Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bolt-lmm/bolt-lmm_2.3.4+dfsg-3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bolt-lmm-2.3.4+dfsg-3_eyqplqh/bolt-lmm_2.3.4+dfsg-3_amd64.buildinfo Get source package info: bolt-lmm=2.3.4+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/bolt-lmm/2.3.4+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-13 automake=1:1.16.3-1 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-1 binutils=2.35.1-5 binutils-common=2.35.1-5 binutils-x86-64-linux-gnu=2.35.1-5 bsdextrautils=2.36.1-3 bsdutils=1:2.36.1-3 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+dd9ef66-5 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=0.21-3 gettext-base=0.21-3 gfortran=4:10.2.0-1 gfortran-10=10.2.1-1 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=1.60 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=2.35.1-5 libblkid1=2.36.1-3 libboost-dev=1.74.0.3 libboost-iostreams-dev=1.74.0.3 libboost-iostreams1.74-dev=1.74.0-5 libboost-iostreams1.74.0=1.74.0-5 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-5 libboost-program-options1.74.0=1.74.0-5 libboost-regex1.74-dev=1.74.0-5 libboost-regex1.74.0=1.74.0-5 libboost1.74-dev=1.74.0-5 libbz2-1.0=1.0.8-4 libc-bin=2.31-6 libc-dev-bin=2.31-6 libc6=2.31-6 libc6-dev=2.31-6 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-1 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-5 libctf0=2.35.1-5 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.3 libdpkg-perl=1.20.5 libelf1=0.182-1 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 libgfortran-10-dev=10.2.1-1 libgfortran5=10.2.1-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-1 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libicu-dev=67.1-5 libicu67=67.1-5 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 liblsan0=10.2.1-1 liblz4-1=1.9.3-1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-3 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnlopt-cxx-dev=2.7.0-4+b2 libnlopt-cxx0=2.7.0-4+b2 libnlopt-dev=2.7.0-4+b2 libnlopt0=2.7.0-4+b2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenblas-dev=0.3.13+ds-1 libopenblas-pthread-dev=0.3.13+ds-1 libopenblas0=0.3.13+ds-1 libopenblas0-pthread=0.3.13+ds-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=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libquadmath0=10.2.1-1 libseccomp2=2.5.0-3+b1 libselinux1=3.1-2+b2 libsigsegv2=2.12-3 libsmartcols1=2.36.1-3 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=247.1-4 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=247.1-4 libunistring2=0.9.10-4 libuuid1=2.36.1-3 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.15-1 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=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 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=2.36.1-3 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/20211009T024746Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201220T203231Z/ 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 bolt-lmm=2.3.4+dfsg-3 && mkdir -p /build/bolt-lmm-rgm07f && dpkg-source --no-check -x /*.dsc /build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg && chown -R builduser:builduser /build/bolt-lmm-rgm07f" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1608648518" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/bolt-lmm-rgm07f /tmp/bolt-lmm-2.3.4+dfsg-3_eyqplqh bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201220T203231Z 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.HbQXxQPetZ 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.HbQXxQPetZ Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-3). 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/20201220T203231Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201220T203231Z 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 (869 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 ... 4621 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 (2.31-6) ... 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/20211009T024746Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201220T203231Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.HbQXxQPetZ Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201220T203231Z 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/20211009T024746Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages [11.9 MB] Fetched 34.6 MB in 29s (1180 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.HbQXxQPetZ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bolt-lmm=2.3.4+dfsg-3 && mkdir -p /build/bolt-lmm-rgm07f && dpkg-source --no-check -x /*.dsc /build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg && chown -R builduser:builduser /build/bolt-lmm-rgm07f"' exec /tmp/mmdebstrap.HbQXxQPetZ Reading package lists... NOTICE: 'bolt-lmm' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bolt-lmm.git Please use: git clone https://salsa.debian.org/med-team/bolt-lmm.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2815 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bolt-lmm 2.3.4+dfsg-3 (dsc) [2254 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bolt-lmm 2.3.4+dfsg-3 (tar) [2805 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bolt-lmm 2.3.4+dfsg-3 (diff) [8304 B] Fetched 2815 kB in 2s (1267 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bolt-lmm_2.3.4+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bolt-lmm in /build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg dpkg-source: info: unpacking bolt-lmm_2.3.4+dfsg.orig.tar.xz dpkg-source: info: unpacking bolt-lmm_2.3.4+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix_makefile.patch dpkg-source: info: applying timer-for-other-arches.patch dpkg-source: info: applying dont-hardcode-glibc-version.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1608648518" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.HbQXxQPetZ dpkg-buildpackage: info: source package bolt-lmm dpkg-buildpackage: info: source version 2.3.4+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j4 clean make[1]: Entering directory '/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg/src' rm -f *.o rm -f bolt make[1]: Leaving directory '/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg/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/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg/src' g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltMain.o -c BoltMain.