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rsangole/fs_error_after_custompackagecompilation.log

Created March 21, 2018 15:19
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fs_error_after_custompackagecompilation
Raw
fs_error_after_custompackagecompilation.log
> install.packages('fs',repos='http://cran.us.r-project.org')
Installing package into ‘/home/hw831/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 2 777k 2 19685 0 0 43174 0 0:00:18 --:--:-- 0:00:18 43168100 777k 100 777k 0 0 639k 0 0:00:01 0:00:01 --:--:-- 640k
* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** libs
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c id.cc -o id.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c utils.cc -o utils.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c file.cc -o file.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c path.cc -o path.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c link.cc -o link.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c fs.cc -o fs.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c dir.cc -o dir.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c error.cc -o error.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c unix/getmode.cc -o unix/getmode.o
g++ -std=c++0x -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c bsd/setmode.c -o bsd/setmode.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c bsd/strmode.c -o bsd/strmode.o
gcc -std=gnu99 -I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -I./libuv/include -I. -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include" -fpic -DU_STATIC_IMPLEMENTATION -O2 -g -c bsd/reallocarray.c -o bsd/reallocarray.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
(cd libuv && CC="gcc -std=gnu99" CFLAGS="-DU_STATIC_IMPLEMENTATION -O2 -g -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="" ./configure --quiet)
make --directory=libuv \
HAVE_DTRACE=0
make[1]: Entering directory '/tmp/RtmpALB79V/R.INSTALL1e3123bd2f5ed/fs/src/libuv'
CC src/libuv_la-fs-poll.lo
CC src/libuv_la-inet.lo
CC src/libuv_la-threadpool.lo
CC src/libuv_la-uv-common.lo
CC src/libuv_la-version.lo
CC src/unix/libuv_la-async.lo
CC src/unix/libuv_la-core.lo
CC src/unix/libuv_la-dl.lo
CC src/unix/libuv_la-fs.lo
CC src/unix/libuv_la-getaddrinfo.lo
CC src/unix/libuv_la-getnameinfo.lo
CC src/unix/libuv_la-loop-watcher.lo
CC src/unix/libuv_la-loop.lo
CC src/unix/libuv_la-pipe.lo
CC src/unix/libuv_la-poll.lo
CC src/unix/libuv_la-process.lo
CC src/unix/libuv_la-signal.lo
CC src/unix/libuv_la-stream.lo
CC src/unix/libuv_la-tcp.lo
CC src/unix/libuv_la-thread.lo
CC src/unix/libuv_la-timer.lo
CC src/unix/libuv_la-tty.lo
CC src/unix/libuv_la-udp.lo
CC src/unix/libuv_la-linux-core.lo
CC src/unix/libuv_la-linux-inotify.lo
CC src/unix/libuv_la-linux-syscalls.lo
CC src/unix/libuv_la-procfs-exepath.lo
CC src/unix/libuv_la-proctitle.lo
CC src/unix/libuv_la-sysinfo-loadavg.lo
CC src/unix/libuv_la-sysinfo-memory.lo
CCLD libuv.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[1]: Leaving directory '/tmp/RtmpALB79V/R.INSTALL1e3123bd2f5ed/fs/src/libuv'
g++ -std=c++0x -shared -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -o fs.so id.o utils.o file.o path.o link.o fs.o dir.o error.o unix/getmode.o RcppExports.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o ./libuv/.libs/libuv.a -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -lR
/usr/bin/ld: id.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
id.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
/usr/lib64/microsoft-r/3.3/lib64/R/share/make/shlib.mk:6: recipe for target 'fs.so' failed
make: *** [fs.so] Error 1
ERROR: compilation failed for package ‘fs’
* removing ‘/home/hw831/R/x86_64-pc-linux-gnu-library/3.3/fs’
Warning in install.packages :
installation of package ‘fs’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpvfzzct/downloaded_packages’
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