Created
November 28, 2020 16:28
-
-
Save mr-c/c8b4c61d511a80bfcae7bef65fde105e to your computer and use it in GitHub Desktop.
Snap 1.0.0 build log
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
| [0mI: Running in no-targz mode[0m | |
| [0mI: pbuilder: network access will be disabled during build[0m | |
| [0mI: Current time: Sat Nov 28 17:18:59 CET 2020[0m | |
| [0mI: pbuilder-time-stamp: 1606580339[0m | |
| [0mI: copying local configuration[0m | |
| [1;33mW: --override-config is not set; not updating apt.conf Read the manpage for details.[0m | |
| [0mI: mounting /proc filesystem[0m | |
| [0mI: mounting /sys filesystem[0m | |
| [0mI: creating /{dev,run}/shm[0m | |
| [0mI: mounting /dev/pts filesystem[0m | |
| [0mI: redirecting /dev/ptmx to /dev/pts/ptmx[0m | |
| [0mI: Mounting /home/michael/.ccache/[0m | |
| [0mI: policy-rc.d already exists[0m | |
| [0mI: Obtaining the cached apt archive contents[0m | |
| [0mI: Setting up ccache[0m | |
| [0mI: Copying source file[0m | |
| [0mI: copying [/home/michael/debian/snap-aligner_1.0.0+dfsg-1.dsc][0m | |
| [0mI: copying [/home/michael/debian/snap-aligner_1.0.0+dfsg.orig.tar.xz][0m | |
| [0mI: copying [/home/michael/debian/snap-aligner_1.0.0+dfsg-1.debian.tar.xz][0m | |
| [0mI: Extracting source[0m | |
| dpkg-source: warning: extracting unsigned source package (snap-aligner_1.0.0+dfsg-1.dsc) | |
| dpkg-source: info: extracting snap-aligner in snap-aligner-1.0.0+dfsg | |
| dpkg-source: info: unpacking snap-aligner_1.0.0+dfsg.orig.tar.xz | |
| dpkg-source: info: unpacking snap-aligner_1.0.0+dfsg-1.debian.tar.xz | |
| dpkg-source: info: using patch list from debian/patches/series | |
| dpkg-source: info: applying non-x86-and-kfreebsd | |
| dpkg-source: info: applying drop-msse | |
| dpkg-source: info: applying spelling | |
| [0mI: Not using root during the build.[0m | |
| [0mI: Installing the build-deps[0m | |
| [0mI: user script /var/cache/pbuilder/build/cow.3850978/tmp/hooks/D05deps starting[0m | |
| + DEPSPATH=/ | |
| + [ -n ] | |
| + set +ex | |
| [0mI: user script /var/cache/pbuilder/build/cow.3850978/tmp/hooks/D05deps finished[0m | |
| [0mI: user script /var/cache/pbuilder/build/cow.3850978/tmp/hooks/D10-man-db starting[0m | |
| I: Preseed man-db/auto-update to false | |
| [0mI: user script /var/cache/pbuilder/build/cow.3850978/tmp/hooks/D10-man-db finished[0m | |
| [0mI: -> Attempting to satisfy build-dependencies[0m | |
| Note, using file '/build/snap-aligner_1.0.0+dfsg-1.dsc' to get the build dependencies | |
| Reading package lists... | |
| Building dependency tree... | |
| Reading state information... | |
| The following NEW packages will be installed: | |
| autoconf automake autopoint autotools-dev bsdextrautils debhelper | |
| dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base | |
| groff-base help2man intltool-debian libarchive-zip-perl libcroco3 | |
| libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 | |
| libicu67 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 | |
| libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db | |
| po-debconf sensible-utils zlib1g-dev | |
| debconf: delaying package configuration, since apt-utils is not installed | |
| 0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded. | |
| Need to get 0 B/19.9 MB of archives. | |
| After this operation, 73.0 MB of additional disk space will be used. | |
| Selecting previously unselected package bsdextrautils. | |
| (Reading database ... | |
| (Reading database ... 5% | |
| (Reading database ... 10% | |
| (Reading database ... 15% | |
| (Reading database ... 20% | |
| (Reading database ... 25% | |
| (Reading database ... 30% | |
| (Reading database ... 35% | |
| (Reading database ... 40% | |
| (Reading database ... 45% | |
| (Reading database ... 50% | |
| (Reading database ... 55% | |
| (Reading database ... 60% | |
| (Reading database ... 65% | |
| (Reading database ... 70% | |
| (Reading database ... 75% | |
| (Reading database ... 80% | |
| (Reading database ... 85% | |
| (Reading database ... 90% | |
| (Reading database ... 95% | |
| (Reading database ... 100% | |
| (Reading database ... 10758 files and directories currently installed.) | |
| Preparing to unpack .../00-bsdextrautils_2.36.1-1_amd64.deb ... | |
| Unpacking bsdextrautils (2.36.1-1) ... | |
| Selecting previously unselected package libuchardet0:amd64. | |
| Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... | |
| Unpacking libuchardet0:amd64 (0.0.7-1) ... | |
| Selecting previously unselected package groff-base. | |
| Preparing to unpack .../02-groff-base_1.22.4-5_amd64.deb ... | |
| Unpacking groff-base (1.22.4-5) ... | |
| Selecting previously unselected package libpipeline1:amd64. | |
| Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... | |
| Unpacking libpipeline1:amd64 (1.5.3-1) ... | |
| Selecting previously unselected package man-db. | |
| Preparing to unpack .../04-man-db_2.9.3-2_amd64.deb ... | |
| Unpacking man-db (2.9.3-2) ... | |
| Selecting previously unselected package liblocale-gettext-perl. | |
| Preparing to unpack .../05-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... | |
| Unpacking liblocale-gettext-perl (1.07-4+b1) ... | |
| Selecting previously unselected package sensible-utils. | |
| Preparing to unpack .../06-sensible-utils_0.0.12+nmu1_all.deb ... | |
| Unpacking sensible-utils (0.0.12+nmu1) ... | |
| Selecting previously unselected package libmagic-mgc. | |
| Preparing to unpack .../07-libmagic-mgc_1%3a5.38-5_amd64.deb ... | |
| Unpacking libmagic-mgc (1:5.38-5) ... | |
| Selecting previously unselected package libmagic1:amd64. | |
| Preparing to unpack .../08-libmagic1_1%3a5.38-5_amd64.deb ... | |
| Unpacking libmagic1:amd64 (1:5.38-5) ... | |
| Selecting previously unselected package file. | |
| Preparing to unpack .../09-file_1%3a5.38-5_amd64.deb ... | |
| Unpacking file (1:5.38-5) ... | |
| Selecting previously unselected package gettext-base. | |
| Preparing to unpack .../10-gettext-base_0.19.8.1-10_amd64.deb ... | |
| Unpacking gettext-base (0.19.8.1-10) ... | |
| Selecting previously unselected package libsigsegv2:amd64. | |
| Preparing to unpack .../11-libsigsegv2_2.12-2_amd64.deb ... | |
| Unpacking libsigsegv2:amd64 (2.12-2) ... | |
| Selecting previously unselected package m4. | |
| Preparing to unpack .../12-m4_1.4.18-4_amd64.deb ... | |
| Unpacking m4 (1.4.18-4) ... | |
| Selecting previously unselected package autoconf. | |
| Preparing to unpack .../13-autoconf_2.69-11.1_all.deb ... | |
| Unpacking autoconf (2.69-11.1) ... | |
| Selecting previously unselected package autotools-dev. | |
| Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... | |
| Unpacking autotools-dev (20180224.1) ... | |
| Selecting previously unselected package automake. | |