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Bolt.o -c Bolt.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParams.o -c BoltParams.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParEstCV.o -c BoltParEstCV.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltReml.o -c BoltReml.cpp Bolt.cpp: In member function ‘void LMM::Bolt::streamBgen(const string&, int, const string&, const string&, double, double, const string&, bool, const std::vector&, bool) const’: Bolt.cpp:2866:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2866 | uint offset; fread(&offset, 4, 1, fin); // cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2867:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2867 | uint H; fread(&H, 4, 1, fin); // cout << "H: " << H << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:2868:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2868 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "BGEN snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2869:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2869 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "BGEN samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2884:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2884 | uint Nrow; fread(&Nrow, 4, 1, fin); // cout << "Nrow: " << Nrow << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2889:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2889 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2890:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2890 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; // cout << "snpID: " << string(snpID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2891:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2891 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2892:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2892 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2893:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2893 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2894:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2894 | fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2901:26: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2901 | uint physpos; fread(&physpos, 4, 1, fin); // cout << "physpos: " << physpos << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2903:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2903 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2909:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2909 | fread(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2910:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2910 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2916:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2916 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2917:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2917 | uint zLen; fread(&zLen, 4, 1, fin); // cout << "zLen: " << zLen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2918:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2918 | fread(zBuf, 1, zLen, fin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp: In member function ‘void LMM::Bolt::streamBgen2(const string&, int, const string&, const string&, double, double, const string&, bool, const std::vector&, bool, int) const’: Bolt.cpp:3188:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3188 | uint offset; fread(&offset, 4, 1, fin); //cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3189:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3189 | uint L_H; fread(&L_H, 4, 1, fin); //cout << "L_H: " << L_H << endl; | ~~~~~^~~~~~~~~~~~~~~~~ Bolt.cpp:3190:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3190 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3192:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3192 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3197:25: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3197 | char magic[5]; fread(magic, 1, 4, fin); magic[4] = '\0'; //cout << "magic bytes: " << string(magic) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:3199:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3199 | uint flags; fread(&flags, 4, 1, fin); //cout << "flags: " << flags << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3231:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3231 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3232:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3232 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; // cout << "snpID: " << string(snpID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3233:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3233 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3234:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3234 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:3237:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3237 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3238:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3238 | fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3247:26: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3247 | uint physpos; fread(&physpos, 4, 1, fin); // cout << "physpos: " << physpos << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3253:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3253 | ushort K; fread(&K, 2, 1, fin); //cout << "K: " << K << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3259:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3259 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3265:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3265 | fread(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3267:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3267 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3273:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3273 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3276:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3276 | uint C; fread(&C, 4, 1, fin); //cout << "C: " << C << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3278:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3278 | uint D; fread(&D, 4, 1, fin); //cout << "D: " << D << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3280:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3280 | fread(&zBufs[B][0], 1, C-4, fin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o CovariateBasis.o -c CovariateBasis.