-
-
Save pwl/742082b99188054d9cfa875d287890a3 to your computer and use it in GitHub Desktop.
sra-tools error
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| $ yaourt -Sa sra-tools | |
| ==> Downloading sra-tools PKGBUILD from AUR... | |
| x .SRCINFO | |
| x PKGBUILD | |
| sra-tools 2.7.0-1 (2016-07-16 20:57) | |
| ( Unsupported package: Potentially dangerous ! ) | |
| ==> sra-tools dependencies: | |
| - libxml2 (already installed) | |
| - file (already installed) | |
| - hdf5 (already installed) | |
| - ngs (already installed) | |
| - ncbi-vdb (already installed) | |
| ==> Continue building sra-tools ? [Y/n] | |
| ==> ----------------------------------- | |
| ==> | |
| ==> Building and installing package | |
| ==> Making package: sra-tools 2.7.0-1 (Thu Nov 17 15:53:05 CET 2016) | |
| ==> Checking runtime dependencies... | |
| ==> Checking buildtime dependencies... | |
| ==> Retrieving sources... | |
| -> Downloading sra-tools-2.7.0.tar.gz... | |
| % Total % Received % Xferd Average Speed Time Time Time Current | |
| Dload Upload Total Spent Left Speed | |
| 100 121 0 121 0 0 282 0 --:--:-- --:--:-- --:--:-- 282 | |
| 100 3703k 0 3703k 0 0 2083k 0 --:--:-- 0:00:01 --:--:-- 3599k | |
| ==> Validating source files with sha256sums... | |
| sra-tools-2.7.0.tar.gz ... Passed | |
| ==> Extracting sources... | |
| -> Extracting sra-tools-2.7.0.tar.gz with bsdtar | |
| ==> Starting prepare()... | |
| ==> Starting build()... | |
| Configuring SRA-TOOLS package | |
| checking system type... Linux | |
| checking OS distributor... Arch | |
| checking machine architecture... x86_64 | |
| checking for supported architecture... x86_64 (64 bits) is supported | |
| checking for supported OS... Linux (linux) is supported | |
| checking for supported tool chain... gcc tool chain is supported | |
| checking for g++... yes | |
| checking whether gcc accepts -Wno-array-bounds... yes | |
| checking whether g++ accepts -static-libstdc++... yes | |
| checking for fuse library... yes | |
| checking for hdf5 library... yes | |
| checking for magic library... yes | |
| checking for xml2 library... yes | |
| checking for ngs-sdk package... | |
| includes... /usr | |
| libraries... /usr/lib64 | |
| includes: /usr/include | |
| libraries: /usr/lib | |
| checking for ncbi-vdb package source files and build results... | |
| includes... /usr/src/ncbi-vdb-2.7.0 | |
| src... /usr/src/ncbi-vdb-2.7.0 | |
| libraries... /home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib | |
| includes: /usr/src/ncbi-vdb-2.7.0/interfaces | |
| libraries: /home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib | |
| ilibraries: /home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib | |
| configure: creating 'build/ld.linux.exe_cmd.sh' | |
| configure: creating 'build/Makefile.config.linux.x86_64' | |
| configure: creating 'Makefile.config' | |
| configure: creating 'reconfigure' | |
| build type: release | |
| build prefix: /home/pawel/ncbi-outdir/sra-tools | |
| build output path: /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel | |
| includedir: /tmp/yaourt-tmp-pawel/aur-sra-tools/pkg/sra-tools/usr/include | |
| bindir: /tmp/yaourt-tmp-pawel/aur-sra-tools/pkg/sra-tools/usr/bin | |
| libdir: /tmp/yaourt-tmp-pawel/aur-sra-tools/pkg/sra-tools/usr/lib | |
| CC = gcc -c | |
| CPP = g++ | |
| configured with: "'--prefix=/tmp/yaourt-tmp-pawel/aur-sra-tools/pkg/sra-tools/usr/' '--with-ngs-sdk-prefix=/usr' '--with-ncbi-vdb-sources=/usr/src/ncbi-vdb-2.7.0'" | |
| make[1]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/shared' | |
| make[2]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/shared' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/shared/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/shared/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/shared -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o toolkit.vers.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/shared/toolkit.vers.c -D__mod_name__=shared -D__file_name__=toolkit.vers -D__file_ext__=c | |
| ar -rc /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib/libtk-version.a toolkit.vers.pic.o | |
| make[2]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/shared' | |
| make[1]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/shared' | |
| make[1]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/util' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o rcexplain.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/rcexplain.c -D__mod_name__=tools/util -D__file_name__=rcexplain -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/rcexplain.2.7.0 -DNDEBUG -m64 rcexplain.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s rcexplain.2.7.0 rcexplain.2 | |
| ln -s rcexplain.2 rcexplain | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o kdbmeta.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/kdbmeta.c -D__mod_name__=tools/util -D__file_name__=kdbmeta -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/kdbmeta.2.7.0 -DNDEBUG -m64 kdbmeta.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s kdbmeta.2.7.0 kdbmeta.2 | |
| ln -s kdbmeta.2 kdbmeta | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o md5cp.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/md5cp.c -D__mod_name__=tools/util -D__file_name__=md5cp -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/md5cp.2.7.0 -DNDEBUG -m64 md5cp.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s md5cp.2.7.0 md5cp.2 | |
| ln -s md5cp.2 md5cp | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-lock.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/vdb-lock.c -D__mod_name__=tools/util -D__file_name__=vdb-lock -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-lock.2.7.0 -DNDEBUG -m64 vdb-lock.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-lock.2.7.0 vdb-lock.2 | |
| ln -s vdb-lock.2 vdb-lock | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-unlock.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/vdb-unlock.c -D__mod_name__=tools/util -D__file_name__=vdb-unlock -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-unlock.2.7.0 -DNDEBUG -m64 vdb-unlock.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-unlock.2.7.0 vdb-unlock.2 | |
| ln -s vdb-unlock.2 vdb-unlock | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o PrintOS.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix/PrintOS.c -D__mod_name__=tools/util -D__file_name__=PrintOS -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o test-sra.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/test-sra.c -D__mod_name__=tools/util -D__file_name__=test-sra -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/test-sra.2.7.0 -DNDEBUG -m64 PrintOS.o test-sra.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s test-sra.2.7.0 test-sra.2 | |
| ln -s test-sra.2 test-sra | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-passwd.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/vdb-passwd.c -D__mod_name__=tools/util -D__file_name__=vdb-passwd -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o syspass.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix/syspass.c -D__mod_name__=tools/util -D__file_name__=syspass -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-passwd.2.7.0 -DNDEBUG -m64 vdb-passwd.o syspass.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-passwd.2.7.0 vdb-passwd.2 | |
| ln -s vdb-passwd.2 vdb-passwd | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/util' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/align-cache' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o align-cache.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache/align-cache.cpp -D__mod_name__=tools/align-cache -D__file_name__=align-cache -D__file_ext__=cpp | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o helper.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache/helper.cpp -D__mod_name__=tools/align-cache -D__file_name__=helper -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/align-cache.2.7.0 -DNDEBUG -m64 align-cache.o helper.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -lload -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s align-cache.2.7.0 align-cache.2 | |
| ln -s align-cache.2 align-cache | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/align-cache' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kar' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o kar-args.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/kar-args.c -D__mod_name__=tools/kar -D__file_name__=kar-args -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o kar.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/kar.c -D__mod_name__=tools/kar -D__file_name__=kar -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/kar.c: In function ‘kar_persist’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/kar.c:1024:15: warning: ‘total_written’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| *num_writ = total_written; | |
| ~~~~~~~~~~^~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/kar.c:980:28: note: ‘total_written’ was declared here | |
| size_t total_expected, total_written; | |
| ^~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/kar.c:956:15: warning: ‘total_written’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| *num_writ = total_written; | |
| ~~~~~~~~~~^~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar/kar.c:911:28: note: ‘total_written’ was declared here | |
| size_t total_expected, total_written; | |
| ^~~~~~~~~~~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/kar.2.7.0 -DNDEBUG -m64 kar-args.o kar.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s kar.2.7.0 kar.2 | |
| ln -s kar.2 kar | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kar' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kqsh' | |
| perl kqsh-thunk.pl -mkdb -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -ikdb/manager.h -ikdb/database.h -ikdb/table.h -ikdb/column.h -ikdb/index.h -ikdb/meta.h -ikdb/namelist.h \ | |
| :KDBManager=mgr :KDatabase=db :KTable=tbl :KColumn=col :KColumnBlob=blob :KIndex=idx :KMetadata=meta :KMDataNode=node -h kqsh-kdb.h -c kqsh-kdb.c || rm kqsh-kdb.c | |
| perl kqsh-thunk.pl -mvdb -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -ivdb/manager.h -ivdb/database.h -ivdb/schema.h -ivdb/table.h -ivdb/cursor.h \ | |
| :VDBManager=mgr VSchemaRuntimeTable=srtt VSchema=schema VTypedecl=td VTypedesc=tdesc :VDatabase=db :VTable=tbl :VCursor=curs -h kqsh-vdb.h -c kqsh-vdb.c || rm kqsh-vdb.c | |
| perl kqsh-thunk.pl -msra -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -isra/sradb.h -isra/wsradb.h -isra/sraschema.h \ | |
| :SRAMgr=mgr SRANamelist=nmlist :SRATable=tbl SRAColumn=col VDBManager=vmgr -h kqsh-sra.h -c kqsh-sra.c || rm kqsh-sra.c | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kqsh' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/std-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kqsh' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kqsh' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-dump' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-context.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-context.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-context -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-coldefs.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-coldefs.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-coldefs -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-tools.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-tools.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-tools -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-str.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-str.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-str -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-helper.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-helper.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-helper -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-filter.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-filter.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-filter -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-formats.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-formats.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-formats -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-redir.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-redir.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-redir -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-fastq.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-fastq.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-fastq -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-bin.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-bin.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-bin -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-interact.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-interact.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-interact -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-repo.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-repo.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-repo -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump-print.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-print.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump-print -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-print.c:1305:13: warning: ‘vdp_print_show_src_and_ranges’ defined but not used [-Wunused-function] | |
| static rc_t vdp_print_show_src_and_ranges( struct num_gen * ranges, uint32_t src_id ) | |
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-print.c:46:0: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-print.c: In function ‘vdp_float’: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64/bitstr.h:35:20: warning: ‘value’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| #define BSWAP( x ) bswap_32 ( x ) | |
| ^~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-print.c:330:19: note: ‘value’ was declared here | |
| float value; | |
| ^~~~~ | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-print.c:46:0: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64/bitstr.h:35:20: warning: ‘value’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| #define BSWAP( x ) bswap_32 ( x ) | |
| ^~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump-print.c:339:20: note: ‘value’ was declared here | |
| double value; | |
| ^~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb_info.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb_info.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb_info -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-dump.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump/vdb-dump.c -D__mod_name__=tools/vdb-dump -D__file_name__=vdb-dump -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-dump.2.7.0 -DNDEBUG -m64 vdb-dump-context.o vdb-dump-coldefs.o vdb-dump-tools.o vdb-dump-str.o vdb-dump-helper.o vdb-dump-filter.o vdb-dump-formats.o vdb-dump-redir.o vdb-dump-fastq.o vdb-dump-bin.o vdb-dump-interact.o vdb-dump-repo.o vdb-dump-print.o vdb_info.o vdb-dump.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-dump.2.7.0 vdb-dump.2 | |
| ln -s vdb-dump.2 vdb-dump | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-dump' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-dump' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o factory.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/factory.c -D__mod_name__=tools/sra-dump -D__file_name__=factory -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fasta_dump.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/fasta_dump.c -D__mod_name__=tools/sra-dump -D__file_name__=fasta_dump -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o core.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/core.c -D__mod_name__=tools/sra-dump -D__file_name__=core -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/fastq.c -D__mod_name__=tools/sra-dump -D__file_name__=fastq -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/fastq-dump.2.7.0 -DNDEBUG -m64 factory.o fasta_dump.o core.o fastq.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s fastq-dump.2.7.0 fastq-dump.2 | |
| ln -s fastq-dump.2 fastq-dump | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sff.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/sff.c -D__mod_name__=tools/sra-dump -D__file_name__=sff -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/sff-dump.2.7.0 -DNDEBUG -m64 factory.o fasta_dump.o core.o sff.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s sff-dump.2.7.0 sff-dump.2 | |
| ln -s sff-dump.2 sff-dump | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o illumina.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/illumina.c -D__mod_name__=tools/sra-dump -D__file_name__=illumina -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/illumina-dump.2.7.0 -DNDEBUG -m64 factory.o fasta_dump.o core.o illumina.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s illumina-dump.2.7.0 illumina-dump.2 | |
| ln -s illumina-dump.2 illumina-dump | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o abi.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump/abi.c -D__mod_name__=tools/sra-dump -D__file_name__=abi -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/abi-dump.2.7.0 -DNDEBUG -m64 factory.o fasta_dump.o core.o abi.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s abi-dump.2.7.0 abi-dump.2 | |
| ln -s abi-dump.2 abi-dump | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-dump' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-pileup' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o dyn_string.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/dyn_string.c -D__mod_name__=tools/sra-pileup -D__file_name__=dyn_string -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cmdline_cmn.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cmdline_cmn.c -D__mod_name__=tools/sra-pileup -D__file_name__=cmdline_cmn -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cmdline_cmn.c: In function ‘foreach_argument’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cmdline_cmn.c:514:20: warning: ‘rc’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| if ( rc == 0 && path != NULL ) | |