| Preparing to unpack .../15-automake_1%3a1.16.2-4_all.deb ... | |
| Unpacking automake (1:1.16.2-4) ... | |
| Selecting previously unselected package autopoint. | |
| Preparing to unpack .../16-autopoint_0.19.8.1-10_all.deb ... | |
| Unpacking autopoint (0.19.8.1-10) ... | |
| Selecting previously unselected package libtool. | |
| Preparing to unpack .../17-libtool_2.4.6-14_all.deb ... | |
| Unpacking libtool (2.4.6-14) ... | |
| Selecting previously unselected package dh-autoreconf. | |
| Preparing to unpack .../18-dh-autoreconf_19_all.deb ... | |
| Unpacking dh-autoreconf (19) ... | |
| Selecting previously unselected package libdebhelper-perl. | |
| Preparing to unpack .../19-libdebhelper-perl_13.2.1_all.deb ... | |
| Unpacking libdebhelper-perl (13.2.1) ... | |
| Selecting previously unselected package libarchive-zip-perl. | |
| Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... | |
| Unpacking libarchive-zip-perl (1.68-1) ... | |
| Selecting previously unselected package libsub-override-perl. | |
| Preparing to unpack .../21-libsub-override-perl_0.09-2_all.deb ... | |
| Unpacking libsub-override-perl (0.09-2) ... | |
| Selecting previously unselected package libfile-stripnondeterminism-perl. | |
| Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.9.0-1_all.deb ... | |
| Unpacking libfile-stripnondeterminism-perl (1.9.0-1) ... | |
| Selecting previously unselected package dh-strip-nondeterminism. | |
| Preparing to unpack .../23-dh-strip-nondeterminism_1.9.0-1_all.deb ... | |
| Unpacking dh-strip-nondeterminism (1.9.0-1) ... | |
| Selecting previously unselected package libelf1:amd64. | |
| Preparing to unpack .../24-libelf1_0.182-1_amd64.deb ... | |
| Unpacking libelf1:amd64 (0.182-1) ... | |
| Selecting previously unselected package dwz. | |
| Preparing to unpack .../25-dwz_0.13-5_amd64.deb ... | |
| Unpacking dwz (0.13-5) ... | |
| Selecting previously unselected package libglib2.0-0:amd64. | |
| Preparing to unpack .../26-libglib2.0-0_2.66.3-1_amd64.deb ... | |
| Unpacking libglib2.0-0:amd64 (2.66.3-1) ... | |
| Selecting previously unselected package libicu67:amd64. | |
| Preparing to unpack .../27-libicu67_67.1-4_amd64.deb ... | |
| Unpacking libicu67:amd64 (67.1-4) ... | |
| Selecting previously unselected package libxml2:amd64. | |
| Preparing to unpack .../28-libxml2_2.9.10+dfsg-6.2_amd64.deb ... | |
| Unpacking libxml2:amd64 (2.9.10+dfsg-6.2) ... | |
| Selecting previously unselected package libcroco3:amd64. | |
| Preparing to unpack .../29-libcroco3_0.6.13-1_amd64.deb ... | |
| Unpacking libcroco3:amd64 (0.6.13-1) ... | |
| Selecting previously unselected package gettext. | |
| Preparing to unpack .../30-gettext_0.19.8.1-10_amd64.deb ... | |
| Unpacking gettext (0.19.8.1-10) ... | |
| Selecting previously unselected package intltool-debian. | |
| Preparing to unpack .../31-intltool-debian_0.35.0+20060710.5_all.deb ... | |
| Unpacking intltool-debian (0.35.0+20060710.5) ... | |
| Selecting previously unselected package po-debconf. | |
| Preparing to unpack .../32-po-debconf_1.0.21_all.deb ... | |
| Unpacking po-debconf (1.0.21) ... | |
| Selecting previously unselected package debhelper. | |
| Preparing to unpack .../33-debhelper_13.2.1_all.deb ... | |
| Unpacking debhelper (13.2.1) ... | |
| Selecting previously unselected package help2man. | |
| Preparing to unpack .../34-help2man_1.47.16_amd64.deb ... | |
| Unpacking help2man (1.47.16) ... | |
| Selecting previously unselected package zlib1g-dev:amd64. | |
| Preparing to unpack .../35-zlib1g-dev_1%3a1.2.11.dfsg-2_amd64.deb ... | |
| Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... | |
| Setting up libpipeline1:amd64 (1.5.3-1) ... | |
| Setting up bsdextrautils (2.36.1-1) ... | |
| update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode | |
| Setting up libicu67:amd64 (67.1-4) ... | |
| Setting up libmagic-mgc (1:5.38-5) ... | |
| Setting up libarchive-zip-perl (1.68-1) ... | |
| Setting up libglib2.0-0:amd64 (2.66.3-1) ... | |
| No schema files found: doing nothing. | |
| Setting up libdebhelper-perl (13.2.1) ... | |
| Setting up libmagic1:amd64 (1:5.38-5) ... | |
| Setting up gettext-base (0.19.8.1-10) ... | |
| Setting up file (1:5.38-5) ... | |
| Setting up autotools-dev (20180224.1) ... | |
| Setting up libsigsegv2:amd64 (2.12-2) ... | |
| Setting up autopoint (0.19.8.1-10) ... | |
| Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... | |
| Setting up sensible-utils (0.0.12+nmu1) ... | |
| Setting up libuchardet0:amd64 (0.0.7-1) ... | |
| Setting up libsub-override-perl (0.09-2) ... | |
| Setting up libelf1:amd64 (0.182-1) ... | |
| Setting up libxml2:amd64 (2.9.10+dfsg-6.2) ... | |
| Setting up liblocale-gettext-perl (1.07-4+b1) ... | |
| Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... | |
| Setting up libtool (2.4.6-14) ... | |
| Setting up m4 (1.4.18-4) ... | |
| Setting up help2man (1.47.16) ... | |
| Setting up libcroco3:amd64 (0.6.13-1) ... | |
| Setting up autoconf (2.69-11.1) ... | |
| Setting up dh-strip-nondeterminism (1.9.0-1) ... | |
| Setting up dwz (0.13-5) ... | |
| Setting up groff-base (1.22.4-5) ... | |
| Setting up automake (1:1.16.2-4) ... | |
| update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode | |
| Setting up gettext (0.19.8.1-10) ... | |
| Setting up man-db (2.9.3-2) ... | |
| Not building database; man-db/auto-update is not 'true'. | |
| Setting up intltool-debian (0.35.0+20060710.5) ... | |
| Setting up po-debconf (1.0.21) ... | |
| Setting up debhelper (13.2.1) ... | |
| Setting up dh-autoreconf (19) ... | |
| Processing triggers for libc-bin (2.31-4) ... | |
| W: --force-yes is deprecated, use one of the options starting with --allow instead. | |
| Reading package lists... | |
| Building dependency tree... | |
| Reading state information... | |
| debian-ports-archive-keyring is already the newest version (2019.11.05). | |
| eatmydata is already the newest version (105-9). | |
| 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. | |
| W: --force-yes is deprecated, use one of the options starting with --allow instead. | |
| [0mI: Copying back the cached apt archive contents[0m | |
| [0mI: Building the package[0m | |
| [0mI: Running cd /build/snap-aligner-1.0.0+dfsg/ && env PATH="/usr/lib/ccache:/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc [0m | |
| dpkg-buildpackage: info: source package snap-aligner | |
| dpkg-buildpackage: info: source version 1.0.0+dfsg-1 | |
| dpkg-buildpackage: info: source distribution UNRELEASED | |
| dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org> | |
| dpkg-source --before-build . | |
| dpkg-buildpackage: info: host architecture amd64 | |
| debian/rules clean | |
| dh clean | |
| debian/rules override_dh_auto_clean | |
| make[1]: Entering directory '/build/snap-aligner-1.0.0+dfsg' | |
