Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/clonalframe/clonalframe_1.2-10+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/clonalframe-1.2-10+b1jv5k2jx3/clonalframe_1.2-10+b1_amd64.buildinfo Get source package info: clonalframe=1.2-10 Source URL: http://snapshot.notset.fr/mr/package/clonalframe/1.2-10/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=1:2.35.1-2 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.3.0-11 dash=0.5.10.2-7 debconf=1.5.74 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 file=1:5.38-4 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.3.0-11 gcc=4:9.2.1-3.1 gcc-10-base=10-20200502-1 gcc-9=9.3.0-11 gcc-9-base=9.3.0-11 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan5=9.3.0-11 libatomic1=10-20200502-1 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=2.35.1-2 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.30-7 libc-dev-bin=2.30-7 libc6=2.30-7 libc6-dev=2.30-7 libcap-ng0=0.7.9-2.1+b2 libcc1-0=10-20200502-1 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 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.8.0-1 libgcc-9-dev=9.3.0-11 libgcc-s1=10-20200502-1 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=10-20200502-1 libgpg-error0=1.37-1 libgsl-dev=2.6+dfsg-2 libgsl25=2.6+dfsg-2 libgslcblas0=2.6+dfsg-2 libicu63=63.2-3 libisl22=0.22.1-1 libitm1=10-20200502-1 liblsan0=10-20200502-1 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-4 libmagic1=1:5.38-4 libmount1=2.35.1-2 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 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=5.30.0-10 libpipeline1=1.5.2-2 libquadmath0=10-20200502-1 libseccomp2=2.4.3-1+b1 libselinux1=3.0-1+b3 libsigsegv2=2.12-2 libsmartcols1=2.35.1-2 libstdc++-9-dev=9.3.0-11 libstdc++6=10-20200502-1 libsub-override-perl=0.09-2 libsystemd0=245.5-2 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10-20200502-1 libubsan1=10-20200502-1 libuchardet0=0.0.6-3 libudev1=245.5-2 libunistring2=0.9.10-2 libuuid1=2.35.1-2 libxml2=2.9.10+dfsg-5 linux-libc-dev=5.6.7-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-2 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=5.30.0-10 perl-base=5.30.0-10 perl-modules-5.30=5.30.0-10 po-debconf=1.0.21 qt5-qmake=5.12.5+dfsg-10 qt5-qmake-bin=5.12.5+dfsg-10 qtchooser=66-2 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-3 tar=1.30+dfsg-7 util-linux=2.35.1-2 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/20200507T210258Z/ 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 clonalframe=1.2-10 && mkdir -p /build/clonalframe-7RGva6 && dpkg-source --no-check -x /*.dsc /build/clonalframe-7RGva6/clonalframe-1.2 && cd /build/clonalframe-7RGva6/clonalframe-1.2 && { printf '%s' 'clonalframe (1.2-10+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libgsl25 -- all/amd64 / i386 Build Daemon (x86-conova-01) Fri, 08 May 2020 00:53:10 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/clonalframe-7RGva6" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/clonalframe-7RGva6/clonalframe-1.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1588899190" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/clonalframe-7RGva6 /tmp/clonalframe-1.2-10+b1jv5k2jx3 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200507T210258Z 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._hW3u75IFn 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._hW3u75IFn Reading package lists... Building dependency tree... util-linux is already the newest version (2.35.1-2). 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/20200507T210258Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200507T210258Z 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 (983 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 ... 4482 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 (2.30-7) ... 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/20200507T210258Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap._hW3u75IFn Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200507T210258Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 21s (1065 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._hW3u75IFn I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d clonalframe=1.2-10 && mkdir -p /build/clonalframe-7RGva6 && dpkg-source --no-check -x /*.dsc /build/clonalframe-7RGva6/clonalframe-1.2 && cd /build/clonalframe-7RGva6/clonalframe-1.2 && { printf '%s' 'clonalframe (1.2-10+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libgsl25 -- all/amd64 / i386 Build Daemon (x86-conova-01) Fri, 08 May 2020 00:53:10 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/clonalframe-7RGva6"' exec /tmp/mmdebstrap._hW3u75IFn Reading package lists... NOTICE: 'clonalframe' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/clonalframe.git Please use: git clone https://salsa.debian.org/med-team/clonalframe.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 53.2 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main clonalframe 1.2-10 (dsc) [2023 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main clonalframe 1.2-10 (tar) [45.5 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main clonalframe 1.2-10 (diff) [5744 B] Fetched 53.2 kB in 0s (798 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'clonalframe_1.2-10.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting clonalframe in /build/clonalframe-7RGva6/clonalframe-1.2 dpkg-source: info: unpacking clonalframe_1.2.orig.tar.gz dpkg-source: info: unpacking clonalframe_1.2-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_gcc-4.6.patch dpkg-source: info: applying no_qtlibs.patch dpkg-source: info: applying glibc2.27.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/clonalframe-7RGva6/clonalframe-1.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1588899190" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap._hW3u75IFn dpkg-buildpackage: info: source package clonalframe dpkg-buildpackage: info: source version 1.2-10+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all/amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory '/build/clonalframe-7RGva6/clonalframe-1.2' dh_clean rm -rf bin build Makefile make[1]: Leaving directory '/build/clonalframe-7RGva6/clonalframe-1.2' debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/clonalframe-7RGva6/clonalframe-1.2' QT_SELECT=5 CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive" dh_auto_configure qmake -makefile "QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now" "QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now" QMAKE_STRIP=: PREFIX=/usr Info: creating stash file /build/clonalframe-7RGva6/clonalframe-1.2/.qmake.stash make[1]: Leaving directory '/build/clonalframe-7RGva6/clonalframe-1.2' dh_auto_build -a make -j4 make[1]: Entering directory '/build/clonalframe-7RGva6/clonalframe-1.2' g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/alignment_xmfa.o src/alignment_xmfa.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/alignment_structure.o src/alignment_structure.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/alignment.o src/alignment.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/boot.o src/boot.cpp src/alignment_structure.cpp: In constructor ‘wb::Alignment_structure::Alignment_structure(char*, int)’: src/alignment_structure.cpp:45:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 45 | if (ch>='0' & ch<='9') | ~~^~~~~ src/alignment.cpp: In member function ‘void wb::Alignment::writeToFile(char*)’: src/alignment.cpp:236:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 236 | char * lets="ATCG"; | ^~~~~~ src/alignment.cpp:241:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 241 | for (unsigned int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wformat=] 61 | printf("Warning: ignoring incomplete fragment %d (does not contain strain %s)\n",v.size(),names[missing]); | ~^ ~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld src/alignment_xmfa.cpp:129:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 129 | for (j=0;j >::size_type’ {aka ‘long unsigned int’} [-Wformat=] 170 | printf("Nb groups=%d\n",groups->size()); | ~^ ~~~~~~~~~~~~~~ | | | | int std::vector >::size_type {aka long unsigned int} | %ld src/burst.cpp:188:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 188 | for (k=1;ksize();k++) | ~^~~~~~~~~~~~ src/burst.cpp:190:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 190 | if (k>=rid->size()) continue; | ~^~~~~~~~~~~~~ src/burst.cpp: In member function ‘void wb::Burst::optimiseFathers(gsl_vector_int*, std::vector >*, int)’: src/burst.cpp:259:42: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 259 | if (slvs->at(prop).size()>current && !descended(prop,i,fathers)) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ src/burst.cpp:252:89: warning: unused parameter ‘f’ [-Wunused-parameter] 252 | void Burst::optimiseFathers(gsl_vector_int * fathers,vector > *slvs,int f) { | ~~~~^ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_ages.o src/move_ages.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_delta.o src/move_delta.cpp src/hashcell.cpp: In member function ‘void wb::HashCell::addNode(wb::Tree*)’: src/hashcell.cpp:51:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 51 | if (l>=t->recMap->size) break; | ~^~~~~~~~~~~~~~~~~ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_gap.o src/move_gap.cpp src/move_ages.cpp: In member function ‘virtual void wb::Move_ages::move(wb::Param*)’: src/move_ages.cpp:60:21: warning: suggest braces around empty body in an ‘else’ statement [-Wempty-body] 60 | } else ;//printf("Age change rejected because out of range\n"); | ^ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_hidden.o src/move_hidden.cpp src/move_delta.cpp: In constructor ‘wb::Move_delta::Move_delta(gsl_rng*, wb::Param*)’: src/move_delta.cpp:24:50: warning: unused parameter ‘p’ [-Wunused-parameter] 24 | Move_delta::Move_delta(gsl_rng * rng,Param * p):Move(rng) { | ~~~~~~~~^ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_hidden2.o src/move_hidden2.cpp src/move_gap.cpp: In constructor ‘wb::Move_gap::Move_gap(gsl_rng*, wb::Param*)’: src/move_gap.cpp:24:46: warning: unused parameter ‘p’ [-Wunused-parameter] 24 | Move_gap::Move_gap(gsl_rng * rng,Param * p) : Move(rng) {} | ~~~~~~~~^ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_mu.o src/move_mu.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_nu.o src/move_nu.cpp src/move_hidden.cpp: In constructor ‘wb::Move_hidden::Move_hidden(gsl_rng*, wb::Param*)’: src/move_hidden.cpp:25:52: warning: unused parameter ‘p’ [-Wunused-parameter] 25 | Move_hidden::Move_hidden(gsl_rng * rng,Param * p) : Move(rng) | ~~~~~~~~^ src/move_hidden.cpp: In member function ‘void wb::Move_hidden::forwardfast(wb::Param*, wb::Tree*)’: src/move_hidden.cpp:127:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 127 | for (unsigned int i=0;ia->polySites,old)- gsl_vector_int_get(p->a->polySites,old-1); | ^ src/move_mu.cpp: In constructor ‘wb::Move_mu::Move_mu(gsl_rng*, wb::Param*)’: src/move_mu.cpp:24:44: warning: unused parameter ‘p’ [-Wunused-parameter] 24 | Move_mu::Move_mu(gsl_rng * rng,Param * p):Move(rng) {} | ~~~~~~~~^ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_rho.o src/move_rho.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move_wb.o src/move_wb.cpp src/move_nu.cpp: In constructor ‘wb::Move_nu::Move_nu(gsl_rng*, wb::Param*)’: src/move_nu.cpp:24:44: warning: unused parameter ‘p’ [-Wunused-parameter] 24 | Move_nu::Move_nu(gsl_rng * rng,Param * p):Move(rng) {} | ~~~~~~~~^ src/move_nu.cpp: In member function ‘virtual void wb::Move_nu::move(wb::Param*)’: src/move_nu.cpp:56:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 56 | if (gsl_vector_char_get(t->recMap,j)==1) | ^ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/move.o src/move.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/param.o src/param.cpp src/move_wb.cpp: In member function ‘virtual void wb::Move_wb::move(wb::Param*)’: src/move_wb.cpp:127:17: warning: unused variable ‘sizeys2’ [-Wunused-variable] 127 | int sizeys2=propLocs(ys,probys,x,p); | ^~~~~~~ src/move_rho.cpp: In constructor ‘wb::Move_rho::Move_rho(gsl_rng*, wb::Param*)’: src/move_rho.cpp:24:46: warning: unused parameter ‘p’ [-Wunused-parameter] 24 | Move_rho::Move_rho(gsl_rng * rng,Param * p):Move(rng) | ~~~~~~~~^ g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/recorder.o src/recorder.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_coal.o src/tree_coal.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_simple.o src/tree_simple.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_upgma.o src/tree_upgma.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree_newick.o src/tree_newick.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/tree.o src/tree.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/util.o src/util.cpp g++ -c -pipe -W -Wall -O3 -static -DHAVE_INLINE -DGSL_RANGE_CHECK_OFF -Isrc -g -O2 -fdebug-prefix-map=/build/clonalframe-7RGva6/clonalframe-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -W -fPIC -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o build/ClonalFrame.o src/ClonalFrame.cpp src/util.cpp: In static member function ‘static void wb::Util::normalize(double*, int)’: src/util.cpp:83:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 83 | for (unsigned int i=0;irec++;} | ~~~^~~~~~~~~ src/tree.cpp:223:29: warning: ‘vals[5]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 223 | {ret+=vals[5];p->rec++;} | ~~~^~~~~~~~~ src/ClonalFrame.cpp: In function ‘gsl_rng* makerng()’: src/ClonalFrame.cpp:83:14: warning: variable ‘rng_seed’ set but not used [-Wunused-but-set-variable] 83 | long int rng_seed; | ^~~~~~~~ src/ClonalFrame.cpp: In function ‘int main(int, char**)’: src/ClonalFrame.cpp:263:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 263 | if (cleanup==true) {a->cleanUp();a->writeToFile("/tmp/out.xmfa");} | ^~~~~~~~~~~~~~~ src/ClonalFrame.cpp:341:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 341 | printf("Time spent in MH in seconds:%d\n",t2-t); | ~^ ~~~~ | | | | int long unsigned int | %ld src/ClonalFrame.cpp: In function ‘gsl_rng* makerng()’: src/ClonalFrame.cpp:96:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 96 | fread(&seed,sizeof(seed),1,devrandom); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o bin/ClonalFrame build/alignment_xmfa.o build/alignment_structure.o build/alignment.o build/boot.o build/burst.o build/consensus.o build/genes.o build/hashcell.o build/move_ages.o build/move_delta.o build/move_gap.o build/move_hidden.o build/move_hidden2.o build/move_mu.o build/move_nu.o build/move_rho.o build/move_wb.o build/move.o build/param.o build/recorder.o build/tree_coal.o build/tree_simple.o build/tree_upgma.o build/tree_newick.o build/tree.o build/util.o build/ClonalFrame.o -lgsl -lgslcblas make[1]: Leaving directory '/build/clonalframe-7RGva6/clonalframe-1.2' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch 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_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'clonalframe-dbgsym' in '../clonalframe-dbgsym_1.2-10+b1_amd64.deb'. dpkg-deb: building package 'clonalframe' in '../clonalframe_1.2-10+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../clonalframe_1.2-10+b1_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/clonalframe-7RGva6 /tmp/clonalframe-1.2-10+b1jv5k2jx3 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap._hW3u75IFn... I: success in 355.0584 seconds md5: clonalframe-dbgsym_1.2-10+b1_amd64.deb: OK md5: clonalframe_1.2-10+b1_amd64.deb: OK sha1: clonalframe-dbgsym_1.2-10+b1_amd64.deb: OK sha1: clonalframe_1.2-10+b1_amd64.deb: OK sha256: clonalframe-dbgsym_1.2-10+b1_amd64.deb: OK sha256: clonalframe_1.2-10+b1_amd64.deb: OK Checksums: OK