| ^ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o out_redir.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/out_redir.c -D__mod_name__=tools/sra-pileup -D__file_name__=out_redir -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o perf_log.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/perf_log.c -D__mod_name__=tools/sra-pileup -D__file_name__=perf_log -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o reref.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/reref.c -D__mod_name__=tools/sra-pileup -D__file_name__=reref -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/reref.c: In function ‘report_on_reference’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/reref.c:204:39: warning: ‘max_ev_at’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| uint64_t from = ( ( max_ev_at - start ) * 5000 ) + 1; | |
| ~~~~~~~~~~~~^~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/reref.c:159:46: note: ‘max_ev_at’ was declared here | |
| int64_t row_id, max_prim_at, max_sec_at, max_ev_at; | |
| ^~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/reref.c:200:12: warning: ‘max_sec_at’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| rc = KOutMsg( "max. SEC:\t%,u\tat row #%,i ( from pos: %,u ... %,u )\n", max_sec, max_sec_at, from, from + 4999 ); | |
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/reref.c:159:34: note: ‘max_sec_at’ was declared here | |
| int64_t row_id, max_prim_at, max_sec_at, max_ev_at; | |
| ^~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/reref.c:194:41: warning: ‘max_prim_at’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| uint64_t from = ( ( max_prim_at - start ) * 5000 ) + 1; | |
| ~~~~~~~~~~~~~~^~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/reref.c:159:21: note: ‘max_prim_at’ was declared here | |
| int64_t row_id, max_prim_at, max_sec_at, max_ev_at; | |
| ^~~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cg_tools.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cg_tools.c -D__mod_name__=tools/sra-pileup -D__file_name__=cg_tools -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cg_tools.c: In function ‘fmt_cigar_elem’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cg_tools.c:570:10: warning: unused variable ‘rc’ [-Wunused-variable] | |
| rc_t rc = string_printf ( dst, 11, &num_writ, "%d%c", cig_oplen, cig_op ); | |
| ^~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cg_tools.c: In function ‘cg_canonical_print_cigar’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cg_tools.c:1721:12: warning: ‘rc’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| return rc; | |
| ^~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/cg_tools.c:1717:12: warning: ‘total_cnt’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| if(total_cnt && op) KOutMsg( "%d%c", total_cnt,op ); | |
| ^~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o report_deletes.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/report_deletes.c -D__mod_name__=tools/sra-pileup -D__file_name__=report_deletes -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ref_regions.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/ref_regions.c -D__mod_name__=tools/sra-pileup -D__file_name__=ref_regions -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o 4na_ascii.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/4na_ascii.c -D__mod_name__=tools/sra-pileup -D__file_name__=4na_ascii -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ref_walker_0.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/ref_walker_0.c -D__mod_name__=tools/sra-pileup -D__file_name__=ref_walker_0 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ref_walker.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/ref_walker.c -D__mod_name__=tools/sra-pileup -D__file_name__=ref_walker -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o walk_debug.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/walk_debug.c -D__mod_name__=tools/sra-pileup -D__file_name__=walk_debug -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pileup_counters.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/pileup_counters.c -D__mod_name__=tools/sra-pileup -D__file_name__=pileup_counters -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pileup_index.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/pileup_index.c -D__mod_name__=tools/sra-pileup -D__file_name__=pileup_index -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pileup_indels.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/pileup_indels.c -D__mod_name__=tools/sra-pileup -D__file_name__=pileup_indels -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pileup_varcount.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/pileup_varcount.c -D__mod_name__=tools/sra-pileup -D__file_name__=pileup_varcount -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pileup_stat.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/pileup_stat.c -D__mod_name__=tools/sra-pileup -D__file_name__=pileup_stat -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pileup_v2.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/pileup_v2.c -D__mod_name__=tools/sra-pileup -D__file_name__=pileup_v2 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sra-pileup.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sra-pileup.c -D__mod_name__=tools/sra-pileup -D__file_name__=sra-pileup -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/sra-pileup.2.7.0 -DNDEBUG -m64 dyn_string.o cmdline_cmn.o out_redir.o perf_log.o reref.o cg_tools.o report_deletes.o ref_regions.o 4na_ascii.o ref_walker_0.o ref_walker.o walk_debug.o pileup_counters.o pileup_index.o pileup_indels.o pileup_varcount.o pileup_stat.o pileup_v2.o sra-pileup.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s sra-pileup.2.7.0 sra-pileup.2 | |
| ln -s sra-pileup.2 sra-pileup | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o inputfiles.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/inputfiles.c -D__mod_name__=tools/sra-pileup -D__file_name__=inputfiles -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o rna_splice_log.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/rna_splice_log.c -D__mod_name__=tools/sra-pileup -D__file_name__=rna_splice_log -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sam-dump-opts.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump-opts.c -D__mod_name__=tools/sra-pileup -D__file_name__=sam-dump-opts -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sam-hdr.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-hdr.c -D__mod_name__=tools/sra-pileup -D__file_name__=sam-hdr -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sam-hdr1.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-hdr1.c -D__mod_name__=tools/sra-pileup -D__file_name__=sam-hdr1 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o matecache.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/matecache.c -D__mod_name__=tools/sra-pileup -D__file_name__=matecache -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o read_fkt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/read_fkt.c -D__mod_name__=tools/sra-pileup -D__file_name__=read_fkt -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sam-aligned.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-aligned.c -D__mod_name__=tools/sra-pileup -D__file_name__=sam-aligned -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sam-unaligned.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-unaligned.c -D__mod_name__=tools/sra-pileup -D__file_name__=sam-unaligned -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o md_flag.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/md_flag.c -D__mod_name__=tools/sra-pileup -D__file_name__=md_flag -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sam-dump.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump.c -D__mod_name__=tools/sra-pileup -D__file_name__=sam-dump -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump.c: In function ‘DumpCGSAM.part.17’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump.c:2752:40: warning: ‘last_cig_op’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| ciglen = last_ciglen + sprintf(dst+last_ciglen,"%d%c",last_cig_oplen,last_cig_op); \ | |
| ^~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump.c:2740:14: note: ‘last_cig_op’ was declared here | |
| char last_cig_op; | |
| ^~~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sam-dump3.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump3.c -D__mod_name__=tools/sra-pileup -D__file_name__=sam-dump3 -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump3.c: In function ‘KMain’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump3.c:477:8: warning: ‘mode’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| rc = init_out_redir( &redir, mode, opts->outputfile, opts->output_buffer_size ); /* from out_redir.c */ | |
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup/sam-dump3.c:468:25: note: ‘mode’ was declared here | |
| enum out_redir_mode mode; | |
| ^~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/sam-dump.2.7.0 -DNDEBUG -m64 inputfiles.o perf_log.o rna_splice_log.o sam-dump-opts.o out_redir.o sam-hdr.o sam-hdr1.o matecache.o read_fkt.o sam-aligned.o sam-unaligned.o md_flag.o cg_tools.o sam-dump.o sam-dump3.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s sam-dump.2.7.0 sam-dump.2 | |
| ln -s sam-dump.2 sam-dump | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-pileup' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/bam-loader' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o bam-loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/bam-loader.c -D__mod_name__=tools/bam-loader -D__file_name__=bam-loader -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o bam.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/bam.c -D__mod_name__=tools/bam-loader -D__file_name__=bam -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/bam.c: In function ‘BAM_FileReadSAM’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/bam.c:2307:9: warning: unused variable ‘n’ [-Wunused-variable] | |
| int n = 0; | |
| ^ | |
| At top level: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/bam.c:2963:17: warning: ‘SequenceLengthFromCIGAR’ defined but not used [-Wunused-function] | |
| static unsigned SequenceLengthFromCIGAR(const BAM_Alignment *self) | |
| ^~~~~~~~~~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/bam.c: In function ‘BAM_FileMake’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/bam.c:1278:18: warning: ‘refSeq’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| self->refSeq = refSeq; | |
| ~~~~~~~~~~~~~^~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/bam.c:1239:16: note: ‘refSeq’ was declared here | |
| BAMRefSeq *refSeq; | |
| ^~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o alignment-writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/alignment-writer.c -D__mod_name__=tools/bam-loader -D__file_name__=alignment-writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o reference-writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/reference-writer.c -D__mod_name__=tools/bam-loader -D__file_name__=reference-writer -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/reference-writer.c: In function ‘ReferenceGetSequence’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/reference-writer.c:564:42: warning: passing argument 2 of ‘ReferenceSeq_Read’ makes integer from pointer without a cast [-Wint-conversion] | |
| return ReferenceSeq_Read(self->rseq, rslt, position, nCIGAR, CIGAR); | |
| ^~~~ | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/reference-writer.h:34:0, | |
| from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/reference-writer.c:39: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/align/writer-reference.h:124:22: note: expected ‘INSDC_coord_zero {aka int}’ but argument is of type ‘char *’ | |
| ALIGN_EXTERN rc_t CC ReferenceSeq_Read(const ReferenceSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len, | |
| ^~~~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/reference-writer.c:564:58: warning: passing argument 4 of ‘ReferenceSeq_Read’ makes pointer from integer without a cast [-Wint-conversion] | |
| return ReferenceSeq_Read(self->rseq, rslt, position, nCIGAR, CIGAR); | |
| ^~~~~~ | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/reference-writer.h:34:0, | |
| from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/reference-writer.c:39: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/align/writer-reference.h:124:22: note: expected ‘uint8_t * {aka unsigned char *}’ but argument is of type ‘unsigned int’ | |
| ALIGN_EXTERN rc_t CC ReferenceSeq_Read(const ReferenceSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len, | |
| ^~~~~~~~~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sequence-writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/sequence-writer.c -D__mod_name__=tools/bam-loader -D__file_name__=sequence-writer -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/sequence-writer.c: In function ‘SequenceWhack’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/sequence-writer.c:490:14: warning: unused variable ‘rc’ [-Wunused-variable] | |
| rc_t rc = VDatabaseOpenTableUpdate(self->db, &tbl, "SEQUENCE"); | |
| ^~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o loader-imp.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/loader-imp.c -D__mod_name__=tools/bam-loader -D__file_name__=loader-imp -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/loader-imp.c: In function ‘ProcessBAM’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/loader-imp.c:1751:44: warning: passing argument 2 of ‘MMArrayGetRead’ from incompatible pointer type [-Wincompatible-pointer-types] | |
| rc_t rc2=MMArrayGetRead(ctx->id2value, (void **)&tmp_value, keyId); | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/loader-imp.c:260:13: note: expected ‘const void ** const’ but argument is of type ‘void **’ | |
| static rc_t MMArrayGetRead(MMArray *const self, void const **const value, uint64_t const element) | |
| ^~~~~~~~~~~~~~ | |
| At top level: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/loader-imp.c:1101:6: warning: ‘LogDupConflict’ defined but not used [-Wunused-function] | |
| rc_t LogDupConflict(char const readName[]) | |
| ^~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/loader-imp.c:911:13: warning: ‘EditUnalignedQualities’ defined but not used [-Wunused-function] | |
| static bool EditUnalignedQualities(uint8_t qual[], bool const hasMismatch[], unsigned readlen) | |
| ^~~~~~~~~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/loader-imp.c:886:13: warning: ‘EditAlignedQualities’ defined but not used [-Wunused-function] | |
| static bool EditAlignedQualities(uint8_t qual[], bool const hasMismatch[], unsigned readlen) | |
| ^~~~~~~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/loader-imp.c:185:20: warning: ‘Print_ctx_value_t’ defined but not used [-Wunused-function] | |
| static char const *Print_ctx_value_t(ctx_value_t const *const self) | |
| ^~~~~~~~~~~~~~~~~ | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o mem-bank.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/mem-bank.cpp -D__mod_name__=tools/bam-loader -D__file_name__=mem-bank -D__file_ext__=cpp | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o low-match-count.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/low-match-count.cpp -D__mod_name__=tools/bam-loader -D__file_name__=low-match-count -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/bam-load.2.7.0 -DNDEBUG -m64 bam-loader.o bam.o alignment-writer.o reference-writer.o sequence-writer.o loader-imp.o mem-bank.o low-match-count.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s bam-load.2.7.0 bam-load.2 | |
| ln -s bam-load.2 bam-load | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/bam-loader' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fastq-loader' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o common-writer.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/common-writer.c -D__mod_name__=tools/fastq-loader -D__file_name__=common-writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sequence-writer.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/sequence-writer.c -D__mod_name__=tools/fastq-loader -D__file_name__=sequence-writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o common-reader.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/common-reader.c -D__mod_name__=tools/fastq-loader -D__file_name__=common-reader -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq-reader.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-reader.c -D__mod_name__=tools/fastq-loader -D__file_name__=fastq-reader -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq-grammar.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-grammar.c -D__mod_name__=tools/fastq-loader -D__file_name__=fastq-grammar -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq-lex.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c -D__mod_name__=tools/fastq-loader -D__file_name__=fastq-lex -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c: In function ‘FASTQ_lex’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c:1113:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] | |
| if ( ! yyg->yy_state_buf ) | |
| ^~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c:1115:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ | |
| if ( ! yyg->yy_state_buf ) | |
| ^~ | |
| At top level: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c:2386:16: warning: ‘yy_top_state’ defined but not used [-Wunused-function] | |
| static int yy_top_state (yyscan_t yyscanner) | |
| ^~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c:1836:16: warning: ‘input’ defined but not used [-Wunused-function] | |
| static int input (yyscan_t yyscanner) | |
| ^~~~~ | |
| ar -rc /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib/libfastqloader.a common-writer.pic.o sequence-writer.pic.o common-reader.pic.o fastq-reader.pic.o fastq-grammar.pic.o fastq-lex.pic.o | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq-loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-loader.c -D__mod_name__=tools/fastq-loader -D__file_name__=fastq-loader -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-loader.c:67:19: warning: ‘option_read’ defined but not used [-Wunused-const-variable=] | |
| static char const option_read[] = "read"; | |
| ^~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-loader.c:58:19: warning: ‘option_input’ defined but not used [-Wunused-const-variable=] | |
| static char const option_input[] = "input"; | |