| dh_auto_clean | |
| make -j8 clean | |
| make[2]: Entering directory '/build/snap-aligner-1.0.0+dfsg' | |
| rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP | |
| make[2]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' | |
| rm -f debian/*.1 | |
| rm -f */*.d */*/*.d | |
| make[1]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' | |
| dh_clean | |
| dpkg-source -b . | |
| dpkg-source: info: using source format '3.0 (quilt)' | |
| dpkg-source: info: building snap-aligner using existing ./snap-aligner_1.0.0+dfsg.orig.tar.xz | |
| dpkg-source: info: using patch list from debian/patches/series | |
| dpkg-source: info: building snap-aligner in snap-aligner_1.0.0+dfsg-1.debian.tar.xz | |
| dpkg-source: info: building snap-aligner in snap-aligner_1.0.0+dfsg-1.dsc | |
| debian/rules binary | |
| dh binary | |
| dh_update_autotools_config | |
| dh_autoreconf | |
| dh_auto_configure | |
| debian/rules override_dh_auto_build | |
| make[1]: Entering directory '/build/snap-aligner-1.0.0+dfsg' | |
| dh_auto_build | |
| make -j8 "INSTALL=install --strip-program=true" | |
| make[2]: Entering directory '/build/snap-aligner-1.0.0+dfsg' | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp | |
| SNAPLib/AlignerContext.cpp: In member function 'void AlignerContext::printStats()': | |
| SNAPLib/AlignerContext.cpp:486:75: warning: format '%lld' expects argument of type 'long long int', but argument 9 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 486 | fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%0.2f%%\t%lld\tt%.0f\n", | |
| | ~~~^ | |
| | | | |
| | long long int | |
| | %ld | |
| ...... | |
| 492 | stats->lvCalls, | |
| | ~~~~~~~~~~~~~~ | |
| | | | |
| | _int64 {aka long int} | |
| SNAPLib/AlignerContext.cpp:486:90: warning: format '%lld' expects argument of type 'long long int', but argument 11 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 486 | fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%0.2f%%\t%lld\tt%.0f\n", | |
| | ~~~^ | |
| | | | |
| | long long int | |
| | %ld | |
| ...... | |
| 494 | stats->totalReads, | |
| | ~~~~~~~~~~~~~~~~~ | |
| | | | |
| | _int64 {aka long int} | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp | |
| SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': | |
| SNAPLib/Error.cpp:89:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 89 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); | |
| | ~~~^ ~~~~~~~~~ | |
| | | | | |
| | long long int _int64 {aka long int} | |
| | %ld | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp | |
| SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': | |
| SNAPLib/Genome.cpp:164:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] | |
| 164 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, (areALTContigsMarked ? GENOME_FLAG_ALT_CONTIGS_MARKED : 0)); | |
| | ~~~^ ~~~~~~ | |
| | | | | |
| | | long int | |
| | long long int | |
| | %ld | |
| SNAPLib/Genome.cpp:174:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 174 | fprintf(saveFile, "%lld %x %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), contigs[i].name); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int _int64 {aka long int} | |
| | %ld | |
| SNAPLib/Genome.cpp:176:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 176 | fprintf(saveFile, "%lld %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), contigs[i].name); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int _int64 {aka long int} | |
| | %ld | |
| SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': | |
| SNAPLib/Genome.cpp:267:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] | |
| 267 | if (1 != sscanf(contigNameBuffer, "%lld", &contigStart)) { | |
| | ~~~^ ~~~~~~~~~~~~ | |
| | | | | |
| | | _int64* {aka long int*} | |
| | long long int* | |
| | %ld | |
| SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool, bool*)': | |
| SNAPLib/Genome.cpp:401:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] | |
| 401 | if (NULL == retval || 2 != sscanf(linebuf,"%lld %d\n", nBases, nContigs)) { | |
| | ~~~^ ~~~~~~ | |
| | | | | |
| | | GenomeDistance* {aka long int*} | |
| | long long int* | |
| | %ld | |
| SNAPLib/Genome.cpp:410:31: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] | |
| 410 | if (3 == sscanf(linebuf, "%lld %d %d\n", nBases, nContigs, &flags)) | |
| | ~~~^ ~~~~~~ | |
| | | | | |
| | | GenomeDistance* {aka long int*} | |
| | long long int* | |
| | %ld | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp | |
| SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)': | |
| SNAPLib/DataReader.cpp:1751:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] | |
| 1751 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int long int | |
| | %ld | |
| SNAPLib/DataReader.cpp:1755:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] | |
| 1755 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int long int | |
| | %ld | |
| SNAPLib/DataReader.cpp:1759:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] | |
| 1759 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int long int | |
| | %ld | |
| SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)': | |
| SNAPLib/DataReader.cpp:1900:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 1900 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int _int64 {aka long int} | |
| | %ld | |
| SNAPLib/DataReader.cpp:1900:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 1900 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | |
| | ~~~^ ~~~~~~ | |
| | | | | |
| | long long int _int64 {aka long int} | |
| | %ld | |
| SNAPLib/DataReader.cpp:1904:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 1904 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset()); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int _int64 {aka long int} | |
| | %ld | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp | |
| SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': | |
| SNAPLib/GenomeIndex.cpp:419:21: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 419 | fprintf(stderr,"%llds\n", (timeInMillis() + 500 - start) / 1000); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int _int64 {aka long int} | |
| | %ld | |
| SNAPLib/GenomeIndex.cpp:794:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] | |
| 794 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int _uint64 {aka long unsigned int} | |
| | %ld | |
| SNAPLib/GenomeIndex.cpp:794:61: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] | |
| 794 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int _uint64 {aka long unsigned int} | |
| | %ld | |
| SNAPLib/GenomeIndex.cpp:794:103: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] | |
| 794 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | |
| | ~~~^ ~~~~~~~~~~~ | |
