Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/l/lagan/lagan_2.0-6_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/lagan-2.0-6441orbgu/lagan_2.0-6_amd64.buildinfo Get source package info: lagan=2.0-6 Source URL: http://snapshot.notset.fr/mr/package/lagan/2.0-6/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 binutils=2.34-6 binutils-common=2.34-6 binutils-x86-64-linux-gnu=2.34-6 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.3.0-10 dash=0.5.10.2-7 debconf=1.5.73 debhelper=13 debianutils=4.9.1 dh-autoreconf=19 dh-strip-nondeterminism=1.8.0-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 fdisk=2.34-0.1 file=1:5.38-4 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.3.0-10 gcc=4:9.2.1-3.1 gcc-10-base=10-20200411-1 gcc-9=9.3.0-10 gcc-9-base=9.3.0-10 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-4 gzip=1.10-2 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-6 libarchive-zip-perl=1.68-1 libasan5=9.3.0-10 libatomic1=10-20200411-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.34-6 libblkid1=2.34-0.1 libboost-dev=1.67.0.2+b1 libboost1.67-dev=1.67.0-17+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.30-4 libc-dev-bin=2.30-4 libc6=2.30-4 libc6-dev=2.30-4 libcap-ng0=0.7.9-2.1+b2 libcc1-0=10-20200411-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.16-1 libcrypt1=1:4.4.16-1 libctf-nobfd0=2.34-6 libctf0=2.34-6 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.251 libdebhelper-perl=13 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libfdisk1=2.34-0.1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.8.0-1 libgcc-9-dev=9.3.0-10 libgcc-s1=10-20200411-1 libgcrypt20=1.8.5-5 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.64.2-1 libgmp10=2:6.2.0+dfsg-4 libgomp1=10-20200411-1 libgpg-error0=1.37-1 libicu63=63.2-3 libisl22=0.22.1-1 libitm1=10-20200411-1 liblsan0=10-20200411-1 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-4 libmagic1=1:5.38-4 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 libncursesw6=6.2-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-9 libpipeline1=1.5.2-2 libquadmath0=10-20200411-1 libseccomp2=2.4.3-1+b1 libselinux1=3.0-1+b3 libsigsegv2=2.12-2 libsmartcols1=2.34-0.1 libstdc++-9-dev=9.3.0-10 libstdc++6=10-20200411-1 libsub-override-perl=0.09-2 libsystemd0=245.4-4 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10-20200411-1 libubsan1=10-20200411-1 libuchardet0=0.0.6-3 libudev1=245.4-4 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libxml2=2.9.10+dfsg-5 linux-libc-dev=5.5.13-2 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.1-1 mawk=1.3.4.20200120-2 ncurses-base=6.2-1 ncurses-bin=6.2-1 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-3 tar=1.30+dfsg-7 util-linux=2.34-0.1 xz-utils=5.2.4-1+b1 zlib1g=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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200526T084721Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200417T040322Z/ 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 lagan=2.0-6 && mkdir -p /build/lagan-5iUdeF && dpkg-source --no-check -x /*.dsc /build/lagan-5iUdeF/lagan-2.0 && chown -R builduser:builduser /build/lagan-5iUdeF" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/lagan-5iUdeF/lagan-2.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1587148751" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/lagan-5iUdeF /tmp/lagan-2.0-6441orbgu bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200417T040322Z 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.cyVKESq715 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.cyVKESq715 Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200417T040322Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200417T040322Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (784 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 ... 4504 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.30-4) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200526T084721Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200417T040322Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.cyVKESq715 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200526T084721Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20200417T040322Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20200526T084721Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200526T084721Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200526T084721Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20200526T084721Z unstable/main amd64 Packages [11.2 MB] Fetched 33.9 MB in 32s (1074 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.cyVKESq715 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d lagan=2.0-6 && mkdir -p /build/lagan-5iUdeF && dpkg-source --no-check -x /*.dsc /build/lagan-5iUdeF/lagan-2.0 && chown -R builduser:builduser /build/lagan-5iUdeF"' exec /tmp/mmdebstrap.cyVKESq715 Reading package lists... NOTICE: 'lagan' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lagan.git Please use: git clone https://salsa.debian.org/med-team/lagan.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 203 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main lagan 2.0-6 (dsc) [1954 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main lagan 2.0-6 (tar) [193 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main lagan 2.0-6 (diff) [7908 B] Fetched 203 kB in 0s (1146 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'lagan_2.0-6.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting lagan in /build/lagan-5iUdeF/lagan-2.0 dpkg-source: info: unpacking lagan_2.0.orig.tar.gz dpkg-source: info: unpacking lagan_2.0-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_define_conflicting_getline.patch dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying ambiuousEnd.patch dpkg-source: info: applying addTest.patch dpkg-source: info: applying adjustPerlPaths.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying gcc9.patch dpkg-source: info: applying gcc10.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/lagan-5iUdeF/lagan-2.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1587148751" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.cyVKESq715 dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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/lagan-5iUdeF/lagan-2.0' dh_auto_clean make -j4 clean make[2]: Entering directory '/build/lagan-5iUdeF/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean make[3]: Entering directory '/build/lagan-5iUdeF/lagan-2.0/src' rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; make clean) make[4]: Entering directory '/build/lagan-5iUdeF/lagan-2.0/src/glocal' rm -f *.o ./*~ *~ core make[4]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0/src/glocal' make[3]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0/src' make[2]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0' rm -f prolagan make[1]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0' 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/lagan-5iUdeF/lagan-2.0' dh_auto_build --sourcedirectory=src cd src && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/lagan-5iUdeF/lagan-2.0/src' gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro order.c: In function ‘doAlign’: order.c:409:5: warning: implicit declaration of function ‘printMFAAlign’; did you mean ‘printBinAlign’? [-Wimplicit-function-declaration] 409 | printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); | ^~~~~~~~~~~~~ | printBinAlign order.c:411:5: warning: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printTextAlign’? [-Wimplicit-function-declaration] 411 | printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); | ^~~~~~~~~~~~~~ | printTextAlign mlagan.c: In function ‘readfile’: mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function ‘main’: mlagan.c:1071:5: warning: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printFASTAAlign’? [-Wimplicit-function-declaration] 1071 | printXMFAAlign(outfile, final); | ^~~~~~~~~~~~~~ | printFASTAAlign fchaos.c: In function ‘readfile’: fchaos.c:357:18: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-z,relro prolagan.c: In function ‘readfile’: prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function ‘main’: prolagan.c:1091:5: warning: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printFASTAAlign’? [-Wimplicit-function-declaration] 1091 | printXMFAAlign(outfile, final); | ^~~~~~~~~~~~~~ | printFASTAAlign multial.c:603:9: warning: ‘gapcache’ is static but used in inline function ‘openGap’ which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: ‘gapcache’ is static but used in inline function ‘contGap’ which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: ‘gapcache’ is static but used in inline function ‘matchscore’ which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: ‘matchcache’ is static but used in inline function ‘matchscore’ which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c:603:9: warning: ‘gapcache’ is static but used in inline function ‘openGap’ which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: ‘gapcache’ is static but used in inline function ‘contGap’ which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: ‘gapcache’ is static but used in inline function ‘matchscore’ which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: ‘matchcache’ is static but used in inline function ‘matchscore’ which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/bin2mf utils/bin2mf.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/bin2bl utils/bin2bl.c -Wl,-z,relro skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/cextract utils/cextract.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/cstat utils/cstat.c -Wl,-z,relro utils/cstat.c: In function ‘cntlets’: utils/cstat.c:51:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 51 | if (!isspace(currchar)) { | ^~~~~~~ utils/cstat.c:52:18: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] 52 | currchar = toupper(currchar); | ^~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro utils/contigorder.c: In function ‘getFileInfo’: utils/contigorder.c:15:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c:26:18: warning: unknown conversion type character ‘&’ in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:16: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function ‘getScores’: utils/contigorder.c:52:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/getlength utils/getlength.c -Wl,-z,relro skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/rc utils/rc.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/seqmerge utils/seqmerge.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-z,relro utils/scorecontigs.c: In function ‘cntlets’: utils/scorecontigs.c:63:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 63 | if (!isspace(currchar)) { | ^~~~~~~ utils/scorecontigs.c:64:18: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] 64 | currchar = toupper(currchar); | ^~~~~~~ utils/scorecontigs.c:65:27: warning: implicit declaration of function ‘isalpha’ [-Wimplicit-function-declaration] 65 | if (!lettersonly || isalpha (currchar)){ | ^~~~~~~ utils/scorecontigs.c: In function ‘main’: utils/scorecontigs.c:384:38: warning: format ‘%s’ expects argument of type ‘char *’, but argument 6 has type ‘char (*)[1024]’ [-Wformat=] 384 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-z,relro g++ -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/Glue utils/Glue.cpp -Wl,-z,relro g++ -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/dotplot utils/dotplot.cpp -Wl,-z,relro gcc -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o ../utils/overlay utils/overlay.c -Wl,-z,relro utils/overlay.c: In function ‘read_align’: utils/overlay.c:119:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 119 | if (!isspace(currchar)) { | ^~~~~~~ utils/overlay.c:120:19: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] 120 | checkchar = toupper(currchar); | ^~~~~~~ utils/overlay.c:134:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 134 | strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/overlay.c:134:45: note: length computed here 134 | strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); | ^~~~~~~~~~~~ utils/Glue.cpp: In function ‘void calculateScoreMatrix(int)’: utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 64 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:72:22: note: in expansion of macro ‘NUCLEOTIDE_MATRIX_FILE’ 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ (cd glocal; make LDFLAGS=-Wl,-z,relro) make[3]: Entering directory '/build/lagan-5iUdeF/lagan-2.0/src/glocal' g++ -Wno-deprecated -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -O3 -I./ -c glocal.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -O3 -I./ -c io.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -O3 -I./ -c rightinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -O3 -I./ -c leftinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -fdebug-prefix-map=/build/lagan-5iUdeF/lagan-2.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -O3 -I./ -c score.cpp -Wl,-z,relro g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm make[3]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0/src' make[1]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0' dh_auto_test -a make -j4 test make[1]: Entering directory '/build/lagan-5iUdeF/lagan-2.0' make -C src make[2]: Entering directory '/build/lagan-5iUdeF/lagan-2.0/src' (cd glocal; make LDFLAGS=-Wl,-z,relro) make[3]: Entering directory '/build/lagan-5iUdeF/lagan-2.0/src/glocal' g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm make[3]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0/src/glocal' make[2]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0/src' (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]" [ok] make[1]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/build/lagan-5iUdeF/lagan-2.0' dh_fixperms find debian -name flipchaos.pl -exec chmod +x \{\} \; make[1]: Leaving directory '/build/lagan-5iUdeF/lagan-2.0' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'lagan' in '../lagan_2.0-6_amd64.deb'. dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-6_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../lagan_2.0-6_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/lagan-5iUdeF /tmp/lagan-2.0-6441orbgu I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.cyVKESq715... I: success in 413.4484 seconds md5: lagan-dbgsym_2.0-6_amd64.deb: OK md5: lagan_2.0-6_amd64.deb: OK sha1: lagan-dbgsym_2.0-6_amd64.deb: OK sha1: lagan_2.0-6_amd64.deb: OK sha256: lagan-dbgsym_2.0-6_amd64.deb: OK sha256: lagan_2.0-6_amd64.deb: OK Checksums: OK