| ^~~~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o loader-imp.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/loader-imp.c -D__mod_name__=tools/fastq-loader -D__file_name__=loader-imp -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o common-writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/common-writer.c -D__mod_name__=tools/fastq-loader -D__file_name__=common-writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sequence-writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/sequence-writer.c -D__mod_name__=tools/fastq-loader -D__file_name__=sequence-writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o common-reader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/common-reader.c -D__mod_name__=tools/fastq-loader -D__file_name__=common-reader -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq-reader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-reader.c -D__mod_name__=tools/fastq-loader -D__file_name__=fastq-reader -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq-grammar.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-grammar.c -D__mod_name__=tools/fastq-loader -D__file_name__=fastq-grammar -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq-lex.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c -D__mod_name__=tools/fastq-loader -D__file_name__=fastq-lex -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c: In function ‘FASTQ_lex’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c:1113:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] | |
| if ( ! yyg->yy_state_buf ) | |
| ^~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c:1115:13: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ | |
| if ( ! yyg->yy_state_buf ) | |
| ^~ | |
| At top level: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c:2386:16: warning: ‘yy_top_state’ defined but not used [-Wunused-function] | |
| static int yy_top_state (yyscan_t yyscanner) | |
| ^~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader/fastq-lex.c:1836:16: warning: ‘input’ defined but not used [-Wunused-function] | |
| static int input (yyscan_t yyscanner) | |
| ^~~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load.2.7.0 -DNDEBUG -m64 fastq-loader.o loader-imp.o common-writer.o sequence-writer.o common-reader.o fastq-reader.o fastq-grammar.o fastq-lex.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s latf-load.2.7.0 latf-load.2 | |
| ln -s latf-load.2 latf-load | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fastq-loader' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/srapath' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o helper.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/helper.c -D__mod_name__=tools/srapath -D__file_name__=helper -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o line_iter.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/line_iter.c -D__mod_name__=tools/srapath -D__file_name__=line_iter -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cgi_request.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/cgi_request.c -D__mod_name__=tools/srapath -D__file_name__=cgi_request -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/cgi_request.c: In function ‘clear_cgi_request_params’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/cgi_request.c:169:12: warning: ‘rc’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| return rc; | |
| ^~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o srapath.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath/srapath.c -D__mod_name__=tools/srapath -D__file_name__=srapath -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/srapath.2.7.0 -DNDEBUG -m64 helper.o line_iter.o cgi_request.o srapath.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s srapath.2.7.0 srapath.2 | |
| ln -s srapath.2 srapath | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/srapath' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-stat' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sra.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat/sra.c -D__mod_name__=tools/sra-stat -D__file_name__=sra -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sra-stat.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat/sra-stat.c -D__mod_name__=tools/sra-stat -D__file_name__=sra-stat -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/sra-stat.2.7.0 -DNDEBUG -m64 sra.o sra-stat.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -lload -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s sra-stat.2.7.0 sra-stat.2 | |
| ln -s sra-stat.2 sra-stat | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-stat' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-copy' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o context.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/context.c -D__mod_name__=tools/vdb-copy -D__file_name__=context -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o helper.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/helper.c -D__mod_name__=tools/vdb-copy -D__file_name__=helper -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o coldefs.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/coldefs.c -D__mod_name__=tools/vdb-copy -D__file_name__=coldefs -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o get_platform.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/get_platform.c -D__mod_name__=tools/vdb-copy -D__file_name__=get_platform -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o namelist_tools.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/namelist_tools.c -D__mod_name__=tools/vdb-copy -D__file_name__=namelist_tools -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o copy_meta.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/copy_meta.c -D__mod_name__=tools/vdb-copy -D__file_name__=copy_meta -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/copy_meta.c: In function ‘enter_version’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/copy_meta.c:326:62: warning: implicit declaration of function ‘KAppVersion’ [-Wimplicit-function-declaration] | |
| rc = string_printf ( buff, sizeof( buff ), NULL, "%.3V", KAppVersion() ); | |
| ^~~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o type_matcher.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/type_matcher.c -D__mod_name__=tools/vdb-copy -D__file_name__=type_matcher -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o redactval.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/redactval.c -D__mod_name__=tools/vdb-copy -D__file_name__=redactval -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o config_values.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/config_values.c -D__mod_name__=tools/vdb-copy -D__file_name__=config_values -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-copy.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/vdb-copy.c -D__mod_name__=tools/vdb-copy -D__file_name__=vdb-copy -D__file_ext__=c | |
| cp /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy/vdb-copy.kfg /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/ncbi/vdb-copy.kfg | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-copy.2.7.0 -DNDEBUG -m64 context.o helper.o coldefs.o get_platform.o namelist_tools.o copy_meta.o type_matcher.o redactval.o config_values.o vdb-copy.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-copy.2.7.0 vdb-copy.2 | |
| ln -s vdb-copy.2 vdb-copy | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-copy' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/rd-filter-redact' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o read-filter-redact.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact/read-filter-redact.c -D__mod_name__=tools/rd-filter-redact -D__file_name__=read-filter-redact -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/read-filter-redact.2.7.0 -DNDEBUG -m64 read-filter-redact.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s read-filter-redact.2.7.0 read-filter-redact.2 | |
| ln -s read-filter-redact.2 read-filter-redact | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/rd-filter-redact' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-config' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o configure.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/configure.cpp -D__mod_name__=tools/vdb-config -D__file_name__=configure -D__file_ext__=cpp | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o util.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/util.cpp -D__mod_name__=tools/vdb-config -D__file_name__=util -D__file_ext__=cpp | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-config.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/vdb-config.c -D__mod_name__=tools/vdb-config -D__file_name__=vdb-config -D__file_ext__=c | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o interactive.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/interactive.cpp -D__mod_name__=tools/vdb-config -D__file_name__=interactive -D__file_ext__=cpp | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-config-model.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config/vdb-config-model.cpp -D__mod_name__=tools/vdb-config -D__file_name__=vdb-config-model -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-config.2.7.0 -DNDEBUG -m64 configure.o util.o vdb-config.o interactive.o vdb-config-model.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltui_cpp -ltui -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-config.2.7.0 vdb-config.2 | |
| ln -s vdb-config.2 vdb-config | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-config' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-info' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/align-info' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-info/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-info/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-info -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o align-info.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-info/align-info.c -D__mod_name__=tools/align-info -D__file_name__=align-info -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/align-info.2.7.0 -DNDEBUG -m64 align-info.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s align-info.2.7.0 align-info.2 | |
| ln -s align-info.2 align-info | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/align-info' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-info' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/qual-recalib-stat' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/std-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/qual-recalib-stat' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/prefetch' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o prefetch.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch/prefetch.c -D__mod_name__=tools/prefetch -D__file_name__=prefetch -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o kfile-no-q.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch/kfile-no-q.c -D__mod_name__=tools/prefetch -D__file_name__=kfile-no-q -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/prefetch.2.7.0 -DNDEBUG -m64 prefetch.o kfile-no-q.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s prefetch.2.7.0 prefetch.2 | |
| ln -s prefetch.2 prefetch | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/prefetch' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-decrypt' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-decrypt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/vdb-decrypt.c -D__mod_name__=tools/vdb-decrypt -D__file_name__=vdb-decrypt -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o shared.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/shared.c -D__mod_name__=tools/vdb-decrypt -D__file_name__=shared -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/shared.c:98:19: warning: ‘CacheLockExt’ defined but not used [-Wunused-const-variable=] | |
| static const char CacheLockExt[] = ".cache.lock"; | |
| ^~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/shared.c:97:19: warning: ‘CacheExt’ defined but not used [-Wunused-const-variable=] | |
| static const char CacheExt[] = ".cache"; | |
| ^~~~~~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-decrypt.2.7.0 -DNDEBUG -m64 vdb-decrypt.o shared.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-decrypt.2.7.0 vdb-decrypt.2 | |
| ln -s vdb-decrypt.2 vdb-decrypt | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-encrypt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt/vdb-encrypt.c -D__mod_name__=tools/vdb-decrypt -D__file_name__=vdb-encrypt -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-encrypt.2.7.0 -DNDEBUG -m64 vdb-encrypt.o shared.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-encrypt.2.7.0 vdb-encrypt.2 | |
| ln -s vdb-encrypt.2 vdb-encrypt | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-decrypt' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-validate' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-validate.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate/vdb-validate.c -D__mod_name__=tools/vdb-validate -D__file_name__=vdb-validate -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate/vdb-validate.c: In function ‘ric_align_generic.isra.9.constprop’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate/vdb-validate.c:1343:5: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| for (chunk = startId; chunk < endId; ) { | |
| ^~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-validate.2.7.0 -DNDEBUG -m64 vdb-validate.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-validate.2.7.0 vdb-validate.2 | |
| ln -s vdb-validate.2 vdb-validate | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o check-corrupt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate/check-corrupt.cpp -D__mod_name__=tools/vdb-validate -D__file_name__=check-corrupt -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/check-corrupt.2.7.0 -DNDEBUG -m64 check-corrupt.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s check-corrupt.2.7.0 check-corrupt.2 | |
| ln -s check-corrupt.2 check-corrupt | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-validate' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-sort' | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o caps.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/caps.c -D__mod_name__=tools/sra-sort -D__file_name__=caps -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o mem.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/mem.c -D__mod_name__=tools/sra-sort -D__file_name__=mem -D__file_ext__=c | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/mem.c:28:0: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/ctx.h:48:23: warning: ‘__file__’ defined but not used [-Wunused-const-variable=] | |
| static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/mem.c:33:1: note: in expansion of macro ‘FILE_ENTRY’ | |
| FILE_ENTRY ( mem ); | |
| ^~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/ctx.h:47:23: warning: ‘__mod__’ defined but not used [-Wunused-const-variable=] | |
| static const char __mod__ [] = "tools/sra-sort"; \ | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/mem.c:33:1: note: in expansion of macro ‘FILE_ENTRY’ | |
| FILE_ENTRY ( mem ); | |
| ^~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o membank.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/membank.c -D__mod_name__=tools/sra-sort -D__file_name__=membank -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o paged-membank.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/paged-membank.c -D__mod_name__=tools/sra-sort -D__file_name__=paged-membank -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o paged-mmapbank.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/paged-mmapbank.c -D__mod_name__=tools/sra-sort -D__file_name__=paged-mmapbank -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o except.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/except.c -D__mod_name__=tools/sra-sort -D__file_name__=except -D__file_ext__=c | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/except.c:34:0: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/klib/status.h:138:0: warning: "STATUS" redefined | |
| #define STATUS( lvl, ... ) \ | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/except.c:30:0: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/status.h:44:0: note: this is the location of the previous definition | |
| #define STATUS( lvl, msg, ... ) \ | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/except.c:28:0: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/ctx.h:48:23: warning: ‘__file__’ defined but not used [-Wunused-const-variable=] | |
| static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/except.c:41:1: note: in expansion of macro ‘FILE_ENTRY’ | |
| FILE_ENTRY ( except ); | |
| ^~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/ctx.h:47:23: warning: ‘__mod__’ defined but not used [-Wunused-const-variable=] | |
| static const char __mod__ [] = "tools/sra-sort"; \ | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/except.c:41:1: note: in expansion of macro ‘FILE_ENTRY’ | |
| FILE_ENTRY ( except ); | |
| ^~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o idx-mapping.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/idx-mapping.c -D__mod_name__=tools/sra-sort -D__file_name__=idx-mapping -D__file_ext__=c | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/idx-mapping.c:28:0: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/ctx.h:48:23: warning: ‘__file__’ defined but not used [-Wunused-const-variable=] | |
| static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/idx-mapping.c:32:1: note: in expansion of macro ‘FILE_ENTRY’ | |
| FILE_ENTRY ( idx-mapping ); | |
| ^~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/ctx.h:47:23: warning: ‘__mod__’ defined but not used [-Wunused-const-variable=] | |
| static const char __mod__ [] = "tools/sra-sort"; \ | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/idx-mapping.c:32:1: note: in expansion of macro ‘FILE_ENTRY’ | |
| FILE_ENTRY ( idx-mapping ); | |