| | | | | |
| | long long int _uint64 {aka long unsigned int} | |
| | %ld | |
| SNAPLib/GenomeIndex.cpp:849:36: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] | |
| 849 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | |
| | ~~~^ | |
| | | | |
| | long long int | |
| | %ld | |
| 850 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | |
| | _uint64 {aka long unsigned int} | |
| SNAPLib/GenomeIndex.cpp:849:50: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] | |
| 849 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | |
| | ~~~^ | |
| | | | |
| | long long int | |
| | %ld | |
| 850 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | |
| | ~~~~~~~~~~~~~~~~~ | |
| | | | |
| | size_t {aka long unsigned int} | |
| SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)': | |
| SNAPLib/GenomeIndex.cpp:1707:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] | |
| 1707 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long int* _int64* {aka long int*} | |
| | %ld | |
| SNAPLib/GenomeIndex.cpp:1707:71: warning: format '%lld' expects argument of type 'long long int*', but argument 10 has type 'size_t*' {aka 'long unsigned int*'} [-Wformat=] | |
| 1707 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | |
| | ~~~^ | |
| | | | |
| | long long int* | |
| | %ld | |
| 1708 | &hashTableKeySize, &hashTablesFileSize, &smallHashTable, &locationSize))) { | |
| | ~~~~~~~~~~~~~~~~~~~ | |
| | | | |
| | size_t* {aka long unsigned int*} | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp | |
| In file included from SNAPLib/PairedAligner.cpp:47: | |
| SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' | |
| 668 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | |
| | ^ | |
| SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' | |
| SNAPLib/PairedAligner.cpp: In member function 'virtual void PairedAlignerContext::runIterationThread()': | |
| SNAPLib/PairedAligner.cpp:618:68: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] | |
| 618 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long unsigned int long unsigned int | |
| | %lu | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp | |
| SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': | |
| SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] | |
| 44 | } | |
| | ^ | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp | |
| SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThread()': | |
| SNAPLib/SingleAligner.cpp:181:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] | |
| 181 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long unsigned int long unsigned int | |
| | %lu | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp | |
| SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': | |
| SNAPLib/Util.cpp:166:28: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] | |
| 166 | sprintf(tempBuf, ",%03lld", x % 1000); | |
| | ~~~~~^ ~~~~~~~~ | |
| | | | | |
| | | _uint64 {aka long unsigned int} | |
| | long long int | |
| | %03ld | |
| SNAPLib/Util.cpp:169:25: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] | |
| 169 | sprintf(tempBuf, "%lld", x); | |
| | ~~~^ ~ | |
| | | | | |
| | | _uint64 {aka long unsigned int} | |
| | long long int | |
| | %ld | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp | |
| In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: | |
| SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' | |
| 668 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | |
| | ^ | |
| SNAPLib/IntersectingPairedEndAligner.h:668:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp | |
| g++ -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp | |
| SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': | |
| SNAPLib/SAM.cpp:1247:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'GenomeLocation' {aka 'long int'} [-Wformat=] | |
| 1247 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu\n", contigs[i].name, end - start); | |
| | ~~~^ ~~~~~~~~~~~ | |
| | | | | |
| | long long unsigned int GenomeLocation {aka long int} | |
| | %lu | |
| SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writePairs(const ReaderContext&, LandauVishkinWithCigar*, AffineGapVectorizedWithCigar*, bool, char*, size_t, size_t*, size_t*, Read**, GenomeLocation*, PairedAlignmentResult*, bool, bool, char*, int*, int*, bool*, bool*) const': | |
| SNAPLib/SAM.cpp:1957:77: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 1957 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s\n", | |
| | ~~~^ | |
| | | | |
| | long long unsigned int | |
| | %lu | |
| ...... | |
| 1961 | positionInContig[whichRead], | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | |
| | GenomeDistance {aka long int} | |
| SNAPLib/SAM.cpp:1957:95: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 1957 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s\n", | |
| | ~~~^ | |
| | | | |
| | long long unsigned int | |
| | %lu | |
| ...... | |
| 1965 | matePositionInContig[whichRead], | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | |
| | GenomeDistance {aka long int} | |
| SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, LandauVishkinWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': | |
| SNAPLib/SAM.cpp:2153:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 2153 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | |
| | ~~~^ | |
| | | | |
| | long long unsigned int | |
| | %lu | |
| ...... | |
| 2157 | positionInContig, | |
| | ~~~~~~~~~~~~~~~~ | |
| | | | |
| | GenomeDistance {aka long int} | |
| SNAPLib/SAM.cpp:2153:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 2153 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | |
| | ~~~^ | |
| | | | |
| | long long unsigned int | |
| | %lu | |
| ...... | |
| 2161 | matePositionInContig, | |
| | ~~~~~~~~~~~~~~~~~~~~ | |
| | | | |
| | GenomeDistance {aka long int} | |
| SNAPLib/SAM.cpp:2153:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 2153 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | |
| | ~~~^ | |
| | | | |
| | long long int | |
| | %ld | |
| ...... | |
| 2162 | templateLength, | |
| | ~~~~~~~~~~~~~~ | |
| | | | |
| | _int64 {aka long int} | |
| SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, AffineGapVectorizedWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': | |
| SNAPLib/SAM.cpp:2358:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 2358 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | |
| | ~~~^ | |
| | | | |
| | long long unsigned int | |
| | %lu | |
| ...... | |
| 2362 | positionInContig, | |
| | ~~~~~~~~~~~~~~~~ | |
| | | | |
| | GenomeDistance {aka long int} | |
| SNAPLib/SAM.cpp:2358:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 2358 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | |
| | ~~~^ | |