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o DataMatrix.o -c DataMatrix.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o FileUtils.o -c FileUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Jackknife.o -c Jackknife.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o LDscoreCalibration.o -c LDscoreCalibration.cpp FileUtils.cpp: In function ‘int FileUtils::checkBgenSample(const string&, const string&, int)’: FileUtils.cpp:275:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 275 | uint offset; fread(&offset, 4, 1, fin); //cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:276:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 276 | uint L_H; fread(&L_H, 4, 1, fin); //cout << "L_H: " << L_H << endl; | ~~~~~^~~~~~~~~~~~~~~~~ FileUtils.cpp:277:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 277 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:279:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 279 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:284:25: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 284 | char magic[5]; fread(magic, 1, 4, fin); magic[4] = '\0'; //cout << "magic bytes: " << string(magic) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:286:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 286 | uint flags; fread(&flags, 4, 1, fin); //cout << "flags: " << flags << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:297:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 297 | uint Nrow; fread(&Nrow, 4, 1, fin); // cout << "Nrow: " << Nrow << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:304:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 304 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << endl; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:305:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 305 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; cout << "first snpID: " << string(snpID) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:307:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 307 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << endl; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:308:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 308 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; cout << "first rsID: " << string(rsID) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:313:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:314:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 314 | fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:323:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 323 | uint bp; fread(&bp, 4, 1, fin); // cout << "bp: " << bp << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:325:28: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 325 | ushort Kheader; fread(&Kheader, 2, 1, fin); //cout << "K: " << K << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:331:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 331 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:332:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 332 | fread(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:334:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 334 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:335:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 335 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:337:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 337 | uint C; fread(&C, 4, 1, fin); //cout << "C: " << C << endl; | ~~~~~^~~~~~~~~~~~~~~ FileUtils.cpp:339:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 339 | uint D; fread(&D, 4, 1, fin); //cout << "D: " << D << endl; | ~~~~~^~~~~~~~~~~~~~~ FileUtils.cpp:341:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 341 | fread(zBuf, 1, C-4, fin); | ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MapInterpolater.o -c MapInterpolater.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MatrixUtils.o -c MatrixUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MemoryUtils.o -c MemoryUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o PhenoBuilder.o -c PhenoBuilder.cpp NonlinearOptMulti.cpp: In function ‘std::vector > NonlinearOptMulti::constrainedNR(double&, boost::numeric::ublas::vector&, const std::vector >&, const boost::numeric::ublas::vector&, const boost::numeric::ublas::matrix&, double)’: NonlinearOptMulti.cpp:230:21: warning: catching polymorphic type ‘class nlopt::roundoff_limited’ by value [-Wcatch-value=] 230 | catch (nlopt::roundoff_limited) { | ^~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o RestrictSnpSet.o -c RestrictSnpSet.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpData.o -c SnpData.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpInfo.o -c SnpInfo.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SpectrumTools.o -c SpectrumTools.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StatsUtils.o -c StatsUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Timer.o -c Timer.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o memcpy.o -c memcpy.cpp g++ -fopenmp -Wl,-z,relro -Wl,-z,now -o bolt BoltMain.o Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o memcpy.o -lboost_program_options -lboost_iostreams -lz -lnlopt -lopenblas -llapack -lgfortran -lpthread -lm make[1]: Leaving directory '/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg/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/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/bolt-lmm-rgm07f/bolt-lmm-2.3.4+dfsg' 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 'bolt-lmm-dbgsym' in '../bolt-lmm-dbgsym_2.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'bolt-lmm' in '../bolt-lmm_2.3.4+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bolt-lmm_2.3.4+dfsg-3_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/bolt-lmm-rgm07f /tmp/bolt-lmm-2.3.4+dfsg-3_eyqplqh I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.HbQXxQPetZ... I: success in 800.5429 seconds md5: bolt-lmm-dbgsym_2.3.4+dfsg-3_amd64.deb: OK md5: bolt-lmm_2.3.4+dfsg-3_amd64.deb: OK sha1: bolt-lmm-dbgsym_2.3.4+dfsg-3_amd64.deb: OK sha1: bolt-lmm_2.3.4+dfsg-3_amd64.deb: OK sha256: bolt-lmm-dbgsym_2.3.4+dfsg-3_amd64.deb: OK sha256: bolt-lmm_2.3.4+dfsg-3_amd64.deb: OK Checksums: OK