| ^~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o map-file.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/map-file.c -D__mod_name__=tools/sra-sort -D__file_name__=map-file -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o col-pair.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/col-pair.c -D__mod_name__=tools/sra-sort -D__file_name__=col-pair -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o row-set.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/row-set.c -D__mod_name__=tools/sra-sort -D__file_name__=row-set -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o simple-row-set.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/simple-row-set.c -D__mod_name__=tools/sra-sort -D__file_name__=simple-row-set -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o mapping-row-set.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/mapping-row-set.c -D__mod_name__=tools/sra-sort -D__file_name__=mapping-row-set -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sorting-row-set.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/sorting-row-set.c -D__mod_name__=tools/sra-sort -D__file_name__=sorting-row-set -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o meta-pair.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/meta-pair.c -D__mod_name__=tools/sra-sort -D__file_name__=meta-pair -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o dir-pair.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/dir-pair.c -D__mod_name__=tools/sra-sort -D__file_name__=dir-pair -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o tbl-pair.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/tbl-pair.c -D__mod_name__=tools/sra-sort -D__file_name__=tbl-pair -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o db-pair.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/db-pair.c -D__mod_name__=tools/sra-sort -D__file_name__=db-pair -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o glob-poslen.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/glob-poslen.c -D__mod_name__=tools/sra-sort -D__file_name__=glob-poslen -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o poslen-col-pair.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/poslen-col-pair.c -D__mod_name__=tools/sra-sort -D__file_name__=poslen-col-pair -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ref-alignid-col.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/ref-alignid-col.c -D__mod_name__=tools/sra-sort -D__file_name__=ref-alignid-col -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o buff-writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/buff-writer.c -D__mod_name__=tools/sra-sort -D__file_name__=buff-writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o id-mapper-col.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/id-mapper-col.c -D__mod_name__=tools/sra-sort -D__file_name__=id-mapper-col -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o capture-first-half-aligned.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/capture-first-half-aligned.c -D__mod_name__=tools/sra-sort -D__file_name__=capture-first-half-aligned -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o csra-tbl.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/csra-tbl.c -D__mod_name__=tools/sra-sort -D__file_name__=csra-tbl -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o csra-pair.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/csra-pair.c -D__mod_name__=tools/sra-sort -D__file_name__=csra-pair -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o run.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/run.c -D__mod_name__=tools/sra-sort -D__file_name__=run -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sra-sort.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/sra-sort.c -D__mod_name__=tools/sra-sort -D__file_name__=sra-sort -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o xcheck-ref-align.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/xcheck-ref-align.c -D__mod_name__=tools/sra-sort -D__file_name__=xcheck-ref-align -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/sra-sort.2.7.0 -DNDEBUG -m64 caps.o mem.o membank.o paged-membank.o paged-mmapbank.o except.o idx-mapping.o map-file.o col-pair.o row-set.o simple-row-set.o mapping-row-set.o sorting-row-set.o meta-pair.o dir-pair.o tbl-pair.o db-pair.o glob-poslen.o poslen-col-pair.o ref-alignid-col.o buff-writer.o id-mapper-col.o capture-first-half-aligned.o csra-tbl.o csra-pair.o run.o sra-sort.o xcheck-ref-align.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s sra-sort.2.7.0 sra-sort.2 | |
| ln -s sra-sort.2 sra-sort | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-sort' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/cache-mgr' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cache-mgr.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr/cache-mgr.c -D__mod_name__=tools/cache-mgr -D__file_name__=cache-mgr -D__file_ext__=c | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr/cache-mgr.c:32:0: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr/cache-mgr.c: In function ‘report_repo.isra.4’: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/klib/log.h:365:56: warning: ‘hint’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| ((((unsigned)lvl) <= KLogLevelGet()) ? pLogErr msg : (rc_t)0) | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr/cache-mgr.c:743:18: note: ‘hint’ was declared here | |
| const char * hint; | |
| ^~~~ | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr/cache-mgr.c:32:0: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/klib/log.h:365:56: warning: ‘rc’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| ((((unsigned)lvl) <= KLogLevelGet()) ? pLogErr msg : (rc_t)0) | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr/cache-mgr.c:741:10: note: ‘rc’ was declared here | |
| rc_t rc, rc1; | |
| ^~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/cache-mgr.2.7.0 -DNDEBUG -m64 cache-mgr.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s cache-mgr.2.7.0 cache-mgr.2 | |
| ln -s cache-mgr.2 cache-mgr | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/cache-mgr' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vcf-loader' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vcf-grammar.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-grammar.c -D__mod_name__=tools/vcf-loader -D__file_name__=vcf-grammar -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vcf-lex.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-lex.c -D__mod_name__=tools/vcf-loader -D__file_name__=vcf-lex -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-lex.c:1544:17: warning: ‘yyunput’ defined but not used [-Wunused-function] | |
| static void yyunput (int c, register char * yy_bp , yyscan_t yyscanner) | |
| ^~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vcf-reader.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-reader.c -D__mod_name__=tools/vcf-loader -D__file_name__=vcf-reader -D__file_ext__=c | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-reader.c:30:0: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-reader.c: In function ‘OpenDataLine’: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/klib/rc.h:92:9: warning: statement with no effect [-Wunused-value] | |
| ( rc_t ) ( rc ) | |
| ^~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-reader.c:231:13: note: in expansion of macro ‘SET_RC_FILE_FUNC_LINE’ | |
| SET_RC_FILE_FUNC_LINE(rc); | |
| ^~~~~~~~~~~~~~~~~~~~~ | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/klib/rc.h:92:9: warning: statement with no effect [-Wunused-value] | |
| ( rc_t ) ( rc ) | |
| ^~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-reader.c:237:9: note: in expansion of macro ‘SET_RC_FILE_FUNC_LINE’ | |
| SET_RC_FILE_FUNC_LINE(rc); | |
| ^~~~~~~~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-reader.c: In function ‘DataItem’: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/klib/rc.h:92:9: warning: statement with no effect [-Wunused-value] | |
| ( rc_t ) ( rc ) | |
| ^~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-reader.c:307:17: note: in expansion of macro ‘SET_RC_FILE_FUNC_LINE’ | |
| SET_RC_FILE_FUNC_LINE(rc); | |
| ^~~~~~~~~~~~~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vcf-database.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader/vcf-database.c -D__mod_name__=tools/vcf-loader -D__file_name__=vcf-database -D__file_ext__=c | |
| ar -rc /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib/libvcfloader.a vcf-grammar.pic.o vcf-lex.pic.o vcf-reader.pic.o vcf-database.pic.o | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vcf-loader' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/copycat' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o copycat.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/copycat.c -D__mod_name__=tools/copycat -D__file_name__=copycat -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ccfileformat.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/ccfileformat.c -D__mod_name__=tools/copycat -D__file_name__=ccfileformat -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/ccfileformat.c:127:19: warning: ‘magicpath’ defined but not used [-Wunused-const-variable=] | |
| static const char magicpath [] = "/usr/share/misc/magic"; | |
| ^~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/ccfileformat.c:105:19: warning: ‘classtable’ defined but not used [-Wunused-const-variable=] | |
| static const char classtable [] = | |
| ^~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cccat.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/cccat.c -D__mod_name__=tools/copycat -D__file_name__=cccat -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cctree.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/cctree.c -D__mod_name__=tools/copycat -D__file_name__=cctree -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cctree-dump.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/cctree-dump.c -D__mod_name__=tools/copycat -D__file_name__=cctree-dump -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cctar.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/cctar.c -D__mod_name__=tools/copycat -D__file_name__=cctar -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ccsra.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/ccsra.c -D__mod_name__=tools/copycat -D__file_name__=ccsra -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ccsubchunk.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/ccsubchunk.c -D__mod_name__=tools/copycat -D__file_name__=ccsubchunk -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ccfile.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat/ccfile.c -D__mod_name__=tools/copycat -D__file_name__=ccfile -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/copycat.2.7.0 -DNDEBUG -m64 copycat.o ccfileformat.o cccat.o cctree.o cctree-dump.o cctar.o ccsra.o ccsubchunk.o ccfile.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -lkff -lmagic-static -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s copycat.2.7.0 copycat.2 | |
| ln -s copycat.2 copycat | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/copycat' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-load' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pstring.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/pstring.c -D__mod_name__=tools/sra-load -D__file_name__=pstring -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o common-xml.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/common-xml.c -D__mod_name__=tools/sra-load -D__file_name__=common-xml -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o experiment-xml.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/experiment-xml.c -D__mod_name__=tools/sra-load -D__file_name__=experiment-xml -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/experiment-xml.c: In function ‘Experiment_FillSegAgrep’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/experiment-xml.c:711:21: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] | |
| const char* b = NULL; | |
| ^ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o run-xml.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/run-xml.c -D__mod_name__=tools/sra-load -D__file_name__=run-xml -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o loader-file.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/loader-file.c -D__mod_name__=tools/sra-load -D__file_name__=loader-file -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o loader-fmt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/loader-fmt.c -D__mod_name__=tools/sra-load -D__file_name__=loader-fmt -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sra-writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/sra-writer.c -D__mod_name__=tools/sra-load -D__file_name__=sra-writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/loader.c -D__mod_name__=tools/sra-load -D__file_name__=loader -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-illumina.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/writer-illumina.c -D__mod_name__=tools/sra-load -D__file_name__=writer-illumina -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-454.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/writer-454.c -D__mod_name__=tools/sra-load -D__file_name__=writer-454 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-ion-torrent.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/writer-ion-torrent.c -D__mod_name__=tools/sra-load -D__file_name__=writer-ion-torrent -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq-fmt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/fastq-fmt.c -D__mod_name__=tools/sra-load -D__file_name__=fastq-fmt -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/fastq-fmt.c: In function ‘FastqLoaderFmt_Version’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/fastq-fmt.c:641:13: warning: implicit declaration of function ‘KAppVersion’ [-Wimplicit-function-declaration] | |
| *vers = KAppVersion(); | |
| ^~~~~~~~~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/fastq-load.2.7.0 -DNDEBUG -m64 pstring.o common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o loader.o writer-illumina.o writer-454.o writer-ion-torrent.o fastq-fmt.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -lkxfs -lkxml -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s fastq-load.2.7.0 fastq-load.2 | |
| ln -s fastq-load.2 fastq-load | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o illumina-fmt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/illumina-fmt.c -D__mod_name__=tools/sra-load -D__file_name__=illumina-fmt -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/illumina-fmt.c: In function ‘IlluminaLoaderFmt_Version’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/illumina-fmt.c:802:13: warning: implicit declaration of function ‘KAppVersion’ [-Wimplicit-function-declaration] | |
| *vers = KAppVersion(); | |
| ^~~~~~~~~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/illumina-load.2.7.0 -DNDEBUG -m64 pstring.o common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o loader.o writer-illumina.o illumina-fmt.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -lkxfs -lkxml -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s illumina-load.2.7.0 illumina-load.2 | |
| ln -s illumina-load.2 illumina-load | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o srf.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/srf.c -D__mod_name__=tools/sra-load -D__file_name__=srf -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o srf-fmt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/srf-fmt.c -D__mod_name__=tools/sra-load -D__file_name__=srf-fmt -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ztr-illumina.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/ztr-illumina.c -D__mod_name__=tools/sra-load -D__file_name__=ztr-illumina -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/ztr-illumina.c: In function ‘undo_mode_80’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/ztr-illumina.c:438:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] | |
| if (dst == NULL) | |
| ^~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/ztr-illumina.c:441:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ | |
| for (i = 0; i != basecount; ++i, u += 4, dst += 4) { | |
| ^~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o srf-illumina.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/srf-illumina.c -D__mod_name__=tools/sra-load -D__file_name__=srf-illumina -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/srf-illumina.c: In function ‘SRFIlluminaLoaderFmt_Version’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/srf-illumina.c:399:13: warning: implicit declaration of function ‘KAppVersion’ [-Wimplicit-function-declaration] | |
| *vers = KAppVersion(); | |
| ^~~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-absolid.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/writer-absolid.c -D__mod_name__=tools/sra-load -D__file_name__=writer-absolid -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ztr-absolid.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/ztr-absolid.c -D__mod_name__=tools/sra-load -D__file_name__=ztr-absolid -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ztr-huffman.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/ztr-huffman.c -D__mod_name__=tools/sra-load -D__file_name__=ztr-huffman -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o srf-absolid.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/srf-absolid.c -D__mod_name__=tools/sra-load -D__file_name__=srf-absolid -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/srf-load.2.7.0 -DNDEBUG -m64 pstring.o common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o loader.o srf.o srf-fmt.o writer-illumina.o ztr-illumina.o srf-illumina.o writer-absolid.o ztr-absolid.o ztr-huffman.o srf-absolid.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -lkxfs -lkxml -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s srf-load.2.7.0 srf-load.2 | |
| ln -s srf-load.2 srf-load | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o absolid-fmt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/absolid-fmt.c -D__mod_name__=tools/sra-load -D__file_name__=absolid-fmt -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/abi-load.2.7.0 -DNDEBUG -m64 pstring.o common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o loader.o writer-absolid.o absolid-fmt.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -lkxfs -lkxml -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s abi-load.2.7.0 abi-load.2 | |
| ln -s abi-load.2 abi-load | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sff-fmt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/sff-fmt.c -D__mod_name__=tools/sra-load -D__file_name__=sff-fmt -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/sff-fmt.c: In function ‘SFFLoaderFmtVersion’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/sff-fmt.c:409:13: warning: implicit declaration of function ‘KAppVersion’ [-Wimplicit-function-declaration] | |
| *vers = KAppVersion(); | |
| ^~~~~~~~~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/sff-load.2.7.0 -DNDEBUG -m64 pstring.o common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o loader.o writer-454.o writer-ion-torrent.o sff-fmt.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -lkxfs -lkxml -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s sff-load.2.7.0 sff-load.2 | |
