Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bambamc/bambamc_0.0.50-6_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bambamc-0.0.50-6ula9e5wj/bambamc_0.0.50-6_amd64.buildinfo Get source package info: bambamc=0.0.50-6 Source URL: http://snapshot.notset.fr/mr/package/bambamc/0.0.50-6/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 apt=2.3.13 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 d-shlibs=0.104 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debian-archive-keyring=2021.1.1 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 gpgv=2.2.27-2 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libapt-pkg6.0=2.3.13 libarchive-zip-perl=1.68-1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37-10 libblkid1=2.37.2-4 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=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdpkg-perl=1.20.9 libelf1=0.186-1 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.1-1 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-4 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libglib2.0-0=2.70.2-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-12 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libnettle8=3.7.3-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-5 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=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libquadmath0=11.2.0-12 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsemanage-common=3.3-1 libsemanage2=3.3-1+b1 libsepol2=3.3-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.7-1 libtasn1-6=4.18.0-4 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libxml2=2.9.12+dfsg-5+b1 libxxhash0=0.8.0-2 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-1 login=1:4.8.1-2 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=6.3-1 ncurses-bin=6.3-1 passwd=1:4.8.1-2 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 pkg-config=0.29.2-1 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=2.37.2-4 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/20211211T024809Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211211T024809Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220102T024729Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211203T090951Z/ 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 bambamc=0.0.50-6 && mkdir -p /build/bambamc-LNr0EZ && dpkg-source --no-check -x /*.dsc /build/bambamc-LNr0EZ/bambamc-0.0.50 && chown -R builduser:builduser /build/bambamc-LNr0EZ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bambamc-LNr0EZ/bambamc-0.0.50 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638734397" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/bambamc-LNr0EZ /tmp/bambamc-0.0.50-6ula9e5wj bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211203T090951Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.Epd960QzGl 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.Epd960QzGl Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). 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/20211203T090951Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211203T090951Z 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 (1032 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 ... 4673 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/20211211T024809Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211211T024809Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220102T024729Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211203T090951Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Epd960QzGl Get:1 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220102T024729Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211203T090951Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220102T024729Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220102T024729Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220102T024729Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220102T024729Z unstable/main amd64 Packages [12.0 MB] Fetched 35.2 MB in 28s (1240 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.Epd960QzGl I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bambamc=0.0.50-6 && mkdir -p /build/bambamc-LNr0EZ && dpkg-source --no-check -x /*.dsc /build/bambamc-LNr0EZ/bambamc-0.0.50 && chown -R builduser:builduser /build/bambamc-LNr0EZ"' exec /tmp/mmdebstrap.Epd960QzGl Reading package lists... NOTICE: 'bambamc' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bambamc.git Please use: git clone https://salsa.debian.org/med-team/bambamc.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 68.7 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main bambamc 0.0.50-6 (dsc) [2099 B] Get:2 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main bambamc 0.0.50-6 (tar) [63.9 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211211T024809Z bookworm/main bambamc 0.0.50-6 (diff) [2668 B] Fetched 68.7 kB in 0s (755 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bambamc_0.0.50-6.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bambamc in /build/bambamc-LNr0EZ/bambamc-0.0.50 dpkg-source: info: unpacking bambamc_0.0.50.orig.tar.gz dpkg-source: info: unpacking bambamc_0.0.50-6.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bambamc-LNr0EZ/bambamc-0.0.50 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638734397" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.Epd960QzGl dpkg-buildpackage: info: source package bambamc dpkg-buildpackage: info: source version 0.0.50-6 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 dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:3: warning: The macro `AC_CANONICAL_SYSTEM' is obsolete. configure.in:3: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.in:3: the top level configure.in:4: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.in:4: You should run autoupdate. m4/libtool.m4:99: AC_PROG_LIBTOOL is expanded from... configure.in:4: the top level configure.in:6: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.in:6: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:1021: AM_CONFIG_HEADER is expanded from... configure.in:6: the top level configure.in:15: warning: The macro `AC_PROG_CC_C99' is obsolete. configure.in:15: You should run autoupdate. ./lib/autoconf/c.m4:1659: AC_PROG_CC_C99 is expanded from... configure.in:15: the top level configure.in:27: warning: The macro `AC_HEADER_STDC' is obsolete. configure.in:27: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.in:27: the top level configure.in:40: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:40: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... configure.in:40: the top level configure.in:68: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:68: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... configure.in:68: the top level configure.in:144: warning: The macro `AC_TRY_LINK' is obsolete. configure.in:144: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... configure.in:144: the top level configure.in:165: warning: AC_OUTPUT should be used without arguments. configure.in:165: You should run autoupdate. autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:4: installing './compile' configure.in:3: installing './config.guess' configure.in:3: installing './config.sub' configure.in:7: installing './install-sh' configure.in:7: installing './missing' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamCollationHash.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamCollatorInterface.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_FormatAlignment.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamCollationHashEntry.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_FormatNumber.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamCollationOutputVector.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamHeaderInfo.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_Hash.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamCollationTempFileGenerator.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamWriter.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_List.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamCollationVector.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_CharBuffer.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_ListNode.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamCollator.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_Chromosome.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_GzipReader.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_LineParsing.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamFileHeader.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamAlignmentPut.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamSingleAlignment.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BamFileDecoder.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_GzipWriter.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_GzipFileDecoder.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_BgzfCompressor.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_LineBuffer.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_SamInfo.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_SamFileDecoder.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_SamBamFileDecoder.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:6: warning: source file 'bambamc/BamBam_StrDup.c' is in a subdirectory, src/Makefile.am:6: but option 'subdir-objects' is disabled src/Makefile.am:40: warning: source file 'test/bamreadertest.c' is in a subdirectory, src/Makefile.am:40: but option 'subdir-objects' is disabled src/Makefile.am:44: warning: source file 'test/bamwritertest.c' is in a subdirectory, src/Makefile.am:44: but option 'subdir-objects' is disabled src/Makefile.am: installing './depcomp' dh_auto_configure -a ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... no checking for mawk... mawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking for egrep... (cached) /bin/grep -E checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib >= 0... yes checking for zlib >= 0... yes checking whether we can compile a zlib program... yes checking for _mkdir... no checking for direct.h... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating ubuntu.sh config.status: creating bambamc.pc config.status: creating src/bambamc/BamBam_Config.h config.status: creating config.h config.status: executing libtool commands config.status: executing depfiles commands dh_auto_build -a make -j10 make[1]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' make all-recursive make[2]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' Making all in src make[3]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o bamreadertest-bamreadertest.o `test -f 'test/bamreadertest.c' || echo './'`test/bamreadertest.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollationHash.lo `test -f 'bambamc/BamBam_BamCollationHash.c' || echo './'`bambamc/BamBam_BamCollationHash.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollatorInterface.lo `test -f 'bambamc/BamBam_BamCollatorInterface.c' || echo './'`bambamc/BamBam_BamCollatorInterface.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_FormatAlignment.lo `test -f 'bambamc/BamBam_FormatAlignment.c' || echo './'`bambamc/BamBam_FormatAlignment.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollationHashEntry.lo `test -f 'bambamc/BamBam_BamCollationHashEntry.c' || echo './'`bambamc/BamBam_BamCollationHashEntry.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_FormatNumber.lo `test -f 'bambamc/BamBam_FormatNumber.c' || echo './'`bambamc/BamBam_FormatNumber.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollationOutputVector.lo `test -f 'bambamc/BamBam_BamCollationOutputVector.c' || echo './'`bambamc/BamBam_BamCollationOutputVector.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamHeaderInfo.lo `test -f 'bambamc/BamBam_BamHeaderInfo.c' || echo './'`bambamc/BamBam_BamHeaderInfo.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_Hash.lo `test -f 'bambamc/BamBam_Hash.c' || echo './'`bambamc/BamBam_Hash.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollationTempFileGenerator.lo `test -f 'bambamc/BamBam_BamCollationTempFileGenerator.c' || echo './'`bambamc/BamBam_BamCollationTempFileGenerator.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationOutputVector.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollationOutputVector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationHashEntry.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollationHashEntry.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_FormatNumber.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_FormatNumber.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollatorInterface.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollatorInterface.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationHash.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollationHash.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamHeaderInfo.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamHeaderInfo.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_FormatAlignment.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_FormatAlignment.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationTempFileGenerator.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollationTempFileGenerator.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationHashEntry.c -o libbambamc_la-BamBam_BamCollationHashEntry.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamWriter.lo `test -f 'bambamc/BamBam_BamWriter.c' || echo './'`bambamc/BamBam_BamWriter.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_Hash.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_Hash.o bambamc/BamBam_Hash.c: In function ‘hash’: bambamc/BamBam_Hash.c:83:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 83 | case 11: c+=((uint32_t)k[10]<<24); | ~^~~~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:84:17: note: here 84 | case 10: c+=((uint32_t)k[9]<<16); | ^~~~ bambamc/BamBam_Hash.c:84:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 84 | case 10: c+=((uint32_t)k[9]<<16); | ~^~~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:85:17: note: here 85 | case 9 : c+=((uint32_t)k[8]<<8); | ^~~~ bambamc/BamBam_Hash.c:85:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 85 | case 9 : c+=((uint32_t)k[8]<<8); | ~^~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:87:17: note: here 87 | case 8 : b+=((uint32_t)k[7]<<24); | ^~~~ bambamc/BamBam_Hash.c:87:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 87 | case 8 : b+=((uint32_t)k[7]<<24); | ~^~~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:88:17: note: here 88 | case 7 : b+=((uint32_t)k[6]<<16); | ^~~~ bambamc/BamBam_Hash.c:88:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 88 | case 7 : b+=((uint32_t)k[6]<<16); | ~^~~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:89:17: note: here 89 | case 6 : b+=((uint32_t)k[5]<<8); | ^~~~ bambamc/BamBam_Hash.c:89:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 89 | case 6 : b+=((uint32_t)k[5]<<8); | ~^~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:90:17: note: here 90 | case 5 : b+=k[4]; | ^~~~ bambamc/BamBam_Hash.c:90:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 90 | case 5 : b+=k[4]; | ~^~~~~~ bambamc/BamBam_Hash.c:91:17: note: here 91 | case 4 : a+=((uint32_t)k[3]<<24); | ^~~~ bambamc/BamBam_Hash.c:91:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 91 | case 4 : a+=((uint32_t)k[3]<<24); | ~^~~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:92:17: note: here 92 | case 3 : a+=((uint32_t)k[2]<<16); | ^~~~ bambamc/BamBam_Hash.c:92:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 92 | case 3 : a+=((uint32_t)k[2]<<16); | ~^~~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:93:17: note: here 93 | case 2 : a+=((uint32_t)k[1]<<8); | ^~~~ bambamc/BamBam_Hash.c:93:27: warning: this statement may fall through [-Wimplicit-fallthrough=] 93 | case 2 : a+=((uint32_t)k[1]<<8); | ~^~~~~~~~~~~~~~~~~~~~~ bambamc/BamBam_Hash.c:94:17: note: here 94 | case 1 : a+=k[0]; | ^~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_FormatNumber.c -o libbambamc_la-BamBam_FormatNumber.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationHash.c -o libbambamc_la-BamBam_BamCollationHash.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationOutputVector.c -o libbambamc_la-BamBam_BamCollationOutputVector.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_FormatAlignment.c -o libbambamc_la-BamBam_FormatAlignment.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamWriter.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamWriter.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationTempFileGenerator.c -o libbambamc_la-BamBam_BamCollationTempFileGenerator.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_Hash.c -o libbambamc_la-BamBam_Hash.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollatorInterface.c -o libbambamc_la-BamBam_BamCollatorInterface.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_List.lo `test -f 'bambamc/BamBam_List.c' || echo './'`bambamc/BamBam_List.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamHeaderInfo.c -o libbambamc_la-BamBam_BamHeaderInfo.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollationVector.lo `test -f 'bambamc/BamBam_BamCollationVector.c' || echo './'`bambamc/BamBam_BamCollationVector.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat 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-Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_List.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_List.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollator.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollator.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_CharBuffer.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_CharBuffer.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 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-I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_Chromosome.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_Chromosome.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_ListNode.c -o libbambamc_la-BamBam_ListNode.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_GzipReader.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_GzipReader.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_CharBuffer.c -o libbambamc_la-BamBam_CharBuffer.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_List.c -o libbambamc_la-BamBam_List.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_LineParsing.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_LineParsing.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollationVector.c -o libbambamc_la-BamBam_BamCollationVector.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_Chromosome.c -o libbambamc_la-BamBam_Chromosome.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_GzipReader.c -o libbambamc_la-BamBam_GzipReader.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamFileHeader.lo `test -f 'bambamc/BamBam_BamFileHeader.c' || echo './'`bambamc/BamBam_BamFileHeader.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamAlignmentPut.lo `test -f 'bambamc/BamBam_BamAlignmentPut.c' || echo './'`bambamc/BamBam_BamAlignmentPut.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamSingleAlignment.lo `test -f 'bambamc/BamBam_BamSingleAlignment.c' || echo './'`bambamc/BamBam_BamSingleAlignment.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BamFileDecoder.lo `test -f 'bambamc/BamBam_BamFileDecoder.c' || echo './'`bambamc/BamBam_BamFileDecoder.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_GzipWriter.lo `test -f 'bambamc/BamBam_GzipWriter.c' || echo './'`bambamc/BamBam_GzipWriter.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_GzipFileDecoder.lo `test -f 'bambamc/BamBam_GzipFileDecoder.c' || echo './'`bambamc/BamBam_GzipFileDecoder.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamFileHeader.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamFileHeader.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_LineParsing.c -o libbambamc_la-BamBam_LineParsing.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamAlignmentPut.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamAlignmentPut.o /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_BgzfCompressor.lo `test -f 'bambamc/BamBam_BgzfCompressor.c' || echo './'`bambamc/BamBam_BgzfCompressor.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamSingleAlignment.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamSingleAlignment.o /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_LineBuffer.lo `test -f 'bambamc/BamBam_LineBuffer.c' || echo './'`bambamc/BamBam_LineBuffer.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_GzipWriter.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_GzipWriter.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamFileDecoder.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamFileDecoder.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BgzfCompressor.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BgzfCompressor.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_GzipFileDecoder.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_GzipFileDecoder.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamCollator.c -o libbambamc_la-BamBam_BamCollator.o >/dev/null 2>&1 bambamc/BamBam_BamSingleAlignment.c: In function ‘BamBam_BamSingleAlignment_LoadAlignment’: bambamc/BamBam_BamSingleAlignment.c:882:48: warning: array subscript has type ‘char’ [-Wchar-subscripts] 882 | if ( ! bambamc_qnameValidTable[*cc] ) | ^~~ bambamc/BamBam_BamSingleAlignment.c:910:65: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare] 910 | if ( ue-BamBam_BamSingleAlignment_GetEncodedCigar(data) < BamBam_BamSingleAlignment_GetNC(data)*sizeof(uint32_t) ) | ^ bambamc/BamBam_BamSingleAlignment.c:957:29: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 957 | if ( ciglen != BamBam_BamSingleAlignment_GetLSeq(data) ) | ^~ bambamc/BamBam_BamSingleAlignment.c:1089:64: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1089 | if ( (ue-auxc) < (3+1+4+ 1*alen) ) | ^ bambamc/BamBam_BamSingleAlignment.c:1098:64: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1098 | if ( (ue-auxc) < (3+1+4+ 2*alen) ) | ^ bambamc/BamBam_BamSingleAlignment.c:1108:64: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1108 | if ( (ue-auxc) < (3+1+4+ 4*alen) ) | ^ /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_SamInfo.lo `test -f 'bambamc/BamBam_SamInfo.c' || echo './'`bambamc/BamBam_SamInfo.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_LineBuffer.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_LineBuffer.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamFileDecoder.c -o libbambamc_la-BamBam_BamFileDecoder.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_GzipWriter.c -o libbambamc_la-BamBam_GzipWriter.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_GzipFileDecoder.c -o libbambamc_la-BamBam_GzipFileDecoder.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_LineBuffer.c -o libbambamc_la-BamBam_LineBuffer.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BgzfCompressor.c -o libbambamc_la-BamBam_BgzfCompressor.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_SamInfo.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_SamInfo.o /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_SamFileDecoder.lo `test -f 'bambamc/BamBam_SamFileDecoder.c' || echo './'`bambamc/BamBam_SamFileDecoder.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_SamBamFileDecoder.lo `test -f 'bambamc/BamBam_SamBamFileDecoder.c' || echo './'`bambamc/BamBam_SamBamFileDecoder.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o libbambamc_la-BamBam_StrDup.lo `test -f 'bambamc/BamBam_StrDup.c' || echo './'`bambamc/BamBam_StrDup.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_SamFileDecoder.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_SamFileDecoder.o gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c -o bamwritertest-bamwritertest.o `test -f 'test/bamwritertest.c' || echo './'`test/bamwritertest.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_SamBamFileDecoder.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_SamBamFileDecoder.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_StrDup.c -fPIC -DPIC -o .libs/libbambamc_la-BamBam_StrDup.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamAlignmentPut.c -o libbambamc_la-BamBam_BamAlignmentPut.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_SamFileDecoder.c -o libbambamc_la-BamBam_SamFileDecoder.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_StrDup.c -o libbambamc_la-BamBam_StrDup.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamFileHeader.c -o libbambamc_la-BamBam_BamFileHeader.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_SamBamFileDecoder.c -o libbambamc_la-BamBam_SamBamFileDecoder.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_SamInfo.c -o libbambamc_la-BamBam_SamInfo.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -c bambamc/BamBam_BamSingleAlignment.c -o libbambamc_la-BamBam_BamSingleAlignment.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -version-info 0:50:0 -Wl,-z,relro -o libbambamc.la -rpath /usr/lib/x86_64-linux-gnu libbambamc_la-BamBam_BamCollationHash.lo libbambamc_la-BamBam_BamCollatorInterface.lo libbambamc_la-BamBam_FormatAlignment.lo libbambamc_la-BamBam_BamCollationHashEntry.lo libbambamc_la-BamBam_FormatNumber.lo libbambamc_la-BamBam_BamCollationOutputVector.lo libbambamc_la-BamBam_BamHeaderInfo.lo libbambamc_la-BamBam_Hash.lo libbambamc_la-BamBam_BamCollationTempFileGenerator.lo libbambamc_la-BamBam_BamWriter.lo libbambamc_la-BamBam_List.lo libbambamc_la-BamBam_BamCollationVector.lo libbambamc_la-BamBam_CharBuffer.lo libbambamc_la-BamBam_ListNode.lo libbambamc_la-BamBam_BamCollator.lo libbambamc_la-BamBam_Chromosome.lo libbambamc_la-BamBam_GzipReader.lo libbambamc_la-BamBam_LineParsing.lo libbambamc_la-BamBam_BamFileHeader.lo libbambamc_la-BamBam_BamAlignmentPut.lo libbambamc_la-BamBam_BamSingleAlignment.lo libbambamc_la-BamBam_BamFileDecoder.lo libbambamc_la-BamBam_GzipWriter.lo libbambamc_la-BamBam_GzipFileDecoder.lo libbambamc_la-BamBam_BgzfCompressor.lo libbambamc_la-BamBam_LineBuffer.lo libbambamc_la-BamBam_SamInfo.lo libbambamc_la-BamBam_SamFileDecoder.lo libbambamc_la-BamBam_SamBamFileDecoder.lo libbambamc_la-BamBam_StrDup.lo -lz libtool: link: gcc -shared -fPIC -DPIC .libs/libbambamc_la-BamBam_BamCollationHash.o .libs/libbambamc_la-BamBam_BamCollatorInterface.o .libs/libbambamc_la-BamBam_FormatAlignment.o .libs/libbambamc_la-BamBam_BamCollationHashEntry.o .libs/libbambamc_la-BamBam_FormatNumber.o .libs/libbambamc_la-BamBam_BamCollationOutputVector.o .libs/libbambamc_la-BamBam_BamHeaderInfo.o .libs/libbambamc_la-BamBam_Hash.o .libs/libbambamc_la-BamBam_BamCollationTempFileGenerator.o .libs/libbambamc_la-BamBam_BamWriter.o .libs/libbambamc_la-BamBam_List.o .libs/libbambamc_la-BamBam_BamCollationVector.o .libs/libbambamc_la-BamBam_CharBuffer.o .libs/libbambamc_la-BamBam_ListNode.o .libs/libbambamc_la-BamBam_BamCollator.o .libs/libbambamc_la-BamBam_Chromosome.o .libs/libbambamc_la-BamBam_GzipReader.o .libs/libbambamc_la-BamBam_LineParsing.o .libs/libbambamc_la-BamBam_BamFileHeader.o .libs/libbambamc_la-BamBam_BamAlignmentPut.o .libs/libbambamc_la-BamBam_BamSingleAlignment.o .libs/libbambamc_la-BamBam_BamFileDecoder.o .libs/libbambamc_la-BamBam_GzipWriter.o .libs/libbambamc_la-BamBam_GzipFileDecoder.o .libs/libbambamc_la-BamBam_BgzfCompressor.o .libs/libbambamc_la-BamBam_LineBuffer.o .libs/libbambamc_la-BamBam_SamInfo.o .libs/libbambamc_la-BamBam_SamFileDecoder.o .libs/libbambamc_la-BamBam_SamBamFileDecoder.o .libs/libbambamc_la-BamBam_StrDup.o -lz -g -O2 -fstack-protector-strong -O3 -Wl,-z -Wl,relro -Wl,-soname -Wl,libbambamc.so.0 -o .libs/libbambamc.so.0.0.50 libtool: link: (cd ".libs" && rm -f "libbambamc.so.0" && ln -s "libbambamc.so.0.0.50" "libbambamc.so.0") libtool: link: (cd ".libs" && rm -f "libbambamc.so" && ln -s "libbambamc.so.0.0.50" "libbambamc.so") libtool: link: ar cr .libs/libbambamc.a libbambamc_la-BamBam_BamCollationHash.o libbambamc_la-BamBam_BamCollatorInterface.o libbambamc_la-BamBam_FormatAlignment.o libbambamc_la-BamBam_BamCollationHashEntry.o libbambamc_la-BamBam_FormatNumber.o libbambamc_la-BamBam_BamCollationOutputVector.o libbambamc_la-BamBam_BamHeaderInfo.o libbambamc_la-BamBam_Hash.o libbambamc_la-BamBam_BamCollationTempFileGenerator.o libbambamc_la-BamBam_BamWriter.o libbambamc_la-BamBam_List.o libbambamc_la-BamBam_BamCollationVector.o libbambamc_la-BamBam_CharBuffer.o libbambamc_la-BamBam_ListNode.o libbambamc_la-BamBam_BamCollator.o libbambamc_la-BamBam_Chromosome.o libbambamc_la-BamBam_GzipReader.o libbambamc_la-BamBam_LineParsing.o libbambamc_la-BamBam_BamFileHeader.o libbambamc_la-BamBam_BamAlignmentPut.o libbambamc_la-BamBam_BamSingleAlignment.o libbambamc_la-BamBam_BamFileDecoder.o libbambamc_la-BamBam_GzipWriter.o libbambamc_la-BamBam_GzipFileDecoder.o libbambamc_la-BamBam_BgzfCompressor.o libbambamc_la-BamBam_LineBuffer.o libbambamc_la-BamBam_SamInfo.o libbambamc_la-BamBam_SamFileDecoder.o libbambamc_la-BamBam_SamBamFileDecoder.o libbambamc_la-BamBam_StrDup.o libtool: link: ranlib .libs/libbambamc.a libtool: link: ( cd ".libs" && rm -f "libbambamc.la" && ln -s "../libbambamc.la" "libbambamc.la" ) /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -Wl,-z,relro -o bamreadertest bamreadertest-bamreadertest.o libbambamc.la -lz /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -Wl,-z,relro -o bamwritertest bamwritertest-bamwritertest.o libbambamc.la -lz libtool: link: gcc -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -Wl,-z -Wl,relro -o .libs/bamwritertest bamwritertest-bamwritertest.o ./.libs/libbambamc.so -lz libtool: link: gcc -g -O2 -ffile-prefix-map=/build/bambamc-LNr0EZ/bambamc-0.0.50=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -rdynamic -Wl,-z -Wl,relro -o .libs/bamreadertest bamreadertest-bamreadertest.o ./.libs/libbambamc.so -lz make[3]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50/src' make[3]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' make[3]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' make[2]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' make[1]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' Making install in src make[2]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50/src' make[3]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50/src' /bin/mkdir -p '/build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libbambamc.la '/build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libbambamc.so.0.0.50 /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.so.0.0.50 libtool: install: (cd /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libbambamc.so.0.0.50 libbambamc.so.0 || { rm -f libbambamc.so.0 && ln -s libbambamc.so.0.0.50 libbambamc.so.0; }; }) libtool: install: (cd /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libbambamc.so.0.0.50 libbambamc.so || { rm -f libbambamc.so && ln -s libbambamc.so.0.0.50 libbambamc.so; }; }) libtool: install: /usr/bin/install -c .libs/libbambamc.lai /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.la libtool: install: /usr/bin/install -c .libs/libbambamc.a /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.a libtool: install: chmod 644 /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.a libtool: install: ranlib /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/include/bambamc' /usr/bin/install -c -m 644 bambamc/BamBam_BamAlignmentPut.h bambamc/BamBam_BamFlagBase.h bambamc/BamBam_FormatAlignment.h bambamc/BamBam_BamCollationHashEntry.h bambamc/BamBam_FormatNumber.h bambamc/BamBam_BamCollationHash.h bambamc/BamBam_BamHeaderInfo.h bambamc/BamBam_GzipReader.h bambamc/BamBam_BamCollationOutputVector.h bambamc/BamBam_BamSingleAlignment.h bambamc/BamBam_Hash.h bambamc/BamBam_BamCollationTempFileGenerator.h bambamc/BamBam_LineParsing.h bambamc/BamBam_BamCollationVector.h bambamc/BamBam_BamWriter.h bambamc/BamBam_List.h bambamc/BamBam_BamCollator.h bambamc/BamBam_CharBuffer.h bambamc/BamBam_ListNode.h bambamc/BamBam_BamCollatorInterface.h bambamc/BamBam_Chromosome.h bambamc/BamBam_MergeHeapEntry.h bambamc/BamBam_BamFileDecoder.h bambamc/BamBam_CollatorState.h bambamc/BamBam_Unused.h bambamc/BamBam_BamFileHeader.h bambamc/BamBam_FastQRead.h bambamc/BamBam_Config.h bambamc/BamBam_GzipWriter.h bambamc/BamBam_GzipFileDecoder.h bambamc/BamBam_BgzfCompressor.h bambamc/BamBam_LineBuffer.h bambamc/BamBam_SamInfo.h bambamc/BamBam_SamFileDecoder.h bambamc/BamBam_SamBamFileDecoder.h bambamc/BamBam_StrDup.h '/build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/include/bambamc' make[3]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50/src' make[2]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50/src' make[2]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' make[3]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 bambamc.pc '/build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make[3]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' make[2]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' make[1]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' debian/rules override_dh_install make[1]: Entering directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ debian/tmp/usr/lib/*/lib*.so Library package automatic movement utility --> zlib1g-dev package exists. set -e install -d -m 755 debian/libbambamc-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libbambamc0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.a debian/libbambamc-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.so debian/libbambamc-dev/usr/lib/x86_64-linux-gnu mv /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.so.0 debian/libbambamc0/usr/lib/x86_64-linux-gnu mv /build/bambamc-LNr0EZ/bambamc-0.0.50/debian/tmp/usr/lib/x86_64-linux-gnu/libbambamc.so.0.0.50 debian/libbambamc0/usr/lib/x86_64-linux-gnu PKGDEV=libbambamc-dev PKGSHL=libbambamc0 install -d -m 755 debian/libbambamc-dev/usr/include mv debian/tmp/usr/include/bambamc debian/libbambamc-dev/usr/include find debian -name "lib*.la" -delete dh_install make[1]: Leaving directory '/build/bambamc-LNr0EZ/bambamc-0.0.50' dh_installdocs -a dh_installchangelogs -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 dpkg-gencontrol: warning: Depends field of package libbambamc-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libbambamc-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libbambamc0-dbgsym' in '../libbambamc0-dbgsym_0.0.50-6_amd64.deb'. dpkg-deb: building package 'libbambamc0' in '../libbambamc0_0.0.50-6_amd64.deb'. dpkg-deb: building package 'libbambamc-dev' in '../libbambamc-dev_0.0.50-6_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bambamc_0.0.50-6_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/bambamc-LNr0EZ /tmp/bambamc-0.0.50-6ula9e5wj I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.Epd960QzGl... I: success in 1306.0452 seconds md5: libbambamc-dev_0.0.50-6_amd64.deb: OK md5: libbambamc0-dbgsym_0.0.50-6_amd64.deb: OK md5: libbambamc0_0.0.50-6_amd64.deb: OK sha1: libbambamc-dev_0.0.50-6_amd64.deb: OK sha1: libbambamc0-dbgsym_0.0.50-6_amd64.deb: OK sha1: libbambamc0_0.0.50-6_amd64.deb: OK sha256: libbambamc-dev_0.0.50-6_amd64.deb: OK sha256: libbambamc0-dbgsym_0.0.50-6_amd64.deb: OK sha256: libbambamc0_0.0.50-6_amd64.deb: OK Checksums: OK