Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/snap-aligner/snap-aligner_1.0.0+dfsg-3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/snap-aligner-1.0.0+dfsg-30z6tr85x/snap-aligner_1.0.0+dfsg-3_amd64.buildinfo Get source package info: snap-aligner=1.0.0+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/snap-aligner/1.0.0+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.4-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3+b1 binutils=2.37-7 binutils-common=2.37-7 binutils-x86-64-linux-gnu=2.37-7 bsdextrautils=2.37.2-3 bsdutils=1:2.37.2-3 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.3.0-11 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.3.0-11 gcc=4:10.2.1-1 gcc-10=10.3.0-11 gcc-10-base=10.3.0-11 gcc-11-base=11.2.0-8 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 help2man=1.48.5 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-8 libatomic1=11.2.0-8 libattr1=1:2.5.1-1 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbinutils=2.37-7 libblkid1=2.37.2-3 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-8 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-7 libctf0=2.37-7 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdpkg-perl=1.20.9 libelf1=0.185-2 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.3.0-11 libgcc-s1=11.2.0-8 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.21-1 libgdbm6=1.21-1 libgmp10=2:6.2.1+dfsg-2 libgomp1=11.2.0-8 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libicu67=67.1-7 libisl23=0.23-1 libitm1=11.2.0-8 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblocale-gettext-perl=1.07-4+b1 liblsan0=11.2.0-8 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-3 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.3-1 libquadmath0=11.2.0-8 libseccomp2=2.5.2-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsimde-dev=0.7.2-4 libsmartcols1=2.37.2-3 libssl1.1=1.1.1l-1 libstdc++-10-dev=10.3.0-11 libstdc++6=11.2.0-8 libsub-override-perl=0.09-2 libsystemd0=247.9-3 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-8 libubsan1=11.2.0-8 libuchardet0=0.0.7-1 libudev1=247.9-3 libunistring2=0.9.10-6 libuuid1=2.37.2-3 libxml2=2.9.12+dfsg-5 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.14.6-3 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 util-linux=2.37.2-3 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211004T210045Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211004T210045Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211001T101807Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d snap-aligner=1.0.0+dfsg-3 && mkdir -p /build/snap-aligner-fM01FF && dpkg-source --no-check -x /*.dsc /build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg && chown -R builduser:builduser /build/snap-aligner-fM01FF" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1633080545" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/snap-aligner-fM01FF /tmp/snap-aligner-1.0.0+dfsg-30z6tr85x bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211001T101807Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.ldEmanynUP as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.ldEmanynUP Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-3). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211001T101807Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211001T101807Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (773 kB/s) Selecting previously unselected package libfakeroot: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 ... 4668 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211004T210045Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211004T210045Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211001T101807Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.ldEmanynUP Get:1 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm InRelease [128 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211001T101807Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.0 MB in 19s (1219 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.ldEmanynUP I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d snap-aligner=1.0.0+dfsg-3 && mkdir -p /build/snap-aligner-fM01FF && dpkg-source --no-check -x /*.dsc /build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg && chown -R builduser:builduser /build/snap-aligner-fM01FF"' exec /tmp/mmdebstrap.ldEmanynUP Reading package lists... NOTICE: 'snap-aligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snap-aligner.git Please use: git clone https://salsa.debian.org/med-team/snap-aligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1072 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main snap-aligner 1.0.0+dfsg-3 (dsc) [2268 B] Get:2 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main snap-aligner 1.0.0+dfsg-3 (tar) [1061 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main snap-aligner 1.0.0+dfsg-3 (diff) [8948 B] Fetched 1072 kB in 1s (1191 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'snap-aligner_1.0.0+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting snap-aligner in /build/snap-aligner-fM01FF/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-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_segfault.patch dpkg-source: info: applying non-x86-and-kfreebsd dpkg-source: info: applying drop-msse dpkg-source: info: applying spelling dpkg-source: info: applying simde I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1633080545" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.ldEmanynUP dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 1.0.0+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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-fM01FF/snap-aligner-1.0.0+dfsg' dh_auto_clean make -j10 clean make[2]: Entering directory '/build/snap-aligner-fM01FF/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-fM01FF/snap-aligner-1.0.0+dfsg' rm -f debian/*.1 rm -f */*.d */*/*.d make[1]: Leaving directory '/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg' dh_auto_build make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg' g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.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 g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.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 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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.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: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]; | ^ g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp 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:866, 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:70:35: note: ‘__builtin___snprintf_chk’ output between 3 and 21 bytes into a destination of size 16 70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | __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:866, 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:70:35: note: ‘__builtin___snprintf_chk’ output between 3 and 21 bytes into a destination of size 16 70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | __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:866, 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:70:35: note: ‘__builtin___snprintf_chk’ output between 3 and 21 bytes into a destination of size 16 70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | __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:866, 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:70:35: note: ‘__builtin___snprintf_chk’ output between 3 and 21 bytes into a destination of size 16 70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o snap-aligner -g -O2 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -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 -ffile-prefix-map=/build/snap-aligner-fM01FF/snap-aligner-1.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -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-fM01FF/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-fM01FF/snap-aligner-1.0.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/snap-aligner/ -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'snap-aligner' in '../snap-aligner_1.0.0+dfsg-3_amd64.deb'. dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_1.0.0+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../snap-aligner_1.0.0+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/snap-aligner-fM01FF /tmp/snap-aligner-1.0.0+dfsg-30z6tr85x I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.ldEmanynUP... I: success in 344.7174 seconds md5: snap-aligner-dbgsym_1.0.0+dfsg-3_amd64.deb: OK md5: snap-aligner_1.0.0+dfsg-3_amd64.deb: OK sha1: snap-aligner-dbgsym_1.0.0+dfsg-3_amd64.deb: OK sha1: snap-aligner_1.0.0+dfsg-3_amd64.deb: OK sha256: snap-aligner-dbgsym_1.0.0+dfsg-3_amd64.deb: OK sha256: snap-aligner_1.0.0+dfsg-3_amd64.deb: OK Checksums: OK