| ln -s sff-load.2 sff-load | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-helicos.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/writer-helicos.c -D__mod_name__=tools/sra-load -D__file_name__=writer-helicos -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o helicos-fmt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/helicos-fmt.c -D__mod_name__=tools/sra-load -D__file_name__=helicos-fmt -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/helicos-load.2.7.0 -DNDEBUG -m64 pstring.o common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o loader.o writer-helicos.o helicos-fmt.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -lkxfs -lkxml -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s helicos-load.2.7.0 helicos-load.2 | |
| ln -s helicos-load.2 helicos-load | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pacbio-fmt.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/pacbio-fmt.c -D__mod_name__=tools/sra-load -D__file_name__=pacbio-fmt -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/pacbio-fmt.c: In function ‘PacBioLoaderXmlFmt_Version’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load/pacbio-fmt.c:100:13: warning: implicit declaration of function ‘KAppVersion’ [-Wimplicit-function-declaration] | |
| *vers = KAppVersion(); | |
| ^~~~~~~~~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/pacbio-loadxml.2.7.0 -DNDEBUG -m64 pstring.o common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o loader.o pacbio-fmt.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -lkxfs -lkxml -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s pacbio-loadxml.2.7.0 pacbio-loadxml.2 | |
| ln -s pacbio-loadxml.2 pacbio-loadxml | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-load' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ccextract' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ccextract' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ccextract/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ccextract/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ccextract -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ccextract.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ccextract/ccextract.c -D__mod_name__=tools/ccextract -D__file_name__=ccextract -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/ccextract.2.7.0 -DNDEBUG -m64 ccextract.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lkxfs -lkxml -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s ccextract.2.7.0 ccextract.2 | |
| ln -s ccextract.2 ccextract | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ccextract' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ccextract' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/pacbio-load' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-context.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-context.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-context -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-tools.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-tools.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-tools -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-zmw.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-zmw.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-zmw -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-basecalls_cmn.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-basecalls_cmn.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-basecalls_cmn -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-sequence.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-sequence.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-sequence -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-consensus.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-consensus.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-consensus -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-consensus.c: In function ‘check_Consensus_totalcount’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-consensus.c:63:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] | |
| if ( res ) | |
| ^~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-consensus.c:66:2: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ | |
| if ( res ) | |
| ^~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-passes.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-passes.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-passes -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-metrics.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-metrics.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-metrics -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-regions.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-regions.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-regions -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pl-progress.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pl-progress.c -D__mod_name__=tools/pacbio-load -D__file_name__=pl-progress -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pacbio-load.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load/pacbio-load.c -D__mod_name__=tools/pacbio-load -D__file_name__=pacbio-load -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/pacbio-load.2.7.0 -DNDEBUG -m64 pl-context.o pl-tools.o pl-zmw.o pl-basecalls_cmn.o pl-sequence.o pl-consensus.o pl-passes.o pl-metrics.o pl-regions.o pl-progress.o pacbio-load.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lkdf5 -lload -Wl,-Bdynamic -lhdf5 -Wl,-Bstatic -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s pacbio-load.2.7.0 pacbio-load.2 | |
| ln -s pacbio-load.2 pacbio-load | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/pacbio-load' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fuse' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o log.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/log.c -D__mod_name__=tools/fuse -D__file_name__=log -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o node.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/node.c -D__mod_name__=tools/fuse -D__file_name__=node -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o accessor.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/accessor.c -D__mod_name__=tools/fuse -D__file_name__=accessor -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o kfile-accessor.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/kfile-accessor.c -D__mod_name__=tools/fuse -D__file_name__=kfile-accessor -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o remote-xml.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/remote-xml.c -D__mod_name__=tools/fuse -D__file_name__=remote-xml -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o remote-cache.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/remote-cache.c -D__mod_name__=tools/fuse -D__file_name__=remote-cache -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o remote-link.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/remote-link.c -D__mod_name__=tools/fuse -D__file_name__=remote-link -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o remote-file.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/remote-file.c -D__mod_name__=tools/fuse -D__file_name__=remote-file -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o remote-directory.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/remote-directory.c -D__mod_name__=tools/fuse -D__file_name__=remote-directory -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o remote-fuser-sys.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix/remote-fuser-sys.c -D__mod_name__=tools/fuse -D__file_name__=remote-fuser-sys -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o remote-fuser.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse/remote-fuser.c -D__mod_name__=tools/fuse -D__file_name__=remote-fuser -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/remote-fuser.2.7.0 -DNDEBUG -m64 log.o node.o accessor.o kfile-accessor.o remote-xml.o remote-cache.o remote-link.o remote-file.o remote-directory.o remote-fuser-sys.o remote-fuser.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -lfuse -lrt -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s remote-fuser.2.7.0 remote-fuser.2 | |
| ln -s remote-fuser.2 remote-fuser | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fuse' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-diff' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o namelist_tools.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/namelist_tools.c -D__mod_name__=tools/vdb-diff -D__file_name__=namelist_tools -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o coldefs.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/coldefs.c -D__mod_name__=tools/vdb-diff -D__file_name__=coldefs -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o vdb-diff.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff/vdb-diff.c -D__mod_name__=tools/vdb-diff -D__file_name__=vdb-diff -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/vdb-diff.2.7.0 -DNDEBUG -m64 namelist_tools.o coldefs.o vdb-diff.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s vdb-diff.2.7.0 vdb-diff.2 | |
| ln -s vdb-diff.2 vdb-diff | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-diff' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kget' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/std-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kget' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ngs-pileup' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/std-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ngs-pileup' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/general-loader' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o general-writer.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/general-writer.cpp -D__mod_name__=tools/general-loader -D__file_name__=general-writer -D__file_ext__=cpp | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/general-writer.cpp: In function ‘int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = short unsigned int; uint8_t = unsigned char]’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/general-writer.cpp:646:17: warning: unused variable ‘ret2’ [-Wunused-variable] | |
| int ret2 = decode_uint16 ( start, start + ret, & val2 ); | |
| ^~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/general-writer.cpp: In function ‘int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = unsigned int; uint8_t = unsigned char]’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/general-writer.cpp:659:17: warning: unused variable ‘ret2’ [-Wunused-variable] | |
| int ret2 = decode_uint32 ( start, start + ret, & val2 ); | |
| ^~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/general-writer.cpp: In function ‘int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = long unsigned int; uint8_t = unsigned char]’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/general-writer.cpp:672:17: warning: unused variable ‘ret2’ [-Wunused-variable] | |
| int ret2 = decode_uint64 ( start, start + ret, & val2 ); | |
| ^~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o utf8-like-int-codec.pic.o -fPIC -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall -D_LIBRARY /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/utf8-like-int-codec.c -D__mod_name__=tools/general-loader -D__file_name__=utf8-like-int-codec -D__file_ext__=c | |
| ar -rc /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib/libgeneral-writer.a.2.7.0 general-writer.pic.o utf8-like-int-codec.pic.o | |
| ln -s libgeneral-writer.a.2.7.0 libgeneral-writer.a.2 | |
| ln -s libgeneral-writer.a.2 libgeneral-writer.a | |
| ln -s libgeneral-writer.a libgeneral-writer-static.a | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o general-loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/general-loader.cpp -D__mod_name__=tools/general-loader -D__file_name__=general-loader -D__file_ext__=cpp | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o protocol-parser.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/protocol-parser.cpp -D__mod_name__=tools/general-loader -D__file_name__=protocol-parser -D__file_ext__=cpp | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o database-loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/database-loader.cpp -D__mod_name__=tools/general-loader -D__file_name__=database-loader -D__file_ext__=cpp | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o utf8-like-int-codec.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/utf8-like-int-codec.c -D__mod_name__=tools/general-loader -D__file_name__=utf8-like-int-codec -D__file_ext__=c | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o main.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/main.cpp -D__mod_name__=tools/general-loader -D__file_name__=main -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/general-loader.2.7.0 -DNDEBUG -m64 general-loader.o protocol-parser.o database-loader.o utf8-like-int-codec.o main.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp-norsrc -lncbi-wvdb-static -lload -ltk-version -Wl,-Bdynamic -lz -lbz2 -ldl -lpthread -Wl,-Bdynamic -lm | |
| ln -s general-loader.2.7.0 general-loader.2 | |
| ln -s general-loader.2 general-loader | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/general-loader' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ref-variation' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -pthread -MD -o var-expand.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp -D__mod_name__=tools/ref-variation -D__file_name__=var-expand -D__file_ext__=cpp | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp:35:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "\""PARAM_ALG_SW"\" means Smith-Waterman. " | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp:36:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "\""PARAM_ALG_RA"\" means Rolling bulldozer algorithm\n", NULL }; | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp:184:13: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%s\n", | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp:184:35: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%s\n", | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp:184:48: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%s\n", | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp:184:72: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%s\n", | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp:184:85: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%s\n", | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/var-expand.cpp:184:109: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%.*s\t%.*s:%"PRSIZE_T"u:%"PRSIZE_T"u:%s\n", | |
| ^ | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -pthread -MD -o common.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/common.cpp -D__mod_name__=tools/ref-variation -D__file_name__=common -D__file_ext__=cpp | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -pthread -MD -o helper.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/helper.cpp -D__mod_name__=tools/ref-variation -D__file_name__=helper -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/var-expand.2.7.0 -DNDEBUG -m64 var-expand.o common.o helper.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -lncbi-ngs-c++ -lncbi-vdb-static -lngs-c++ -ltk-version -lncbi-vdb -lload -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s var-expand.2.7.0 var-expand.2 | |
| ln -s var-expand.2 var-expand | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ref-variation' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fastdump' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o helper.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/helper.c -D__mod_name__=tools/fastdump -D__file_name__=helper -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o index.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/index.c -D__mod_name__=tools/fastdump -D__file_name__=index -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o lookup_writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/lookup_writer.c -D__mod_name__=tools/fastdump -D__file_name__=lookup_writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o lookup_reader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/lookup_reader.c -D__mod_name__=tools/fastdump -D__file_name__=lookup_reader -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/lookup_reader.c: In function ‘loop_until_key_found’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/lookup_reader.c:167:18: warning: ‘found_len’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| curr += found_len; | |
| ~~~~~^~~~~~~~~~~~ | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o file_printer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/file_printer.c -D__mod_name__=tools/fastdump -D__file_name__=file_printer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o merge_sorter.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/merge_sorter.c -D__mod_name__=tools/fastdump -D__file_name__=merge_sorter -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sorter.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/sorter.c -D__mod_name__=tools/fastdump -D__file_name__=sorter -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cmn_iter.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/cmn_iter.c -D__mod_name__=tools/fastdump -D__file_name__=cmn_iter -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o raw_read_iter.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/raw_read_iter.c -D__mod_name__=tools/fastdump -D__file_name__=raw_read_iter -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o special_iter.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/special_iter.c -D__mod_name__=tools/fastdump -D__file_name__=special_iter -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastq_iter.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/fastq_iter.c -D__mod_name__=tools/fastdump -D__file_name__=fastq_iter -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o join.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/join.c -D__mod_name__=tools/fastdump -D__file_name__=join -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o fastdump.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump/fastdump.c -D__mod_name__=tools/fastdump -D__file_name__=fastdump -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/fastdump.2.7.0 -DNDEBUG -m64 helper.o index.o lookup_writer.o lookup_reader.o file_printer.o merge_sorter.o sorter.o cmn_iter.o raw_read_iter.o special_iter.o fastq_iter.o join.o fastdump.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s fastdump.2.7.0 fastdump.2 | |