| | | | |
| | long long unsigned int | |
| | %lu | |
| ...... | |
| 2366 | matePositionInContig, | |
| | ~~~~~~~~~~~~~~~~~~~~ | |
| | | | |
| | GenomeDistance {aka long int} | |
| SNAPLib/SAM.cpp:2358:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] | |
| 2358 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s\n", | |
| | ~~~^ | |
| | | | |
| | long long int | |
| | %ld | |
| ...... | |
| 2367 | templateLength, | |
| | ~~~~~~~~~~~~~~ | |
| | | | |
| | _int64 {aka long int} | |
| SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': | |
| SNAPLib/SAM.cpp:2687:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 2687 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long unsigned int GenomeDistance {aka long int} | |
| | %lu | |
| SNAPLib/SAM.cpp:2690:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 2690 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long unsigned int GenomeDistance {aka long int} | |
| | %lu | |
| SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': | |
| SNAPLib/SAM.cpp:2777:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 2777 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long unsigned int GenomeDistance {aka long int} | |
| | %lu | |
| SNAPLib/SAM.cpp:2780:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] | |
| 2780 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | |
| | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| | | | | |
| | long long unsigned int GenomeDistance {aka long int} | |
| | %lu | |
| SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': | |
| SNAPLib/SAM.cpp:1183:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] | |
| 1183 | commandLine[0] = '\0'; | |
| | ~~~~~~~~~~~~~~~^~~~~~ | |
| SNAPLib/SAM.cpp:1182:40: note: at offset 0 to an object with size 0 allocated by 'operator new []' here | |
| 1182 | commandLine = new char[commandLineSize]; | |
| | ^ | |
| SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': | |
| SNAPLib/SAM.cpp:2687:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] | |
| 2687 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | |
| | ^~~~ | |
| SNAPLib/SAM.cpp:2687:54: note: directive argument in the range [1, 9223372036854775807] | |
| 2687 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | |
| | ^~~~~~~ | |
| In file included from /usr/include/stdio.h:867, | |
| from /usr/include/c++/10/cstdio:42, | |
| from /usr/include/c++/10/fstream:41, | |
| from SNAPLib/stdafx.h:14, | |
| from SNAPLib/SAM.cpp:19: | |
| /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 | |
| 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| 68 | __bos (__s), __fmt, __va_arg_pack ()); | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| SNAPLib/SAM.cpp:2690:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] | |
| 2690 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | |
| | ^~~~ | |
| SNAPLib/SAM.cpp:2690:52: note: directive argument in the range [1, 9223372036854775807] | |
| 2690 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | |
| | ^~~~~~~ | |
| In file included from /usr/include/stdio.h:867, | |
| from /usr/include/c++/10/cstdio:42, | |
| from /usr/include/c++/10/fstream:41, | |
| from SNAPLib/stdafx.h:14, | |
| from SNAPLib/SAM.cpp:19: | |
| /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 | |
| 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| 68 | __bos (__s), __fmt, __va_arg_pack ()); | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': | |
| SNAPLib/SAM.cpp:2777:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] | |
| 2777 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | |
| | ^~~~ | |
| SNAPLib/SAM.cpp:2777:54: note: directive argument in the range [1, 9223372036854775807] | |
| 2777 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | |
| | ^~~~~~~ | |
| In file included from /usr/include/stdio.h:867, | |
| from /usr/include/c++/10/cstdio:42, | |
| from /usr/include/c++/10/fstream:41, | |
| from SNAPLib/stdafx.h:14, | |
| from SNAPLib/SAM.cpp:19: | |
| /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 | |
| 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| 68 | __bos (__s), __fmt, __va_arg_pack ()); | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| SNAPLib/SAM.cpp:2780:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] | |
| 2780 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | |
| | ^~~~ | |
| SNAPLib/SAM.cpp:2780:52: note: directive argument in the range [1, 9223372036854775807] | |
| 2780 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | |
| | ^~~~~~~ | |
| In file included from /usr/include/stdio.h:867, | |
| from /usr/include/c++/10/cstdio:42, | |
| from /usr/include/c++/10/fstream:41, | |
| from SNAPLib/stdafx.h:14, | |
| from SNAPLib/SAM.cpp:19: | |
| /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 | |
| 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| 68 | __bos (__s), __fmt, __va_arg_pack ()); | |
| | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| g++ -o snap-aligner -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz | |
| g++ -o unit_tests -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz | |
| echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o | |
| SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o | |
| echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o | |
| SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o | |
| g++ -o SNAPCommand -g -O2 -fdebug-prefix-map=/build/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -MMD -ISNAPLib -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz | |
| make[2]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' | |
| help2man --no-discard-stderr --no-info --version-string="1.0.0" \ | |
| --name "scalable nucleotide alignment program" \ | |
| --help-option=" " ./snap-aligner > debian/snap-aligner.1 | |
| for option in index single paired; do help2man \ | |
| --no-discard-stderr --no-info --version-string="1.0.0" \ | |
| --include=debian/snap-aligner-${option}-man-include \ | |
| --help-option=" " "./snap-aligner ${option}" > \ | |
| debian/snap-aligner-${option}.1; done | |
| help2man --no-discard-stderr --no-info --version-string="1.0.0" \ | |
| --name "scalable nucleotide alignment program" \ | |
| --help-option=" " ./SNAPCommand > debian/SNAPCommand.1 | |
| make[1]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' | |
| debian/rules override_dh_auto_test | |
| make[1]: Entering directory '/build/snap-aligner-1.0.0+dfsg' | |
| dh_auto_test | |
| ./unit_tests | |
| AffineGapTest: | |
| - synthetic: [OK] | |
| AffineGapVectorizedTest: | |
| - equal strings: [OK] | |
| - one deletion: [OK] | |
| - long deletion: [OK] | |
| - long insertion: [OK] | |
| - synthetic: [OK] | |
| EventTest: | |
| - many waiters: [OK] | |
| - single waiters: [OK] | |
| LandauVishkinTest: | |
| - equal strings: [OK] | |
| - prefixes: [OK] | |
| - non-equal strings: [OK] | |
| - overly distant strings: [OK] | |
| - CIGAR strings: [OK] | |
| ProbabilityDistanceTest: | |
| - basic probabilities: [OK] | |
| - indels: [OK] | |
| 15 / 15 tests passed. | |
| make[1]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' | |
| create-stamp debian/debhelper-build-stamp | |
| dh_testroot | |
| dh_prep | |
| dh_auto_install | |
| dh_install | |
| dh_installdocs | |
| dh_installchangelogs | |
| debian/rules override_dh_installexamples | |
| make[1]: Entering directory '/build/snap-aligner-1.0.0+dfsg' | |
| dh_installexamples | |
| find debian/snap-aligner/usr/share/doc/snap-aligner/examples -print0 | xargs -0 chmod a-x | |
| make[1]: Leaving directory '/build/snap-aligner-1.0.0+dfsg' | |
| dh_installman | |
| dh_perl | |
| dh_link | |
| dh_strip_nondeterminism | |
| dh_compress | |
| dh_fixperms | |
| dh_missing | |
| dh_dwz -a | |
| dh_strip -a | |
| dh_makeshlibs -a | |
| dh_shlibdeps -a | |
| dh_installdeb | |
| dh_gencontrol | |
| dh_md5sums | |
| dh_builddeb | |
| dpkg-deb: building package 'snap-aligner' in '../snap-aligner_1.0.0+dfsg-1_amd64.deb'. | |
| dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_1.0.0+dfsg-1_amd64.deb'. | |
| dpkg-genbuildinfo | |
| dpkg-genchanges >../snap-aligner_1.0.0+dfsg-1_amd64.changes | |
| dpkg-genchanges: info: including full source code in upload | |
| dpkg-source --after-build . | |
| dpkg-buildpackage: info: full upload (original source is included) | |
| [0mI: copying local configuration[0m | |
| [0mI: user script /var/cache/pbuilder/build/cow.3850978/tmp/hooks/B20autopkgtest starting[0m | |
| + cd /build/snap-aligner-1.0.0+dfsg/debian/.. | |
| + '[' '!' -f debian/tests/control ']' | |
| + '[' '!' -f debian/files ']' | |
| + OPTS= | |
| + '[' -n '' ']' | |
| + unset newpid_name | |
| + apt-cache policy newpid | |
| + grep -q newpid: | |
| + echo 'The newpid package seems to be available, considering for installation' | |
| The newpid package seems to be available, considering for installation | |
| + newpid_name=newpid | |
| + apt-get install -y autopkgtest apt-utils pbuilder newpid | |
| Reading package lists... | |
| Building dependency tree... | |
| Reading state information... | |
| The following additional packages will be installed: | |
| debootstrap libcap2 libcap2-bin libexpat1 libncurses6 libprocps8 libpsl5 | |
| libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline8 | |
| mailcap media-types mime-support procps python3 python3-chardet | |
| python3-debian python3-minimal python3-pkg-resources python3-six python3.8 | |
| python3.8-minimal readline-common wget | |
| Suggested packages: | |
| lxc lxd ovmf qemu-efi-aarch64 qemu-efi-arm qemu-system qemu-utils schroot | |
| vmdb2 ubuntu-archive-keyring squid-deb-proxy-client gdebi-core python3-doc | |
| python3-tk python3-venv python3-setuptools python3.8-venv python3.8-doc | |
| binfmt-support readline-doc | |
| Recommended packages: | |
| autodep8 gnupg arch-test libpam-cap libgpm2 publicsuffix devscripts fakeroot | |
| net-tools | iproute2 sudo psmisc python3-apt ca-certificates | |
| The following NEW packages will be installed: | |
| apt-utils autopkgtest debootstrap libcap2 libcap2-bin libexpat1 libncurses6 | |
| libprocps8 libpsl5 libpython3-stdlib libpython3.8-minimal | |
| libpython3.8-stdlib libreadline8 mailcap media-types mime-support newpid | |
| pbuilder procps python3 python3-chardet python3-debian python3-minimal | |
| python3-pkg-resources python3-six python3.8 python3.8-minimal | |
| readline-common wget | |
| debconf: delaying package configuration, since apt-utils is not installed | |
| 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. | |
| Need to get 0 B/8209 kB of archives. | |
| After this operation, 29.9 MB of additional disk space will be used. | |
| Selecting previously unselected package libpython3.8-minimal:amd64. | |
| (Reading database ... | |
| (Reading database ... 5% | |
| (Reading database ... 10% | |
| (Reading database ... 15% | |
| (Reading database ... 20% | |
| (Reading database ... 25% | |
| (Reading database ... 30% | |
| (Reading database ... 35% | |
| (Reading database ... 40% | |
| (Reading database ... 45% | |
| (Reading database ... 50% | |
| (Reading database ... 55% | |
| (Reading database ... 60% | |
| (Reading database ... 65% | |
| (Reading database ... 70% | |
| (Reading database ... 75% | |
| (Reading database ... 80% | |
| (Reading database ... 85% | |
| (Reading database ... 90% | |
| (Reading database ... 95% | |
| (Reading database ... 100% | |
| (Reading database ... 12846 files and directories currently installed.) | |
| Preparing to unpack .../libpython3.8-minimal_3.8.6-1_amd64.deb ... | |
| Unpacking libpython3.8-minimal:amd64 (3.8.6-1) ... | |
| Selecting previously unselected package libexpat1:amd64. | |
| Preparing to unpack .../libexpat1_2.2.10-1_amd64.deb ... | |
| Unpacking libexpat1:amd64 (2.2.10-1) ... | |
| Selecting previously unselected package python3.8-minimal. | |
| Preparing to unpack .../python3.8-minimal_3.8.6-1_amd64.deb ... | |
| Unpacking python3.8-minimal (3.8.6-1) ... | |
| Setting up libpython3.8-minimal:amd64 (3.8.6-1) ... | |
| Setting up libexpat1:amd64 (2.2.10-1) ... | |
| Setting up python3.8-minimal (3.8.6-1) ... | |
| Selecting previously unselected package python3-minimal. | |
| (Reading database ... | |
| (Reading database ... 5% | |
| (Reading database ... 10% | |
| (Reading database ... 15% | |
| (Reading database ... 20% | |
| (Reading database ... 25% | |
| (Reading database ... 30% | |
| (Reading database ... 35% | |
| (Reading database ... 40% | |
| (Reading database ... 45% | |
| (Reading database ... 50% | |
| (Reading database ... 55% | |
| (Reading database ... 60% | |
| (Reading database ... 65% | |
| (Reading database ... 70% | |
| (Reading database ... 75% | |
| (Reading database ... 80% | |
| (Reading database ... 85% | |
| (Reading database ... 90% | |
| (Reading database ... 95% | |
| (Reading database ... 100% | |
| (Reading database ... 13138 files and directories currently installed.) | |
| Preparing to unpack .../0-python3-minimal_3.8.6-1_amd64.deb ... | |
| Unpacking python3-minimal (3.8.6-1) ... | |
| Selecting previously unselected package media-types. | |
| Preparing to unpack .../1-media-types_1.0.1_all.deb ... | |
| Unpacking media-types (1.0.1) ... | |
| Selecting previously unselected package mailcap. | |
| Preparing to unpack .../2-mailcap_3.67_all.deb ... | |
| Unpacking mailcap (3.67) ... | |
| Selecting previously unselected package mime-support. | |
| Preparing to unpack .../3-mime-support_3.66_all.deb ... | |
| Unpacking mime-support (3.66) ... | |
| Selecting previously unselected package readline-common. | |
| Preparing to unpack .../4-readline-common_8.1~rc2-2_all.deb ... | |
| Unpacking readline-common (8.1~rc2-2) ... | |
| Selecting previously unselected package libreadline8:amd64. | |
| Preparing to unpack .../5-libreadline8_8.1~rc2-2_amd64.deb ... | |
| Unpacking libreadline8:amd64 (8.1~rc2-2) ... | |
| Selecting previously unselected package libpython3.8-stdlib:amd64. | |
| Preparing to unpack .../6-libpython3.8-stdlib_3.8.6-1_amd64.deb ... | |
| Unpacking libpython3.8-stdlib:amd64 (3.8.6-1) ... | |
| Selecting previously unselected package python3.8. | |
| Preparing to unpack .../7-python3.8_3.8.6-1_amd64.deb ... | |
| Unpacking python3.8 (3.8.6-1) ... | |
| Selecting previously unselected package libpython3-stdlib:amd64. | |
| Preparing to unpack .../8-libpython3-stdlib_3.8.6-1_amd64.deb ... | |
| Unpacking libpython3-stdlib:amd64 (3.8.6-1) ... | |
| Setting up python3-minimal (3.8.6-1) ... | |
| Selecting previously unselected package python3. | |
| (Reading database ... | |
| (Reading database ... 5% | |
| (Reading database ... 10% | |
| (Reading database ... 15% | |
| (Reading database ... 20% | |
| (Reading database ... 25% | |
| (Reading database ... 30% | |
| (Reading database ... 35% | |
| (Reading database ... 40% | |
| (Reading database ... 45% | |
| (Reading database ... 50% | |
| (Reading database ... 55% | |
| (Reading database ... 60% | |
| (Reading database ... 65% | |
| (Reading database ... 70% | |
| (Reading database ... 75% | |
| (Reading database ... 80% | |
| (Reading database ... 85% | |
| (Reading database ... 90% | |
| (Reading database ... 95% | |
| (Reading database ... 100% | |
| (Reading database ... 13563 files and directories currently installed.) | |
| Preparing to unpack .../00-python3_3.8.6-1_amd64.deb ... | |
| Unpacking python3 (3.8.6-1) ... | |
| Selecting previously unselected package apt-utils. | |
| Preparing to unpack .../01-apt-utils_2.1.11_amd64.deb ... | |
| Unpacking apt-utils (2.1.11) ... | |
| Selecting previously unselected package libncurses6:amd64. | |
| Preparing to unpack .../02-libncurses6_6.2+20200918-1_amd64.deb ... | |
| Unpacking libncurses6:amd64 (6.2+20200918-1) ... | |
| Selecting previously unselected package libprocps8:amd64. | |
| Preparing to unpack .../03-libprocps8_2%3a3.3.16-5_amd64.deb ... | |
| Unpacking libprocps8:amd64 (2:3.3.16-5) ... | |
| Selecting previously unselected package procps. | |
| Preparing to unpack .../04-procps_2%3a3.3.16-5_amd64.deb ... | |
| Unpacking procps (2:3.3.16-5) ... | |
| Selecting previously unselected package libpsl5:amd64. | |
| Preparing to unpack .../05-libpsl5_0.21.0-1.1_amd64.deb ... | |
| Unpacking libpsl5:amd64 (0.21.0-1.1) ... | |
| Selecting previously unselected package wget. | |
| Preparing to unpack .../06-wget_1.20.3-1+b3_amd64.deb ... | |
| Unpacking wget (1.20.3-1+b3) ... | |
| Selecting previously unselected package python3-pkg-resources. | |
| Preparing to unpack .../07-python3-pkg-resources_50.3.0-1_all.deb ... | |
| Unpacking python3-pkg-resources (50.3.0-1) ... | |
| Selecting previously unselected package python3-chardet. | |
| Preparing to unpack .../08-python3-chardet_3.0.4-7_all.deb ... | |
| Unpacking python3-chardet (3.0.4-7) ... | |
| Selecting previously unselected package python3-six. | |
| Preparing to unpack .../09-python3-six_1.15.0-2_all.deb ... | |
| Unpacking python3-six (1.15.0-2) ... | |
| Selecting previously unselected package python3-debian. | |
| Preparing to unpack .../10-python3-debian_0.1.38_all.deb ... | |
| Unpacking python3-debian (0.1.38) ... | |
| Selecting previously unselected package autopkgtest. | |
| Preparing to unpack .../11-autopkgtest_5.15_all.deb ... | |
| Unpacking autopkgtest (5.15) ... | |
| Selecting previously unselected package debootstrap. | |
| Preparing to unpack .../12-debootstrap_1.0.123_all.deb ... | |
| Unpacking debootstrap (1.0.123) ... | |
| Selecting previously unselected package libcap2:amd64. | |
| Preparing to unpack .../13-libcap2_1%3a2.44-1_amd64.deb ... | |
| Unpacking libcap2:amd64 (1:2.44-1) ... | |
| Selecting previously unselected package libcap2-bin. | |
| Preparing to unpack .../14-libcap2-bin_1%3a2.44-1_amd64.deb ... | |
| Unpacking libcap2-bin (1:2.44-1) ... | |
| Selecting previously unselected package newpid. | |
| Preparing to unpack .../15-newpid_13_amd64.deb ... | |
| Unpacking newpid (13) ... | |
| Selecting previously unselected package pbuilder. | |
| Preparing to unpack .../16-pbuilder_0.230.4_all.deb ... | |
| Unpacking pbuilder (0.230.4) ... | |
| Setting up media-types (1.0.1) ... | |
| Setting up libpsl5:amd64 (0.21.0-1.1) ... | |
| Setting up apt-utils (2.1.11) ... | |
| Setting up wget (1.20.3-1+b3) ... | |
| Setting up libcap2:amd64 (1:2.44-1) ... | |
| Setting up libcap2-bin (1:2.44-1) ... | |
| Setting up libncurses6:amd64 (6.2+20200918-1) ... | |
| Setting up mailcap (3.67) ... | |
| Setting up readline-common (8.1~rc2-2) ... | |
| Setting up libprocps8:amd64 (2:3.3.16-5) ... | |
| Setting up debootstrap (1.0.123) ... | |
| Setting up mime-support (3.66) ... | |
| Setting up pbuilder (0.230.4) ... | |
| Setting up libreadline8:amd64 (8.1~rc2-2) ... | |
| Setting up newpid (13) ... | |
| Setting up procps (2:3.3.16-5) ... | |
| update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode | |
| Setting up libpython3.8-stdlib:amd64 (3.8.6-1) ... | |
| Setting up python3.8 (3.8.6-1) ... | |
| Setting up libpython3-stdlib:amd64 (3.8.6-1) ... | |
| Setting up python3 (3.8.6-1) ... | |
| Setting up python3-six (1.15.0-2) ... | |
| Setting up python3-pkg-resources (50.3.0-1) ... | |
| Setting up python3-chardet (3.0.4-7) ... | |
| Setting up python3-debian (0.1.38) ... | |
| Setting up autopkgtest (5.15) ... | |
| Processing triggers for man-db (2.9.3-2) ... | |
| Not building database; man-db/auto-update is not 'true'. | |
| Processing triggers for libc-bin (2.31-4) ... | |
| + mkdir -p /build/autopkgtest.out | |
| + which autopkgtest | |
| + newpid autopkgtest --output-dir /build/autopkgtest.out --summary /build/autopkgtest.summary /build/snap-aligner-dbgsym_1.0.0+dfsg-1_amd64.deb /build/snap-aligner_1.0.0+dfsg-1_amd64.deb /build/snap-aligner-1.0.0+dfsg -- autopkgtest-virt-null | |
| autopkgtest [16:21:43]: starting date: 2020-11-28 | |
| autopkgtest [16:21:43]: version 5.15 | |
| autopkgtest [16:21:43]: host mrc-tux; command line: /usr/bin/autopkgtest --output-dir /build/autopkgtest.out --summary /build/autopkgtest.summary /build/snap-aligner-dbgsym_1.0.0+dfsg-1_amd64.deb /build/snap-aligner_1.0.0+dfsg-1_amd64.deb /build/snap-aligner-1.0.0+dfsg -- autopkgtest-virt-null | |
| autopkgtest [16:21:43]: testbed dpkg architecture: amd64 | |
| autopkgtest [16:21:43]: testbed running kernel: Linux 5.9.0-3-amd64 #1 SMP Debian 5.9.9-1 (2020-11-19) | |
| autopkgtest [16:21:43]: @@@@@@@@@@@@@@@@@@@@ built-tree /build/snap-aligner-1.0.0+dfsg | |
| autopkgtest [16:21:43]: testing package snap-aligner version 1.0.0+dfsg-1 | |
| autopkgtest [16:21:43]: test run-unit-test: preparing testbed | |
| Get:1 file:/tmp/autopkgtest.uAkRfu/binaries InRelease | |
| Ign:1 file:/tmp/autopkgtest.uAkRfu/binaries InRelease | |
| Get:2 file:/tmp/autopkgtest.uAkRfu/binaries Release [816 B] | |
| Get:2 file:/tmp/autopkgtest.uAkRfu/binaries Release [816 B] | |
| Get:3 file:/tmp/autopkgtest.uAkRfu/binaries Release.gpg | |
| Ign:3 file:/tmp/autopkgtest.uAkRfu/binaries Release.gpg | |
| Get:4 file:/tmp/autopkgtest.uAkRfu/binaries Packages [2095 B] | |
| Reading package lists... | |
| Reading package lists... | |
| Building dependency tree... | |
| Reading state information... | |
| Correcting dependencies...Starting pkgProblemResolver with broken count: 0 | |
| Starting 2 pkgProblemResolver with broken count: 0 | |
| Done | |
| Done | |
| Starting pkgProblemResolver with broken count: 0 | |
| Starting 2 pkgProblemResolver with broken count: 0 | |
| Done | |
| The following additional packages will be installed: | |
| snap-aligner | |
| The following NEW packages will be installed: | |
| snap-aligner | |
| 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. | |
| 1 not fully installed or removed. | |
| Need to get 0 B/725 kB of archives. | |
| After this operation, 1670 kB of additional disk space will be used. | |
| Get:1 file:/tmp/autopkgtest.uAkRfu/binaries snap-aligner 1.0.0+dfsg-1 [725 kB] | |
| Selecting previously unselected package snap-aligner. | |
| (Reading database ... | |
| (Reading database ... 5% | |
| (Reading database ... 10% | |
| (Reading database ... 15% | |
| (Reading database ... 20% | |
| (Reading database ... 25% | |
| (Reading database ... 30% | |
| (Reading database ... 35% | |
| (Reading database ... 40% | |
| (Reading database ... 45% | |
| (Reading database ... 50% | |
| (Reading database ... 55% | |
| (Reading database ... 60% | |
| (Reading database ... 65% | |
| (Reading database ... 70% | |
| (Reading database ... 75% | |
| (Reading database ... 80% | |
| (Reading database ... 85% | |
| (Reading database ... 90% | |
| (Reading database ... 95% | |
| (Reading database ... 100% | |
| (Reading database ... 14215 files and directories currently installed.) | |
| Preparing to unpack .../binaries/./snap-aligner.deb ... | |
| Unpacking snap-aligner (1.0.0+dfsg-1) ... | |
| Setting up snap-aligner (1.0.0+dfsg-1) ... | |
| Setting up autopkgtest-satdep (0) ... | |
| Processing triggers for man-db (2.9.3-2) ... | |
| Not building database; man-db/auto-update is not 'true'. | |
| (Reading database ... 14252 files and directories currently installed.) | |
| Removing autopkgtest-satdep (0) ... | |
| autopkgtest [16:21:47]: test run-unit-test: [----------------------- | |
| .: | |
| correct-fq-datatest.sam | |
| correct-fq-datatest2.sam | |
| correct-sam-datatest.sam | |
| correct-sam-datatest2.sam | |
| datatest.bam | |
| datatest.fa | |
| datatest.fq | |
| datatest.sam | |
| datatest2.fa | |
| ref | |
| ./ref: | |
| datatest | |
| datatest2 | |
| output.sam | |
| ./ref/datatest: | |
| Genome | |
| GenomeIndex | |
| ./ref/datatest2: | |
| Genome | |
| GenomeIndex | |
| [93m[1mTest 1[0m | |
| Welcome to SNAP version 1.0.0. | |
| Auto-set key size to 6 | |
| Auto-set locationSize to 4 | |
| Hash table slack 0.300000 | |
| Loading FASTA file 'datatest.fa' into memory...0s | |
| Genome has 1 contigs, of which 0 are ALTs | |
| Saving genome...Computing bias table. | |
| 0s | |
| Bias computation: 0 / 1202 | |
| Computed bias table in 0s | |
| Allocating memory for hash tables...0s | |
| Building hash tables. | |
| 0(0%) seeds occur more than once, total of 0(0%) genome locations are not unique, 498(41%) bad seeds, 0 both complements used 500 no string | |
| Hash table build took 0s | |
| Building overflow table. | |
| Overflow table build and hash table save took 0s | |
| Saving overflow table...0s | |
| Index build and save took 0s (1202 bases/s) | |
| [92m[1mPassed[0m | |
| [93m[1mTest 2[0m | |
| Welcome to SNAP version 1.0.0. | |
| Auto-set key size to 5 | |
| Auto-set locationSize to 4 | |
| Hash table slack 0.300000 | |
| Loading FASTA file 'datatest2.fa' into memory...0s | |
| Genome has 2 contigs, of which 0 are ALTs | |
| Saving genome...Computing bias table. | |
| 0s | |
| Bias computation: 0 / 1904 | |
| Computed bias table in 0s | |
| Allocating memory for hash tables...0s | |
| Building hash tables. | |
| 145(7%) seeds occur more than once, total of 290(15%) genome locations are not unique, 997(52%) bad seeds, 0 both complements used 522 no string | |
| Hash table build took 0s | |
| Building overflow table. | |
| Overflow table build and hash table save took 0s | |
| Saving overflow table...0s | |
| Index build and save took 0s (1904 bases/s) | |
| [92m[1mPassed[0m | |
| [93m[1mTest 3[0m | |
| Welcome to SNAP version 1.0.0. | |
| Loading index from directory... snap-aligner: OpenMemoryMappedFile datatest/OverflowTable mmap failed: Invalid argument | |
| /tmp/autopkgtest.uAkRfu/tree/debian/tests/run-unit-test: line 37: 157 Segmentation fault (core dumped) snap-aligner single datatest datatest.fq -o output.sam | |
| autopkgtest [16:21:48]: test run-unit-test: -----------------------] | |
| autopkgtest [16:21:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - | |
| run-unit-test FAIL non-zero exit status 139 | |
| autopkgtest [16:21:48]: @@@@@@@@@@@@@@@@@@@@ summary | |
| run-unit-test FAIL non-zero exit status 139 | |
| autopkgtest [16:21:48]: Binaries: resetting testbed apt configuration | |
| Hit:1 http://deb.debian.org/debian bullseye InRelease | |
| Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [39.7 kB] | |
| Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 Packages [205 kB] | |
| Fetched 245 kB in 1s (281 kB/s) | |
| Reading package lists... | |
| + EXIT=4 | |
| + tar -caf /build/autopkgtest.tar.gz /build/autopkgtest.out | |
| tar: Removing leading `/' from member names | |
| tar: Removing leading `/' from hard link targets | |
| + exit 0 | |
| [0mI: user script /var/cache/pbuilder/build/cow.3850978/tmp/hooks/B20autopkgtest finished[0m | |
| [0mI: Copying back the cached apt archive contents[0m | |
| [0mI: unmounting /home/michael/.ccache/ filesystem[0m | |
| [0mI: unmounting dev/ptmx filesystem[0m | |
| [0mI: unmounting dev/pts filesystem[0m | |
| [0mI: unmounting dev/shm filesystem[0m | |
| [0mI: unmounting proc filesystem[0m | |
| [0mI: unmounting sys filesystem[0m | |
| [0mI: Current time: Sat Nov 28 17:22:08 CET 2020[0m | |
| [0mI: pbuilder-time-stamp: 1606580528[0m |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment