Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bio-eagle/bio-eagle_2.4.1-3+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bio-eagle-2.4.1-3+b14a8vyj8f/bio-eagle_2.4.1-3+b1_amd64.buildinfo Get source package info: bio-eagle=2.4.1-3 Source URL: http://snapshot.notset.fr/mr/package/bio-eagle/2.4.1-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.3-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1-1 binutils=2.35.1-4 binutils-common=2.35.1-4 binutils-x86-64-linux-gnu=2.35.1-4 bsdextrautils=2.36.1-2 bsdutils=1:2.36.1-2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-1 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.3 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+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.1-1 gcc=4:10.2.0-1 gcc-10=10.2.1-1 gcc-10-base=10.2.1-1 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 icu-devtools=67.1-5 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.1-1 libatomic1=10.2.1-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1+b1 libbinutils=2.35.1-4 libblkid1=2.36.1-2 libboost-dev=1.74.0.2 libboost-iostreams-dev=1.74.0.2 libboost-iostreams1.74-dev=1.74.0-3+b1 libboost-iostreams1.74.0=1.74.0-3+b1 libboost-program-options-dev=1.74.0.2 libboost-program-options1.74-dev=1.74.0-3+b1 libboost-program-options1.74.0=1.74.0-3+b1 libboost-regex1.74-dev=1.74.0-3+b1 libboost-regex1.74.0=1.74.0-3+b1 libboost1.74-dev=1.74.0-3+b1 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-5 libc-dev-bin=2.31-5 libc6=2.31-5 libc6-dev=2.31-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-1 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-4 libctf0=2.35.1-4 libcurl3-gnutls=7.72.0-1 libcurl4-gnutls-dev=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.3 libdeflate-dev=1.6-1 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.1-1 libgcc-s1=10.2.1-1 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.1-1 libglib2.0-0=2.66.3-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-3 libgomp1=10.2.1-1 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.6-2 libhts-dev=1.11-2 libhts3=1.11-2 libicu-dev=67.1-5 libicu67=67.1-5 libidn2-0=2.3.0-4 libisl23=0.23-1 libitm1=10.2.1-1 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.1-1 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=2.36.1-2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenblas-dev=0.3.12+ds-2 libopenblas-pthread-dev=0.3.12+ds-2 libopenblas0=0.3.12+ds-2 libopenblas0-pthread=0.3.12+ds-2 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 libpcre2-8-0=10.35-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.1 libquadmath0=10.2.1-1 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+b1 libselinux1=3.1-2+b2 libsigsegv2=2.12-2 libsmartcols1=2.36.1-2 libssh2-1=1.9.0-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-1 libstdc++6=10.2.1-1 libsub-override-perl=0.09-2 libsystemd0=247.1-3 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.1-1 libubsan1=10.2.1-1 libuchardet0=0.0.7-1 libudev1=247.1-3 libunistring2=0.9.10-4 libuuid1=2.36.1-2 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.11-1 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+20201114-1 ncurses-bin=6.2+20201114-1 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=1.32+dfsg-1 util-linux=2.36.1-2 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/20201212T153433Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201210T083846Z/ 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 bio-eagle=2.4.1-3 && mkdir -p /build/bio-eagle-Cd8bv6 && dpkg-source --no-check -x /*.dsc /build/bio-eagle-Cd8bv6/bio-eagle-2.4.1 && cd /build/bio-eagle-Cd8bv6/bio-eagle-2.4.1 && { printf '%s' 'bio-eagle (2.4.1-3+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against boost 1.74 -- amd64 / i386 Build Daemon (x86-ubc-01) Sat, 12 Dec 2020 09:04:58 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/bio-eagle-Cd8bv6" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bio-eagle-Cd8bv6/bio-eagle-2.4.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607763898" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/bio-eagle-Cd8bv6 /tmp/bio-eagle-2.4.1-3+b14a8vyj8f bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201210T083846Z 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.0QGAq3Y7u0 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.0QGAq3Y7u0 Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-2). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201210T083846Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201210T083846Z 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 (1080 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 ... 4616 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 (2.31-5) ... 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/20201212T153433Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201210T083846Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.0QGAq3Y7u0 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201212T153433Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201210T083846Z 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/20201212T153433Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201212T153433Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201212T153433Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201212T153433Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 30s (1141 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.0QGAq3Y7u0 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bio-eagle=2.4.1-3 && mkdir -p /build/bio-eagle-Cd8bv6 && dpkg-source --no-check -x /*.dsc /build/bio-eagle-Cd8bv6/bio-eagle-2.4.1 && cd /build/bio-eagle-Cd8bv6/bio-eagle-2.4.1 && { printf '%s' 'bio-eagle (2.4.1-3+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against boost 1.74 -- amd64 / i386 Build Daemon (x86-ubc-01) Sat, 12 Dec 2020 09:04:58 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/bio-eagle-Cd8bv6"' exec /tmp/mmdebstrap.0QGAq3Y7u0 Reading package lists... NOTICE: 'bio-eagle' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bio-eagle.git Please use: git clone https://salsa.debian.org/med-team/bio-eagle.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1639 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bio-eagle 2.4.1-3 (dsc) [2210 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bio-eagle 2.4.1-3 (tar) [1628 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bio-eagle 2.4.1-3 (diff) [8668 B] Fetched 1639 kB in 1s (1205 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bio-eagle_2.4.1-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bio-eagle in /build/bio-eagle-Cd8bv6/bio-eagle-2.4.1 dpkg-source: info: unpacking bio-eagle_2.4.1.orig.tar.gz dpkg-source: info: unpacking bio-eagle_2.4.1-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile_config.patch dpkg-source: info: applying non_x86_malloc I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bio-eagle-Cd8bv6/bio-eagle-2.4.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607763898" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.0QGAq3Y7u0 dpkg-buildpackage: info: source package bio-eagle dpkg-buildpackage: info: source version 2.4.1-3+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j4 clean make[1]: Entering directory '/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1/src' rm -f *.o rm -f eagle make[1]: Leaving directory '/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary-arch dh binary-arch --sourcedirectory=src dh_update_autotools_config -a -O--sourcedirectory=src dh_autoreconf -a -O--sourcedirectory=src dh_auto_configure -a -O--sourcedirectory=src dh_auto_build -a -O--sourcedirectory=src cd src && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1/src' g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleMain.o -c EagleMain.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o DipTreePBWT.o -c DipTreePBWT.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Eagle.o -c Eagle.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleImpMiss.o -c EagleImpMiss.cpp EagleMain.cpp: In function ‘void phaseWithRef(EAGLE::EagleParams&, Timer&, double, int, char**)’: EagleMain.cpp:109:17: warning: unused variable ‘hapBitsTptr’ [-Wunused-variable] 109 | HapBitsT *hapBitsTptr = NULL; | ^~~~~~~~~~~ EagleMain.cpp:110:17: warning: unused variable ‘hapHedgePtr’ [-Wunused-variable] 110 | HapHedge *hapHedgePtr = NULL; | ^~~~~~~~~~~ EagleMain.cpp:104:25: warning: unused variable ‘timeImpMissing’ [-Wunused-variable] 104 | double timeMN2 = 0, timeImpMissing = 0; | ^~~~~~~~~~~~~~ EagleMain.cpp: In function ‘int main(int, char**)’: EagleMain.cpp:448:61: warning: unused variable ‘timeImpMissing’ [-Wunused-variable] 448 | double t23 = timer.get_time(); timer.update_time(); double timeImpMissing = 0; | ^~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleParams.o -c EagleParams.cpp Eagle.cpp: In member function ‘void EAGLE::Eagle::readPhaseConfs(const string&)’: Eagle.cpp:3108:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3108 | fread(phaseConfs, 1, 2*N*Mseg64*64, fout); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp: In function ‘void EAGLE::bcf_hdr_append_eagle_version(bcf_hdr_t*, int, char**)’: Eagle.cpp:3221:17: warning: ignoring return value of ‘int bcf_hdr_sync(bcf_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3221 | bcf_hdr_sync(hdr); | ~~~~~~~~~~~~^~~~~ Eagle.cpp: In member function ‘void EAGLE::Eagle::writeVcf(const string&, const std::vector&, const string&, int, double, double, const string&, bool, bool, int, char**) const’: Eagle.cpp:3248:18: warning: ignoring return value of ‘int bcf_hdr_write(htsFile*, bcf_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3248 | bcf_hdr_write(out, hdr); | ~~~~~~~~~~~~~^~~~~~~~~~ Eagle.cpp:3270:13: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3270 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ Eagle.cpp:3282:13: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3282 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ Eagle.cpp:3347:13: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3347 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ Eagle.cpp: In member function ‘void EAGLE::Eagle::writeVcfNonRef(const string&, const string&, int, int, double, double, const string&, bool, bool, int, char**) const’: Eagle.cpp:3388:18: warning: ignoring return value of ‘int bcf_hdr_write(htsFile*, bcf_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3388 | bcf_hdr_write(out, hdr); | ~~~~~~~~~~~~~^~~~~~~~~~ Eagle.cpp:3467:11: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3467 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EaglePBWT.o -c EaglePBWT.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o FileUtils.o -c FileUtils.cpp Eagle.cpp: In member function ‘std::string EAGLE::Eagle::computePhaseString(uint64, uint64, uint64, const std::vector&, const std::vector&, uint64, double, bool) const’: Eagle.cpp:1124:43: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] 1124 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~ Eagle.cpp:1124:31: note: directive argument in the range [1, 2147483647] 1124 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 12 and 339 bytes into a destination of size 20 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp:1156:41: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] 1156 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~ Eagle.cpp:1156:29: note: directive argument in the range [0, 2147483647] 1156 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 12 and 339 bytes into a destination of size 20 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp: In member function ‘void EAGLE::Eagle::printMatch(uint64, uint64, uint64, const EAGLE::Match&, double (*)[4]) const’: Eagle.cpp:1197:43: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] 1197 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~ Eagle.cpp:1197:31: note: directive argument in the range [0, 2147483647] 1197 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 12 and 339 bytes into a destination of size 20 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o GenoData.o -c GenoData.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o HapHedge.o -c HapHedge.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MapInterpolater.o -c MapInterpolater.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MemoryUtils.o -c MemoryUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o StaticMultimap.o -c StaticMultimap.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o SyncedVcfData.o -c SyncedVcfData.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Timer.o -c Timer.cpp SyncedVcfData.cpp: In member function ‘std::vector > EAGLE::SyncedVcfData::processVcfs(const string&, const string&, const string&, bool, int&, int, double, double, std::vector&, std::vector&, const string&, const string&, int, std::vector > >&, bool, std::vector&)’: SyncedVcfData.cpp:228:18: warning: ignoring return value of ‘int bcf_hdr_write(htsFile*, bcf_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 228 | bcf_hdr_write(out, tgt_hdr); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ SyncedVcfData.cpp:262:42: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 262 | if (outputUnphased && tgt) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:270:35: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 270 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:287:35: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 287 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:293:35: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 293 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:303:35: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 303 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:321:35: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 321 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:377:11: warning: ignoring return value of ‘int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 377 | bcf_write(out, tgt_hdr, tgt); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp: In function ‘void EAGLE::process_ref_genotypes(int, int, int32_t*, bool, bool, std::vector&, int&, int&, uint&)’: SyncedVcfData.cpp:97:14: warning: ‘haps[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 97 | if (haps[0] != haps[1] && ((w=18000*(w&65535)+(w>>16))&1)) | ~~~~~~^ SyncedVcfData.cpp:97:25: warning: ‘haps[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 97 | if (haps[0] != haps[1] && ((w=18000*(w&65535)+(w>>16))&1)) | ~~~~~~^ g++ -fopenmp -Wl,-z,relro -Wl,-z,now -o eagle EagleMain.o DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o -lhts -lboost_program_options -lboost_iostreams -lz -lopenblas -lpthread -lm make[1]: Leaving directory '/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1/src' dh_auto_test -a -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=src dh_prep -a -O--sourcedirectory=src dh_auto_install -a -O--sourcedirectory=src dh_install -a -O--sourcedirectory=src dh_installdocs -a -O--sourcedirectory=src debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/bio-eagle-Cd8bv6/bio-eagle-2.4.1' dh_installman -a -O--sourcedirectory=src dh_installsystemduser -a -O--sourcedirectory=src dh_perl -a -O--sourcedirectory=src dh_link -a -O--sourcedirectory=src dh_strip_nondeterminism -a -O--sourcedirectory=src dh_compress -a -O--sourcedirectory=src dh_fixperms -a -O--sourcedirectory=src dh_missing -a -O--sourcedirectory=src dh_dwz -a -a -O--sourcedirectory=src dh_strip -a -a -O--sourcedirectory=src dh_makeshlibs -a -a -O--sourcedirectory=src dh_shlibdeps -a -a -O--sourcedirectory=src dh_installdeb -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dh_md5sums -a -O--sourcedirectory=src dh_builddeb -a -O--sourcedirectory=src dpkg-deb: building package 'bio-eagle' in '../bio-eagle_2.4.1-3+b1_amd64.deb'. dpkg-deb: building package 'bio-eagle-dbgsym' in '../bio-eagle-dbgsym_2.4.1-3+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bio-eagle_2.4.1-3+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/bio-eagle-Cd8bv6 /tmp/bio-eagle-2.4.1-3+b14a8vyj8f I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.0QGAq3Y7u0... I: success in 632.7133 seconds md5: bio-eagle-dbgsym_2.4.1-3+b1_amd64.deb: OK md5: bio-eagle_2.4.1-3+b1_amd64.deb: OK sha1: bio-eagle-dbgsym_2.4.1-3+b1_amd64.deb: OK sha1: bio-eagle_2.4.1-3+b1_amd64.deb: OK sha256: bio-eagle-dbgsym_2.4.1-3+b1_amd64.deb: OK sha256: bio-eagle_2.4.1-3+b1_amd64.deb: OK Checksums: OK