| ln -s fastdump.2 fastdump | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fastdump' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/cg-load' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o cg-load.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/cg-load.c -D__mod_name__=tools/cg-load -D__file_name__=cg-load -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o factory-evidence-intervals.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/factory-evidence-intervals.c -D__mod_name__=tools/cg-load -D__file_name__=factory-evidence-intervals -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o factory-evidence-dnbs.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/factory-evidence-dnbs.c -D__mod_name__=tools/cg-load -D__file_name__=factory-evidence-dnbs -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o factory-mappings.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/factory-mappings.c -D__mod_name__=tools/cg-load -D__file_name__=factory-mappings -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o factory-reads.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/factory-reads.c -D__mod_name__=tools/cg-load -D__file_name__=factory-reads -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o factory-tag-lfr.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/factory-tag-lfr.c -D__mod_name__=tools/cg-load -D__file_name__=factory-tag-lfr -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o f1_3.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/f1_3.c -D__mod_name__=tools/cg-load -D__file_name__=f1_3 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o f1_5.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/f1_5.c -D__mod_name__=tools/cg-load -D__file_name__=f1_5 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o f1_7.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/f1_7.c -D__mod_name__=tools/cg-load -D__file_name__=f1_7 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o f2_0.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/f2_0.c -D__mod_name__=tools/cg-load -D__file_name__=f2_0 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o f2_2.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/f2_2.c -D__mod_name__=tools/cg-load -D__file_name__=f2_2 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o f2_5.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/f2_5.c -D__mod_name__=tools/cg-load -D__file_name__=f2_5 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o file.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/file.c -D__mod_name__=tools/cg-load -D__file_name__=file -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o file-version-factory.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/file-version-factory.c -D__mod_name__=tools/cg-load -D__file_name__=file-version-factory -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o formats.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/formats.c -D__mod_name__=tools/cg-load -D__file_name__=formats -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-algn.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/writer-algn.c -D__mod_name__=tools/cg-load -D__file_name__=writer-algn -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-evidence-dnbs.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/writer-evidence-dnbs.c -D__mod_name__=tools/cg-load -D__file_name__=writer-evidence-dnbs -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-evidence-intervals.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/writer-evidence-intervals.c -D__mod_name__=tools/cg-load -D__file_name__=writer-evidence-intervals -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer-seq.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load/writer-seq.c -D__mod_name__=tools/cg-load -D__file_name__=writer-seq -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/cg-load.2.7.0 -DNDEBUG -m64 cg-load.o factory-evidence-intervals.o factory-evidence-dnbs.o factory-mappings.o factory-reads.o factory-tag-lfr.o f1_3.o f1_5.o f1_7.o f2_0.o f2_2.o f2_5.o file.o file-version-factory.o formats.o writer-algn.o writer-evidence-dnbs.o writer-evidence-intervals.o writer-seq.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lload -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s cg-load.2.7.0 cg-load.2 | |
| ln -s cg-load.2 cg-load | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/cg-load' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pileup-stats' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/pileup-stats' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pileup-stats/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pileup-stats/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pileup-stats -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pileup-stats.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pileup-stats/pileup-stats.cpp -D__mod_name__=tools/pileup-stats -D__file_name__=pileup-stats -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/pileup-stats.2.7.0 -DNDEBUG -m64 pileup-stats.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/usr/lib -Wl,-Bstatic -lkapp -lgeneral-writer -lncbi-ngs-c++ -lncbi-vdb-static -lngs-c++ -ltk-version -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s pileup-stats.2.7.0 pileup-stats.2 | |
| ln -s pileup-stats.2 pileup-stats | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/pileup-stats' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pileup-stats' | |
| make[1]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools' | |
| ==> Starting check()... | |
| make[1]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/shared' | |
| make[2]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/shared' | |
| make[2]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/std'. | |
| make[2]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/shared' | |
| make[1]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/shared' | |
| make[1]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/util' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o testld.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/testld.c -D__mod_name__=tools/util -D__file_name__=testld -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/testld -DNDEBUG -m64 testld.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o txt2kdb.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/txt2kdb.c -D__mod_name__=tools/util -D__file_name__=txt2kdb -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/txt2kdb -DNDEBUG -m64 txt2kdb.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o rowwritetest.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/rowwritetest.c -D__mod_name__=tools/util -D__file_name__=rowwritetest -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/rowwritetest.c: In function ‘run’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/rowwritetest.c:287:0: warning: "STATUS" redefined | |
| #define STATUS(action) (action FORMAT, tablePath, name) | |
| In file included from /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/rowwritetest.c:11:0: | |
| /usr/src/ncbi-vdb-2.7.0/interfaces/klib/status.h:138:0: note: this is the location of the previous definition | |
| #define STATUS( lvl, ... ) \ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/rowwritetest -DNDEBUG -m64 rowwritetest.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o sortreadtest.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/sortreadtest.c -D__mod_name__=tools/util -D__file_name__=sortreadtest -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/sortreadtest -DNDEBUG -m64 sortreadtest.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pacbio-correct.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pacbio-correct.c -D__mod_name__=tools/util -D__file_name__=pacbio-correct -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/pacbio-correct.2.7.0 -DNDEBUG -m64 pacbio-correct.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s pacbio-correct.2.7.0 pacbio-correct.2 | |
| ln -s pacbio-correct.2 pacbio-correct | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o crc32sum.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/crc32sum.c -D__mod_name__=tools/util -D__file_name__=crc32sum -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/crc32sum -DNDEBUG -m64 crc32sum.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o samview.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/samview.c -D__mod_name__=tools/util -D__file_name__=samview -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/samview -DNDEBUG -m64 samview.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o kdb-index.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/kdb-index.c -D__mod_name__=tools/util -D__file_name__=kdb-index -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/kdb-index.2.7.0 -DNDEBUG -m64 kdb-index.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s kdb-index.2.7.0 kdb-index.2 | |
| ln -s kdb-index.2 kdb-index | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o pseudo-aligner.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp -D__mod_name__=tools/util -D__file_name__=pseudo-aligner -D__file_ext__=cpp | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp: In constructor ‘Settings::Settings(std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp:69:9: warning: ‘Settings::templateLength’ will be initialized after [-Wreorder] | |
| int templateLength; | |
| ^~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp:68:9: warning: ‘int Settings::readLength’ [-Wreorder] | |
| int readLength; | |
| ^~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp:71:5: warning: when initialized here [-Wreorder] | |
| Settings(map<string, string> &args) | |
| ^~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp:68:9: warning: ‘Settings::readLength’ will be initialized after [-Wreorder] | |
| int readLength; | |
| ^~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp:66:9: warning: ‘int Settings::coverageTarget’ [-Wreorder] | |
| int coverageTarget; | |
| ^~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp:71:5: warning: when initialized here [-Wreorder] | |
| Settings(map<string, string> &args) | |
| ^~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp: In function ‘std::pair<unsigned int, unsigned int> make_read_pair(unsigned int)’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp:359:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| if (pos2 + settings->readLength <= settings->lengthTarget) | |
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp: In function ‘void usage(const string&, bool)’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/pseudo-aligner.cpp:451:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] | |
| for (int i = 0; i < Settings::paramNames().size(); ++i) { | |
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/pseudo-aligner -DNDEBUG -m64 pseudo-aligner.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -lz -lbz2 -ldl -lpthread -Wl,-Bdynamic -lm | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o schema-replace.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util/schema-replace.c -D__mod_name__=tools/util -D__file_name__=schema-replace -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/schema-replace.2.7.0 -DNDEBUG -m64 schema-replace.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s schema-replace.2.7.0 schema-replace.2 | |
| ln -s schema-replace.2 schema-replace | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/util' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/util' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/align-cache' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/align-cache' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-cache' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kar' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kar' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kar' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kqsh' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kqsh' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kqsh' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kqsh' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-dump' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-dump' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-dump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-dump' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-dump' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-dump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-pileup' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-pileup' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-pileup' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/bam-loader' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o samview.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader/samview.c -D__mod_name__=tools/bam-loader -D__file_name__=samview -D__file_ext__=c | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/samview.2.7.0 -DNDEBUG -m64 bam.o samview.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s samview.2.7.0 samview.2 | |
| ln -s samview.2 samview | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/bam-loader' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/bam-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fastq-loader' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fastq-loader' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastq-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/srapath' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/srapath' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/srapath' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-stat' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-stat' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-stat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-copy' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-copy' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-copy' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/rd-filter-redact' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o test-read-write-cursor.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact/test-read-write-cursor.c -D__mod_name__=tools/rd-filter-redact -D__file_name__=test-read-write-cursor -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/test-read-write-cursor.2.7.0 -DNDEBUG -m64 test-read-write-cursor.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -Wl,-Bdynamic -lncbi-wvdb -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s test-read-write-cursor.2.7.0 test-read-write-cursor.2 | |
| ln -s test-read-write-cursor.2 test-read-write-cursor | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/rd-filter-redact' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/rd-filter-redact' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-config' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-config' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-config' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-info' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/align-info' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/align-info' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/align-info' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/qual-recalib-stat' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o namelist_tools.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/namelist_tools.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=namelist_tools -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o context.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/context.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=context -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o columns.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/columns.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=columns -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o ref_exclude.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/ref_exclude.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=ref_exclude -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o spot_position.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/spot_position.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=spot_position -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o stat_mod_2.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/stat_mod_2.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=stat_mod_2 -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o reader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/reader.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=reader -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/writer.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=writer -D__file_ext__=c | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o qual-recalib-stat.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat/qual-recalib-stat.c -D__mod_name__=tools/qual-recalib-stat -D__file_name__=qual-recalib-stat -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/qual-recalib-stat.2.7.0 -DNDEBUG -m64 namelist_tools.o context.o columns.o ref_exclude.o spot_position.o stat_mod_2.o reader.o writer.o qual-recalib-stat.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s qual-recalib-stat.2.7.0 qual-recalib-stat.2 | |
| ln -s qual-recalib-stat.2 qual-recalib-stat | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/qual-recalib-stat' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/qual-recalib-stat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/prefetch' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/prefetch' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/prefetch' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-decrypt' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-decrypt' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-decrypt' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-validate' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-validate' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-validate' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-sort' | |
| gcc -c -DNDEBUG -m64 -std=gnu99 -fgnu89-inline -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o dump-blob-boundaries.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort/dump-blob-boundaries.c -D__mod_name__=tools/sra-sort -D__file_name__=dump-blob-boundaries -D__file_ext__=c | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/dump-blob-boundaries -DNDEBUG -m64 dump-blob-boundaries.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -lncbi-vdb -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-sort' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-sort' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/cache-mgr' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/cache-mgr' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cache-mgr' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vcf-loader' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vcf-loader' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/copycat' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/copycat' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/copycat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-load' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/sra-load' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/sra-load' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ccextract' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ccextract' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ccextract' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ccextract' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/pacbio-load' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/pacbio-load' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pacbio-load' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fuse' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fuse' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fuse' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-diff' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/vdb-diff' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vdb-diff' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kget' | |
| gcc -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o kget.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget/kget.c -D__mod_name__=tools/kget -D__file_name__=kget -D__file_ext__=c | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget/kget.c: In function ‘full_download.isra.5’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget/kget.c:738:44: warning: ‘outfile’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| rc = KDirectoryCreateFile ( dir, &dst, false, 0664, kcmInit, outfile ); | |
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| gcc -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/kget.2.7.0 -DNDEBUG -m64 kget.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s kget.2.7.0 kget.2 | |
| ln -s kget.2 kget | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/kget' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/kget' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ngs-pileup' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -I /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/ngs/ngs-c++ -MD -o ngs-pileup.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup/ngs-pileup.cpp -D__mod_name__=tools/ngs-pileup -D__file_name__=ngs-pileup -D__file_ext__=cpp | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup/ngs-pileup.cpp: In member function ‘void NGS_Pileup::TargetReference::Process(std::ostream&)’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable ‘next’ [-Wunused-variable] | |
| bool next = i -> nextPileup (); | |
| ^~~~ | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -I /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/ngs/ngs-c++ -MD -o main.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup/main.cpp -D__mod_name__=tools/ngs-pileup -D__file_name__=main -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/ngs-pileup.2.7.0 -DNDEBUG -m64 ngs-pileup.o main.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -lncbi-ngs-c++ -lncbi-vdb-static -lngs-c++ -ltk-version -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s ngs-pileup.2.7.0 ngs-pileup.2 | |
| ln -s ngs-pileup.2 ngs-pileup | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ngs-pileup' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ngs-pileup' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/general-loader' | |
| c++ -DNDEBUG -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/gw-dumper /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/gw-dumper.cpp /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader/utf8-like-int-codec.c -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/general-loader' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ref-variation' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -pthread -MD -o ref-variation.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp -D__mod_name__=tools/ref-variation -D__file_name__=ref-variation -D__file_ext__=cpp | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:229:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "\""COUNT_STRAND_NONE_STR"\" - do not count (default). " | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:230:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "\""COUNT_STRAND_COUNTERALIGNED_STR"\" - as in Illumina. " | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:231:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "\""COUNT_STRAND_COALIGNED_STR"\" - as in 454 or IonTorrent. ", NULL }; | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:236:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "\""PARAM_ALG_SW"\" means Smith-Waterman. " | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:237:9: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] | |
| "\""PARAM_ALG_RA"\" means Rolling bulldozer algorithm\n", NULL }; | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp: In instantiation of ‘int NSRefVariation::find_alignment_in_pileup_db(const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, size_t, TLock*, size_t, NSRefVariation::coverage_info*, size_t) [with TLock = KProc::CKLock; size_t = long unsigned int]’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:877:47: required from ‘void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, TLock*, size_t, NSRefVariation::coverage_info*) [with TLock = KProc::CKLock; size_t = long unsigned int]’ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:917:43: required from ‘void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const std::vector<KSearch::CVRefVariation>*, TLock*, size_t) [with TLock = KProc::CKLock; size_t = long unsigned int]’ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:957:51: required from ‘void NSRefVariation::find_alignments(const char*, const std::vector<KSearch::CVRefVariation>*, TLock*, size_t, const NSRefVariation::CInputRuns*, KApp::CProgressBar*) [with TLock = KProc::CKLock; size_t = long unsigned int]’ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:1049:44: required from here | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:569:28: warning: unused variable ‘allele_size’ [-Wunused-variable] | |
| size_t allele_size = obj.GetAlleleSize(); | |
| ^~~~~~~~~~~ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp: In instantiation of ‘int NSRefVariation::find_alignment_in_pileup_db(const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, size_t, TLock*, size_t, NSRefVariation::coverage_info*, size_t) [with TLock = CNoMutex; size_t = long unsigned int]’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:877:47: required from ‘void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, TLock*, size_t, NSRefVariation::coverage_info*) [with TLock = CNoMutex; size_t = long unsigned int]’ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:917:43: required from ‘void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const std::vector<KSearch::CVRefVariation>*, TLock*, size_t) [with TLock = CNoMutex; size_t = long unsigned int]’ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:957:51: required from ‘void NSRefVariation::find_alignments(const char*, const std::vector<KSearch::CVRefVariation>*, TLock*, size_t, const NSRefVariation::CInputRuns*, KApp::CProgressBar*) [with TLock = CNoMutex; size_t = long unsigned int]’ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:1076:48: required from here | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation/ref-variation.cpp:569:28: warning: unused variable ‘allele_size’ [-Wunused-variable] | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/ref-variation.2.7.0 -DNDEBUG -m64 ref-variation.o common.o helper.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -lncbi-ngs-c++ -lncbi-vdb-static -lngs-c++ -ltk-version -lncbi-vdb -lload -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| ln -s ref-variation.2.7.0 ref-variation.2 | |
| ln -s ref-variation.2 ref-variation | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/ref-variation' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/ref-variation' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fastdump' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/fastdump' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/fastdump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/cg-load' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/cg-load' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/cg-load' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pileup-stats' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/pileup-stats' | |
| make[3]: Nothing to be done for '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/all-cmn'. | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/tools/pileup-stats' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/pileup-stats' | |
| make[1]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools' | |
| make[1]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/kget' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/kget' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/align-info' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/align-info' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/align-cache' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/align-cache' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-dump' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-dump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/ref-variation' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/ref-variation' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-validate' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-validate' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/kar' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/kar' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/copycat' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/copycat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastdump' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastdump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-copy' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-copy' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/qual-recalib-stat' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/qual-recalib-stat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/sra-pileup' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/sra-pileup' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/srapath' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/srapath' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fuse' | |
| make[2]: Nothing to be done for 'std'. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fuse' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o wb-test-fastq.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/wb-test-fastq.cpp -D__mod_name__=test/fastq-loader -D__file_name__=wb-test-fastq -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/wb-test-fastq -DNDEBUG -m64 wb-test-fastq.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -lktst -lfastqloader -lload -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o test-fastq-loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/test-fastq-loader.cpp -D__mod_name__=test/fastq-loader -D__file_name__=test-fastq-loader -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-fastq-loader -DNDEBUG -m64 test-fastq-loader.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -lktst -lfastqloader -lload -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader' | |
| find: ‘/home/pawel/ncbi’: No such file or directory | |
| HOST=krowa | |
| OS=linux | |
| USER=pawel | |
| running 1.1 | |
| running 1.2 | |
| running 1.3 | |
| running 1.4 | |
| running 2.1 | |
| running 2.1.1 | |
| running 2.2 | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load returned 3, expected 0 | |
| command executed: | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.2.fastq --quality PHRED_33 -o /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.2/obj 1>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.2/load.stdout 2>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.2/load.stderr | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.2.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.2.fastq:2:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - Too many bad records: records: 2, bad records: 1, bad records percentage: 0.50, allowed percentage: 0.05 | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID' | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - accession="obj" errors="1" status="failure" | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - load failed | |
| running 2.3 | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load returned 3, expected 0 | |
| command executed: | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.3.fastq --quality PHRED_33 -o /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.3/obj 1>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.3/load.stdout 2>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.3/load.stderr | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.3.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.3.fastq:2:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.3.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.3.fastq:4:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - Too many bad records: records: 4, bad records: 2, bad records percentage: 0.50, allowed percentage: 0.05 | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID' | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - accession="obj" errors="2" status="failure" | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - load failed | |
| running 2.4 | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load returned 3, expected 0 | |
| command executed: | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.4.fastq --quality PHRED_33 -o /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.4/obj 1>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.4/load.stdout 2>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/2.4/load.stderr | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.4.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.4.fastq:6:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.4.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/2.4.fastq:8:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - Too many bad records: records: 4, bad records: 2, bad records percentage: 0.50, allowed percentage: 0.05 | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID' | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - accession="obj" errors="2" status="failure" | |
| 2016-11-17T14:55:15 latf-load.2.7 err: data invalid while closing table - load failed | |
| running 2.5 | |
| running 2.6 | |
| running 2.7 | |
| running 2.8 | |
| running 2.8.1 | |
| running 2.9 | |
| running 2.9.1 | |
| running 3.1 | |
| running 3.2 | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load returned 3, expected 0 | |
| command executed: | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.2a.fastq /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.2b.fastq --quality PHRED_33 -o /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/3.2/obj 1>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/3.2/load.stdout 2>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/3.2/load.stderr | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.2b.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.2b.fastq:1:1:syntax error, unexpected '+' | |
| 2016-11-17T14:55:15 latf-load.2.7 err: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.2b.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 err: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.2b.fastq:2:1:syntax error, unexpected $undefined | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID' | |
| 2016-11-17T14:55:15 latf-load.2.7 err: format unsupported while parsing file - accession="obj" errors="2" status="failure" | |
| 2016-11-17T14:55:15 latf-load.2.7 err: format unsupported while parsing file - load failed | |
| running 3.3 | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load returned 3, expected 0 | |
| command executed: | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.3a.fastq /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.3b.fastq --quality PHRED_33 -o /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/3.3/obj 1>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/3.3/load.stdout 2>/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/actual/3.3/load.stderr | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.3a.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 warn: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.3a.fastq:1:1:syntax error, unexpected '+' | |
| 2016-11-17T14:55:15 latf-load.2.7 err: file="/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.3a.fastq" | |
| 2016-11-17T14:55:15 latf-load.2.7 err: /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader/input/3.3a.fastq:2:1:syntax error, unexpected $undefined | |
| 2016-11-17T14:55:15 latf-load.2.7 err: format unsupported while parsing file - accession="obj" errors="2" status="failure" | |
| 2016-11-17T14:55:15 latf-load.2.7 err: format unsupported while parsing file - load failed | |
| running 4.1 | |
| running 4.2 | |
| running 4.3 | |
| running 4.3.1 | |
| running 4.4 | |
| running 4.5 | |
| running 4.5.1 | |
| running 4.6 | |
| running 4.6.1 | |
| running 4.7 | |
| running 5.0 | |
| running 6.0 | |
| running 7.1 | |
| running 7.2 | |
| running 7.3 | |
| running 8.0 | |
| running 8.1 | |
| running 9.0 | |
| running 10.0 | |
| running 11.0 | |
| running 11.1 | |
| running 12.0 | |
| running 12.1 | |
| running 12.2 | |
| running 13.0 | |
| running 13.1 | |
| running 14.0 | |
| ++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| Run /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/wb-test-fastq | |
| Running 99 test cases... | |
| *** No errors detected | |
| ++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| Run /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-fastq-loader | |
| Running 1 test case... | |
| *** No errors detected | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastq-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/vcf-loader' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/vcf-loader -MD -o test-vcf-loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp -D__mod_name__=test/vcf-loader -D__file_name__=test-vcf-loader -D__file_ext__=cpp | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp: In destructor ‘VcfReaderFixture::~VcfReaderFixture()’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp:443:81: warning: throw will always call terminate() [-Wterminate] | |
| throw logic_error(string("~VcfReaderFixture: VcfReaderWhack failed")); | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp:443:81: note: in C++11 destructors default to noexcept | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp:446:84: warning: throw will always call terminate() [-Wterminate] | |
| throw logic_error(string("~VcfReaderFixture: KDirectoryRelease failed")); | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp:446:84: note: in C++11 destructors default to noexcept | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp: In destructor ‘VcfDatabaseFixture::~VcfDatabaseFixture()’: | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp:624:86: warning: throw will always call terminate() [-Wterminate] | |
| throw logic_error(string("~VcfDatabaseFixture: VDBManagerRelease failed")); | |
| ^ | |
| /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader/test-vcf-loader.cpp:624:86: note: in C++11 destructors default to noexcept | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-vcf-loader -DNDEBUG -m64 test-vcf-loader.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -lktst -lncbi-wvdb -lvcfloader -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/vcf-loader' | |
| ++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| Run /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-vcf-loader | |
| Running 20 test cases... | |
| *** No errors detected | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vcf-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/kget' | |
| File "test_kget.py", line 119 | |
| print "-" * 80 | |
| ^ | |
| SyntaxError: Missing parentheses in call to 'print' | |
| make[2]: *** [Makefile:44: download] Error 1 | |
| make[2]: Target 'runtests' not remade because of errors. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/kget' | |
| make[1]: *** [/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/Makefile.targets:90: kget_runtests] Error 2 | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/general-loader' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -MD -o test-general-loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/test-general-loader.cpp -D__mod_name__=test/general-loader -D__file_name__=test-general-loader -D__file_ext__=cpp | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -MD -o testsource.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/testsource.cpp -D__mod_name__=test/general-loader -D__file_name__=testsource -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-general-loader -DNDEBUG -m64 test-general-loader.o testsource.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp-norsrc -lncbi-wvdb-static -lload -lktst -Wl,-Bdynamic -lz -lbz2 -ldl -lpthread -Wl,-Bdynamic -lm | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/general-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/general-loader' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -MD -o test-general-writer.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/test-general-writer.cpp -D__mod_name__=test/general-loader -D__file_name__=test-general-writer -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-general-writer -DNDEBUG -m64 test-general-writer.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -Wl,-Bstatic -lgeneral-writer -Wl,-Bdynamic -lz -lbz2 -ldl -lpthread -Wl,-Bdynamic -lm | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/general-loader' | |
| make[3]: Entering directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/general-loader' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/tools/general-loader -MD -o test-gw-dumper.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader/test-gw-dumper.cpp -D__mod_name__=test/general-loader -D__file_name__=test-gw-dumper -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-gw-dumper -DNDEBUG -m64 test-gw-dumper.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lgeneral-writer -Wl,-Bdynamic -lz -lbz2 -ldl -lpthread -Wl,-Bdynamic -lm | |
| make[3]: Leaving directory '/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/obj/test/general-loader' | |
| running test case 1 | |
| running test case 1packed | |
| running test case 1override | |
| running test case 1override | |
| running test case 2 | |
| running test case 2packed | |
| running test case 3 | |
| running test case 3packed | |
| running test case 4 | |
| running test case 4packed | |
| running test case 5packed | |
| running test case 6 | |
| running test case 6packed | |
| ++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| Run /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-general-loader | |
| Unpacked protocol: Running 62 test cases... | |
| *** No errors detected | |
| Packed protocol: Running 62 test cases... | |
| *** No errors detected | |
| ++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| Run /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-general-writer | |
| CreateGw Success | |
| --------------------------------- | |
| addTable Success | |
| --------------------------------- | |
| addColumn Success | |
| --------------------------------- | |
| dbAddDatabase Success | |
| --------------------------------- | |
| dbAddTable Success | |
| --------------------------------- | |
| write Success | |
| --------------------------------- | |
| setDBMetadataNode Success | |
| --------------------------------- | |
| setTblMetadataNode Success | |
| --------------------------------- | |
| setColMetadataNode Success | |
| --------------------------------- | |
| setProgMsg Success | |
| --------------------------------- | |
| Attempting add table after endStream | |
| state violation adding table | |
| addTable correctly failed | |
| endStream Success | |
| --------------------------------- | |
| ++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| Run /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/test-gw-dumper | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/general-loader' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o bio-end/makeinputs.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall bio-end/makeinputs.cpp -D__mod_name__=test/vschema -D__file_name__=bio-end/makeinputs -D__file_ext__=cpp | |
| bio-end/makeinputs.cpp: In function ‘void run(const char*, bool, const int32_t*, const int32_t*, const int8_t*, int)’: | |
| bio-end/makeinputs.cpp:75:16: warning: ‘gw’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| delete gw; | |
| ^~ | |
| g++ -static-libstdc++ -static-libgcc -o ./bio-end-makeinputs -DNDEBUG -m64 bio-end/makeinputs.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -Wl,-Bstatic -lgeneral-writer -Wl,-Bdynamic -lz -lbz2 -ldl -lpthread -Wl,-Bdynamic -lm | |
| running test bio-end:excl-1 | |
| running test bio-end:excl-2 | |
| running test bio-end:excl-3 | |
| running test bio-end:excl-4 | |
| running test bio-end:incl-1 | |
| bio-end tests executed successfuly | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o idx-text/makeinputs.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall idx-text/makeinputs.cpp -D__mod_name__=test/vschema -D__file_name__=idx-text/makeinputs -D__file_ext__=cpp | |
| idx-text/makeinputs.cpp: In function ‘void run(const char*, TestCaseType, const string*, int)’: | |
| idx-text/makeinputs.cpp:101:16: warning: ‘gw’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| delete gw; | |
| ^~ | |
| idx-text/makeinputs.cpp:57:21: warning: ‘db_schema’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| const char* db_schema; | |
| ^~~~~~~~~ | |
| g++ -static-libstdc++ -static-libgcc -o ./idx-text-makeinputs -DNDEBUG -m64 idx-text/makeinputs.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -Wl,-Bstatic -lgeneral-writer -Wl,-Bdynamic -lz -lbz2 -ldl -lpthread -Wl,-Bdynamic -lm | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o idx-text/checklookup.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall idx-text/checklookup.cpp -D__mod_name__=test/vschema -D__file_name__=idx-text/checklookup -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o ./idx-text-checklookup -DNDEBUG -m64 idx-text/checklookup.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -Wl,-Bstatic -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| running test idx-text:ci-1 | |
| running test idx-text:ci-2 | |
| running test idx-text:ci-3 | |
| running test idx-text:ci-4 | |
| running test idx-text:ci-5 | |
| running test idx-text:cs-1 | |
| running test idx-text:cs-2 | |
| running test idx-text:cs-3 | |
| idx-text tests executed successfuly | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vschema' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/align-info' | |
| Usage: | |
| align-info [options] <db-path> | |
| Summary: | |
| Print database alignment information | |
| Parameters: | |
| db-path Path to the database | |
| Options: | |
| -a|--all print all information | |
| -r|--ref print refseq information [default] | |
| -b|--bam print bam header (if present) | |
| -Q|--qual print quality statistics (if present) | |
| -H|--headers print headers for output blocks | |
| -h|--help Output brief explanation for the program. | |
| -V|--version Display the version of the program then | |
| quit. | |
| -L|--log-level <level> Logging level as number or enum string. One | |
| of (fatal|sys|int|err|warn|info|debug) or | |
| (0-6) Current/default is warn | |
| -v|--verbose Increase the verbosity of the program | |
| status messages. Use multiple times for more | |
| verbosity. Negates quiet. | |
| -q|--quiet Turn off all status messages for the | |
| program. Negated by verbose. | |
| --option-file <file> Read more options and parameters from the | |
| file. | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/align-info : 2.7.0 | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/align-info' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/align-cache' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/align-cache' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-dump' | |
| g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/interfaces/override -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-dump/linux -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-dump/unix -I/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-dump -I/usr/src/ncbi-vdb-2.7.0/interfaces/ -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc/x86_64 -I/usr/src/ncbi-vdb-2.7.0/interfaces/cc/gcc -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/linux -I/usr/src/ncbi-vdb-2.7.0/interfaces/os/unix -I/usr/src/ncbi-vdb-2.7.0/interfaces/ext -I/usr/include -I. -MD -o makedb.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall makedb.cpp -D__mod_name__=test/vdb-dump -D__file_name__=makedb -D__file_ext__=cpp | |
| g++ -static-libstdc++ -static-libgcc -o /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/test-bin/vdb-dump-makedb -DNDEBUG -m64 makedb.o -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -L/home/pawel/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -Wl,-Bstatic -lkapp -lktst -lncbi-wvdb -Wl,-Bdynamic -ldl -lpthread -lxml2 -Wl,-Bdynamic -lm | |
| testing vdb-dump... | |
| 2016-11-17T14:57:28 vdb-dump.2.7 err: name incorrect while evaluating path within network system module - Scheme is 'https' | |
| 2016-11-17T14:57:28 vdb-dump.2.7 err: name incorrect while evaluating path within network system module - log failure: RC(rcText,rcString,rcConverting,rcBuffer,rcInsufficient) in 'error with http open '$(U)'' | |
| 2016-11-17T14:57:28 vdb-dump.2.7 int: item not found while constructing within virtual database module - the path 'SRR056386' cannot be opened as vdb-database or vdb-table | |
| 2016-11-17T14:57:28 vdb-dump.2.7 int: item not found while constructing within virtual database module - Maybe it is a legacy table. If so, specify a schema with the -S option | |
| 2016-11-17T14:57:28 vdb-dump.2.7 err: KDirectoryRelease() -> RC(rcVDB,rcNoTarg,rcConstructing,rcItem = rcLastObject_v1_0,rcNotFound) | |
| make[2]: *** [Makefile:66: vdb-dump] Error 3 | |
| make[2]: Target 'runtests' not remade because of errors. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-dump' | |
| make[1]: *** [/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/Makefile.targets:90: vdb-dump_runtests] Error 2 | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/ref-variation' | |
| 2016-11-17T14:57:28 vdb-config.2.7 int: path not found while opening node within configuration module - /repository/site | |
| no access to repository, skipping ref-variation test... | |
| 2016-11-17T14:57:28 vdb-config.2.7 int: path not found while opening node within configuration module - /repository/site | |
| no access to repository, skipping var-expand test... | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/ref-variation' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-validate' | |
| Starting vdb-validate tests... | |
| All vdb-validate tests succeed | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-validate' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/kar' | |
| Starting kar tests... | |
| Testing create mode... | |
| Testing create mode with existing archive... | |
| Testing force: -f create mode... | |
| Testing option variation --create ... | |
| Testing option variation --directory ... | |
| Testing option variation --force ... | |
| Testing md5: --md5 mode... | |
| Testing test mode... | |
| Testing option variation --test ... | |
| Testing longlist: -l mode... | |
| Testing extract mode... | |
| Testing extract mode --extract... | |
| could not locate old kar tool to run comparisons | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/kar' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/copycat' | |
| Starting copycat tests... | |
| <REDACTABLE_TYPES>INSDC:color:text,INSDC:x2cs:bin,INSDC:2cs:bin,INSDC:2cs:packed,INSDC:dna:text,INSDC:4na:bin,INSDC:4na:packed,INSDC:x2na:bin,INSDC:2na:bin,INSDC:2na:packed,NCBI:SRA:pos16,INSDC:quality:phred,INSDC:quality:log_odds,NCBI:qual4,INSDC:position:one,INSDC:position:zero,NCBI:fsamp4,NCBI:isamp1</REDACTABLE_TYPES> | |
| <INSDC_2cs_bin>2</INSDC_2cs_bin> | |
| <INSDC_2na_bin>2</INSDC_2na_bin> | |
| <INSDC_x2cs_bin>1</INSDC_x2cs_bin> | |
| <INSDC_x2na_bin>1</INSDC_x2na_bin> | |
| <kfg>/home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin</kfg> | |
| /home/pawel/ncbi-outdir/sra-tools/linux/gcc/x86_64/rel/bin/ncbi/vdb-copy.kfg | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/copycat' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastdump' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fastdump' | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-copy' | |
| Traceback (most recent call last): | |
| File "/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/check-exit-code.py", line 72, in <module> | |
| in_err = check_stream ( popca.stderr ) | |
| File "/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/check-exit-code.py", line 51, in check_stream | |
| if line.startswith ( "Usage:" ): | |
| TypeError: startswith first arg must be bytes or a tuple of bytes, not str | |
| make[2]: *** [Makefile:45: check_exit_code] Error 1 | |
| make[2]: Target 'runtests' not remade because of errors. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/vdb-copy' | |
| make[1]: *** [/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/Makefile.targets:90: vdb-copy_runtests] Error 2 | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/qual-recalib-stat' | |
| Traceback (most recent call last): | |
| File "/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/check-exit-code.py", line 72, in <module> | |
| in_err = check_stream ( popca.stderr ) | |
| File "/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/check-exit-code.py", line 51, in check_stream | |
| if line.startswith ( "Usage:" ): | |
| TypeError: startswith first arg must be bytes or a tuple of bytes, not str | |
| make[2]: *** [Makefile:45: check_exit_code] Error 1 | |
| make[2]: Target 'runtests' not remade because of errors. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/qual-recalib-stat' | |
| make[1]: *** [/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/Makefile.targets:90: qual-recalib-stat_runtests] Error 2 | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/sra-pileup' | |
| Traceback (most recent call last): | |
| File "/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/check-exit-code.py", line 71, in <module> | |
| in_out = check_stream ( popca.stdout ) | |
| File "/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/check-exit-code.py", line 51, in check_stream | |
| if line.startswith ( "Usage:" ): | |
| TypeError: startswith first arg must be bytes or a tuple of bytes, not str | |
| make[2]: *** [Makefile:45: check_exit_code] Error 1 | |
| make[2]: Target 'runtests' not remade because of errors. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/sra-pileup' | |
| make[1]: *** [/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/Makefile.targets:90: sra-pileup_runtests] Error 2 | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/srapath' | |
| Traceback (most recent call last): | |
| File "/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/check-exit-code.py", line 72, in <module> | |
| in_err = check_stream ( popca.stderr ) | |
| File "/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/check-exit-code.py", line 51, in check_stream | |
| if line.startswith ( "Usage:" ): | |
| TypeError: startswith first arg must be bytes or a tuple of bytes, not str | |
| make[2]: *** [Makefile:45: check_exit_code] Error 1 | |
| make[2]: Target 'runtests' not remade because of errors. | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/srapath' | |
| make[1]: *** [/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/build/Makefile.targets:90: srapath_runtests] Error 2 | |
| make[2]: Entering directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fuse' | |
| make[2]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test/fuse' | |
| make[1]: Target 'by_default' not remade because of errors. | |
| make[1]: Leaving directory '/tmp/yaourt-tmp-pawel/aur-sra-tools/src/sra-tools-2.7.0/test' | |
| make: *** [Makefile:48: test] Error 2 | |
| ==> ERROR: A failure occurred in check(). | |
| Aborting... | |
| ==> ERROR: Makepkg was unable to build sra-tools. | |
| ==> Restart building sra-tools ? [y/N] | |
| ==> ---------------------------------- | |
| ==> |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment