Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/a/allelecount/allelecount_4.2.1-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/allelecount-4.2.1-18aw6jbc4/allelecount_4.2.1-1_amd64.buildinfo Get source package info: allelecount=4.2.1-1 Source URL: http://snapshot.notset.fr/mr/package/allelecount/4.2.1-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-3 binutils-common=2.35.1-3 binutils-x86-64-linux-gnu=2.35.1-3 bsdextrautils=2.36.1-1 bsdutils=1:2.36.1-1 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-17 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.39-3 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-17 gcc=4:10.2.0-1 gcc-10=10.2.0-17 gcc-10-base=10.2.0-17 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-17 libatomic1=10.2.0-17 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libb-debug-perl=1.26-2 libbinutils=2.35.1-3 libblkid1=2.36.1-1 libbrotli1=1.0.9-2+b1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-17 libcom-err2=1.45.6-1 libconst-fast-perl=0.014-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-3 libctf0=2.35.1-3 libcurl3-gnutls=7.72.0-1 libcurl4-gnutls-dev=7.72.0-1 libdata-optlist-perl=0.110-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdeflate-dev=1.6-1 libdeflate0=1.6-1 libdevel-cover-perl=1.36-1+b2 libdevel-symdump-perl=2.18-3 libdpkg-perl=1.20.5 libelf1=0.182-1 libffi7=3.3-5 libfile-slurp-perl=9999.32-1 libfile-stripnondeterminism-perl=1.9.0-1 libfile-which-perl=1.23-1 libgcc-10-dev=10.2.0-17 libgcc-s1=10.2.0-17 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.3-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.6.15-4 libgomp1=10.2.0-17 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libhogweed6=3.6-2 libhtml-parser-perl=3.75-1+b1 libhtml-tagset-perl=3.20-4 libhts-dev=1.11-2 libhts3=1.11-2 libicu67=67.1-4 libidn2-0=2.3.0-4 libipc-system-simple-perl=1.30-1 libisl22=0.22.1-1 libitm1=10.2.0-17 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.0-17 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnettle8=3.6-2 libnghttp2-14=1.41.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libparams-util-perl=1.102-1+b1 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpod-coverage-perl=0.23-2 libpod-parser-perl=1.63-2 libpsl5=0.21.0-1.1 libquadmath0=10.2.0-17 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36.1-1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-17 libstdc++6=10.2.0-17 libsub-exporter-perl=0.987-1 libsub-exporter-progressive-perl=0.001013-1 libsub-install-perl=0.928-1 libsub-override-perl=0.09-2 libsystemd0=246.6-3 libtasn1-6=4.16.0-2 libtest-fatal-perl=0.016-1 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtry-tiny-perl=0.30-1 libtsan0=10.2.0-17 libubsan1=10.2.0-17 libuchardet0=0.0.7-1 libudev1=246.6-3 libunistring2=0.9.10-4 liburi-perl=5.05-1 libuuid1=2.36.1-1 libxml2=2.9.10+dfsg-6.2 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36.1-1 xz-utils=5.2.4-1+b1 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201202T151734Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201119T152556Z/ 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 allelecount=4.2.1-1 && mkdir -p /build/allelecount-h75VdX && dpkg-source --no-check -x /*.dsc /build/allelecount-h75VdX/allelecount-4.2.1 && chown -R builduser:builduser /build/allelecount-h75VdX" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/allelecount-h75VdX/allelecount-4.2.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605960011" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/allelecount-h75VdX /tmp/allelecount-4.2.1-18aw6jbc4 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201119T152556Z 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.fwUahO7dGC 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.fwUahO7dGC Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (514 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 ... 4690 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... 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/20201202T151734Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201119T152556Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.fwUahO7dGC Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201119T152556Z 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/20201202T151734Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201202T151734Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 30s (1146 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.fwUahO7dGC I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d allelecount=4.2.1-1 && mkdir -p /build/allelecount-h75VdX && dpkg-source --no-check -x /*.dsc /build/allelecount-h75VdX/allelecount-4.2.1 && chown -R builduser:builduser /build/allelecount-h75VdX"' exec /tmp/mmdebstrap.fwUahO7dGC Reading package lists... NOTICE: 'allelecount' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/allelecount.git Please use: git clone https://salsa.debian.org/med-team/allelecount.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1407 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main allelecount 4.2.1-1 (dsc) [2399 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main allelecount 4.2.1-1 (tar) [1389 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main allelecount 4.2.1-1 (diff) [15.2 kB] Fetched 1407 kB in 1s (1093 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'allelecount_4.2.1-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting allelecount in /build/allelecount-h75VdX/allelecount-4.2.1 dpkg-source: info: unpacking allelecount_4.2.1.orig.tar.gz dpkg-source: info: unpacking allelecount_4.2.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/allelecount-h75VdX/allelecount-4.2.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605960011" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.fwUahO7dGC dpkg-buildpackage: info: source package allelecount dpkg-buildpackage: info: source version 4.2.1-1 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/allelecount-h75VdX/allelecount-4.2.1' dh_auto_clean --sourcedirectory=c cd c && make -j4 clean make[2]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1/c' rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno make[2]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1/c' dh_auto_clean --sourcedirectory=perl make[1]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1' dh_auto_configure --sourcedirectory=c dh_auto_configure --sourcedirectory=perl cd perl && perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/allelecount-h75VdX/allelecount-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/allelecount-h75VdX/allelecount-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now" Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for alleleCount Writing MYMETA.yml and MYMETA.json make[1]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1' dh_auto_build --sourcedirectory=c cd c && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1/c' rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno mkdir -p ./bin mkdir -p ./htslib_tmp #Do some magic to ensure we compile ALLELECOUNT with the static libhts.a rather than libhts.so ln -fs /libhts.a ./htslib_tmp/libhts.a gcc -O3 -DALLELECOUNTER_VERSION='"4.2.1"' -g -O2 -fdebug-prefix-map=/build/allelecount-h75VdX/allelecount-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic -c src/bam_access.c -o src/bam_access.o src/bam_access.c: In function ‘pileupCounts’: src/bam_access.c:132:56: warning: ‘pre_b’ may be used uninitialized in this function [-Wmaybe-uninitialized] 132 | if(!(p->is_del) && qual >= min_base_qual && (absent || pre_b != c)){ | ~~~~~~~~^~~~~~~~~~~~~~ gcc -O3 -DALLELECOUNTER_VERSION='"4.2.1"' -I/usr/local//include -Isrc/ -I/ -rdynamic -g -O2 -fdebug-prefix-map=/build/allelecount-h75VdX/allelecount-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -o ./bin/alleleCounter ./src/bam_access.o -L./htslib_tmp -L/usr/local//lib -lhts -lpthread -lz -lbz2 -llzma -lm -ldl ./src/alleleCounter.c -Wl,-z,relro -Wl,-z,now gcc -O3 -DALLELECOUNTER_VERSION='"4.2.1"' -g -O2 -fdebug-prefix-map=/build/allelecount-h75VdX/allelecount-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic ./src/bam_access.o -L./htslib_tmp -lhts -lpthread -lz -lbz2 -llzma -lm -ldl -L/usr/local//lib -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now tests/bam_access_tests.c -o tests/bam_access_tests tests/bam_access_tests.c: In function ‘test_bam_access_get_position_base_counts’: tests/bam_access_tests.c:45:6: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] 45 | int res = bam_access_get_position_base_counts(chr,pos,stats,0,NULL); | ^~~ sh ./tests/runtests.sh Running unit tests: ---- RUNNING: ./tests/bam_access_tests Performing pileup of 11250 reads at 1 198661939 ALL TESTS PASSED Tests run: 1 tests/bam_access_tests PASS remove tmp hts location rm -rf ./htslib_tmp Binaries have been compiled. make[2]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1/c' dh_auto_build --sourcedirectory=perl cd perl && make -j4 make[2]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1/perl' cp lib/Sanger/CGP/AlleleCount.pm blib/lib/Sanger/CGP/AlleleCount.pm cp lib/Sanger/CGP/AlleleCount/Genotype.pm blib/lib/Sanger/CGP/AlleleCount/Genotype.pm cp bin/alleleCounter.pl blib/script/alleleCounter.pl "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounter.pl Manifying 1 pod document Manifying 1 pod document make[2]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1/perl' make[1]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1' dh_auto_test --sourcedirectory=c cd c && make -j4 test make[2]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1/c' sh ./tests/runtests.sh Running unit tests: ---- RUNNING: ./tests/bam_access_tests Performing pileup of 11250 reads at 1 198661939 ALL TESTS PASSED Tests run: 1 tests/bam_access_tests PASS make[2]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1/c' dh_auto_test --sourcedirectory=perl cd perl && make -j4 test TEST_VERBOSE=1 make[2]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1/perl' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/1_pm_compile.t .. ok 1 - use Sanger::CGP::AlleleCount; ok 2 - use Sanger::CGP::AlleleCount::Genotype; ok 3 - Check version inheritance exists (Sanger::CGP::AlleleCount) ok 4 - Check version inheritance exists (Sanger::CGP::AlleleCount::Genotype) ok 5 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' 1..5 ok t/2_pl_compile.t .. ok 1 - Compilation check: /build/allelecount-h75VdX/allelecount-4.2.1/perl/t/../bin/alleleCounter.pl 1..1 ok t/genotype.t ...... ok 1 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' ok 2 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' ok 3 - Check execution of loci profile (BAM) ok 4 - Expected result for defaults (BAM) ok 5 - Check execution of loci profile (BAM, pbq=20) ok 6 - Expected result for defaults (BAM, pbq=20) ok 7 - Check execution of loci profile (BAM, mapq=1) ok 8 - Expected result for defaults (BAM, mapq=1) ok 9 - Check execution of snp6 loci profile (BAM) ok 10 - Expected result for defaults (BAM) ok 11 - Check execution of snp6 loci profile (BAM, pbq=20) ok 12 - Expected result for defaults (BAM, pbq=20) ok 13 - Check execution of snp6 loci profile (BAM, mapq=1) ok 14 - Expected result for defaults (BAM, mapq>0) ok 15 - Check execution of loci profile (CRAM) ok 16 - Expected result for defaults (CRAM) ok 17 - Check execution of loci profile (CRAM, pbq=20) ok 18 - Expected result for defaults (CRAM, pbq=20) ok 19 - Check execution of loci profile (CRAM, mapq=1) ok 20 - Expected result for defaults (CRAM, mapq=1) ok 21 - Check execution of snp6 loci profile (CRAM) ok 22 - Expected result for defaults (CRAM) ok 23 - Check execution of snp6 loci profile (CRAM, pbq=20) ok 24 - Expected result for defaults (CRAM, pbq=20) ok 25 - Check execution of snp6 loci profile (CRAM, mapq=1) ok 26 - Expected result for defaults (CRAM, mapq=1) 1..26 ok All tests successful. Files=3, Tests=32, 2 wallclock secs ( 0.05 usr 0.00 sys + 0.72 cusr 0.13 csys = 0.90 CPU) Result: PASS make[2]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1/perl' make[1]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1' dh_auto_install --sourcedirectory=c dh_auto_install --sourcedirectory=perl cd perl && make -j4 install DESTDIR=/build/allelecount-h75VdX/allelecount-4.2.1/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/allelecount-h75VdX/allelecount-4.2.1/perl' Manifying 1 pod document Manifying 1 pod document Installing /build/allelecount-h75VdX/allelecount-4.2.1/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount.pm Installing /build/allelecount-h75VdX/allelecount-4.2.1/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/Genotype.pm Installing /build/allelecount-h75VdX/allelecount-4.2.1/debian/tmp/usr/share/man/man1/alleleCounter.pl.1p Installing /build/allelecount-h75VdX/allelecount-4.2.1/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::Genotype.3pm Installing /build/allelecount-h75VdX/allelecount-4.2.1/debian/tmp/usr/bin/alleleCounter.pl make[2]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1/perl' make[1]: Leaving directory '/build/allelecount-h75VdX/allelecount-4.2.1' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'allelecount' in '../allelecount_4.2.1-1_amd64.deb'. dpkg-deb: building package 'allelecount-dbgsym' in '../allelecount-dbgsym_4.2.1-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../allelecount_4.2.1-1_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/allelecount-h75VdX /tmp/allelecount-4.2.1-18aw6jbc4 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.fwUahO7dGC... I: success in 604.8986 seconds md5: allelecount-dbgsym_4.2.1-1_amd64.deb: OK md5: allelecount_4.2.1-1_amd64.deb: OK sha1: allelecount-dbgsym_4.2.1-1_amd64.deb: OK sha1: allelecount_4.2.1-1_amd64.deb: OK sha256: allelecount-dbgsym_4.2.1-1_amd64.deb: OK sha256: allelecount_4.2.1-1_amd64.deb: OK Checksums: OK