Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bolt-lmm/bolt-lmm_2.3.6+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bolt-lmm-2.3.6+dfsg-139464p7z/bolt-lmm_2.3.6+dfsg-1_amd64.buildinfo Get source package info: bolt-lmm=2.3.6+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/bolt-lmm/2.3.6+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binutils=2.37-9 binutils-common=2.37-9 binutils-x86-64-linux-gnu=2.37-9 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-2 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 gfortran=4:11.2.0-2 gfortran-11=11.2.0-12 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 icu-devtools=67.1-7 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libbinutils=2.37-9 libblkid1=2.37.2-4 libboost-dev=1.74.0.3 libboost-iostreams-dev=1.74.0.3 libboost-iostreams1.74-dev=1.74.0-12 libboost-iostreams1.74.0=1.74.0-12 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-12 libboost-program-options1.74.0=1.74.0-12 libboost-regex1.74-dev=1.74.0-12 libboost-regex1.74.0=1.74.0-12 libboost1.74-dev=1.74.0-12 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-9 libctf0=2.37-9 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdpkg-perl=1.20.9 libelf1=0.186-1 libfile-stripnondeterminism-perl=1.12.0-2 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran-11-dev=11.2.0-12 libgfortran5=11.2.0-12 libgmp10=2:6.2.1+dfsg-3 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libicu-dev=67.1-7 libicu67=67.1-7 libisl23=0.24-2 libitm1=11.2.0-12 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libnlopt-cxx-dev=2.7.0-5 libnlopt-cxx0=2.7.0-5 libnlopt-dev=2.7.0-5 libnlopt0=2.7.0-5 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenblas-dev=0.3.18+ds-2 libopenblas-pthread-dev=0.3.18+ds-2 libopenblas0=0.3.18+ds-2 libopenblas0-pthread=0.3.18+ds-2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libquadmath0=11.2.0-12 libseccomp2=2.5.2-2 libselinux1=3.3-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.6-2 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.6-2 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.16-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.3-1 ncurses-bin=6.3-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 util-linux=2.37.2-4 xz-utils=5.2.5-2 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/20211122T030439Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211122T030439Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211216T085418Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211118T084946Z/ 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=2.3.6+dfsg-1 && mkdir -p /build/bolt-lmm-wSMza4 && dpkg-source --no-check -x /*.dsc /build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg && chown -R builduser:builduser /build/bolt-lmm-wSMza4" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637336679" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/bolt-lmm-wSMza4 /tmp/bolt-lmm-2.3.6+dfsg-139464p7z bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211118T084946Z 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.UhYuq5WwRW 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.UhYuq5WwRW Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). 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/20211118T084946Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1024 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 ... 4669 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211122T030439Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211122T030439Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211216T085418Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211118T084946Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.UhYuq5WwRW Get:1 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages [12.0 MB] Fetched 35.3 MB in 45s (788 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.UhYuq5WwRW I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bolt-lmm=2.3.6+dfsg-1 && mkdir -p /build/bolt-lmm-wSMza4 && dpkg-source --no-check -x /*.dsc /build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg && chown -R builduser:builduser /build/bolt-lmm-wSMza4"' exec /tmp/mmdebstrap.UhYuq5WwRW 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/20211122T030439Z bookworm/main bolt-lmm 2.3.6+dfsg-1 (dsc) [2229 B] Get:2 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main bolt-lmm 2.3.6+dfsg-1 (tar) [2804 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211122T030439Z bookworm/main bolt-lmm 2.3.6+dfsg-1 (diff) [8492 B] Fetched 2815 kB in 2s (1289 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bolt-lmm_2.3.6+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bolt-lmm in /build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg dpkg-source: info: unpacking bolt-lmm_2.3.6+dfsg.orig.tar.xz dpkg-source: info: unpacking bolt-lmm_2.3.6+dfsg-1.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-wSMza4/bolt-lmm-2.3.6+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637336679" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.UhYuq5WwRW dpkg-buildpackage: info: source package bolt-lmm dpkg-buildpackage: info: source version 2.3.6+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi 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 -j10 clean make[1]: Entering directory '/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg/src' rm -f *.o rm -f bolt make[1]: Leaving directory '/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+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 -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg/src' g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltMain.o -c BoltMain.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Bolt.o -c Bolt.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParams.o -c BoltParams.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParEstCV.o -c BoltParEstCV.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltReml.o -c BoltReml.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o CovariateBasis.o -c CovariateBasis.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o DataMatrix.o -c DataMatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o FileUtils.o -c FileUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Jackknife.o -c Jackknife.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o LDscoreCalibration.o -c LDscoreCalibration.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MapInterpolater.o -c MapInterpolater.cpp FileUtils.cpp: In function ‘int FileUtils::checkBgenSample(const string&, const string&, int)’: FileUtils.cpp:265:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 265 | uint offset; fread(&offset, 4, 1, fin); //cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:266:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 266 | uint L_H; fread(&L_H, 4, 1, fin); //cout << "L_H: " << L_H << endl; | ~~~~~^~~~~~~~~~~~~~~~~ FileUtils.cpp:267:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 267 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:269:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 269 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:274:25: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 274 | char magic[5]; fread(magic, 1, 4, fin); magic[4] = '\0'; //cout << "magic bytes: " << string(magic) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:276:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 276 | uint flags; fread(&flags, 4, 1, fin); //cout << "flags: " << flags << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:287:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 287 | uint Nrow; fread(&Nrow, 4, 1, fin); // cout << "Nrow: " << Nrow << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:294:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 294 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << endl; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:295:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 295 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; cout << "first snpID: " << string(snpID) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:297:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 297 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << endl; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:298:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 298 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; cout << "first rsID: " << string(rsID) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:303:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 303 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:304:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 304 | fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:313:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | uint bp; fread(&bp, 4, 1, fin); // cout << "bp: " << bp << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:315:28: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 315 | ushort Kheader; fread(&Kheader, 2, 1, fin); //cout << "K: " << K << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:321:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 321 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:322:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 322 | fread(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:324:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 324 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:325:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 325 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:327:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 327 | uint C; fread(&C, 4, 1, fin); //cout << "C: " << C << endl; | ~~~~~^~~~~~~~~~~~~~~ FileUtils.cpp:329:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 329 | uint D; fread(&D, 4, 1, fin); //cout << "D: " << D << endl; | ~~~~~^~~~~~~~~~~~~~~ FileUtils.cpp:331:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 331 | fread(zBuf, 1, C-4, fin); | ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MatrixUtils.o -c MatrixUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MemoryUtils.o -c MemoryUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o PhenoBuilder.o -c PhenoBuilder.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o RestrictSnpSet.o -c RestrictSnpSet.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpData.o -c SnpData.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) { | ^~~~~~~~~~~~~~~~ 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:2881:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2881 | uint offset; fread(&offset, 4, 1, fin); // cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2882:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2882 | uint H; fread(&H, 4, 1, fin); // cout << "H: " << H << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:2883:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2883 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "BGEN snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2884:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2884 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "BGEN samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2899:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2899 | uint Nrow; fread(&Nrow, 4, 1, fin); // cout << "Nrow: " << Nrow << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2904:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2904 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2905:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2905 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; // cout << "snpID: " << string(snpID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2906:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2906 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2907:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2907 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2908:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2908 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << 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(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2916:26: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2916 | uint physpos; fread(&physpos, 4, 1, fin); // cout << "physpos: " << physpos << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2918:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2918 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2924:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2924 | fread(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2925:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2925 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2931:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2931 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2932:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2932 | uint zLen; fread(&zLen, 4, 1, fin); // cout << "zLen: " << zLen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2933:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2933 | 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:3203:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3203 | uint offset; fread(&offset, 4, 1, fin); //cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3204:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3204 | uint L_H; fread(&L_H, 4, 1, fin); //cout << "L_H: " << L_H << endl; | ~~~~~^~~~~~~~~~~~~~~~~ Bolt.cpp:3205:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3205 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3207:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3207 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3212:25: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3212 | char magic[5]; fread(magic, 1, 4, fin); magic[4] = '\0'; //cout << "magic bytes: " << string(magic) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:3214:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3214 | uint flags; fread(&flags, 4, 1, fin); //cout << "flags: " << flags << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3246:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3246 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3247:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3247 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; // cout << "snpID: " << string(snpID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3248:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3248 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3249:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3249 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:3252:23: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3252 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3253:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3253 | fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3262:26: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3262 | uint physpos; fread(&physpos, 4, 1, fin); // cout << "physpos: " << physpos << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3268:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3268 | ushort K; fread(&K, 2, 1, fin); //cout << "K: " << K << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3274:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3274 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ 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(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3282:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3282 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3288:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3288 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3291:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3291 | uint C; fread(&C, 4, 1, fin); //cout << "C: " << C << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3293:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3293 | uint D; fread(&D, 4, 1, fin); //cout << "D: " << D << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3295:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3295 | fread(&zBufs[B][0], 1, C-4, fin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpInfo.o -c SnpInfo.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SpectrumTools.o -c SpectrumTools.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StatsUtils.o -c StatsUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Timer.o -c Timer.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o memcpy.o -c memcpy.cpp In file included from Bolt.cpp:55: In member function ‘LMM::Bolt::VarCompData& LMM::Bolt::VarCompData::operator=(const LMM::Bolt::VarCompData&)’, inlined from ‘double LMM::Bolt::estLogDelta(double*, double*, const std::vector&, int, double, int, double, int, bool) const’ at Bolt.cpp:2218:16: Bolt.hpp:54:12: warning: ‘nextVCs.LMM::Bolt::VarCompData::sigma2K’ may be used uninitialized [-Wmaybe-uninitialized] 54 | struct VarCompData { | ^~~~~~~~~~~ Bolt.cpp: In member function ‘double LMM::Bolt::estLogDelta(double*, double*, const std::vector&, int, double, int, double, int, bool) const’: Bolt.cpp:2187:19: note: ‘nextVCs’ declared here 2187 | VarCompData nextVCs; | ^~~~~~~ Bolt.cpp: In member function ‘std::string LMM::Bolt::getSnpStats(const string&, int, int, double, const string&, const string&, double, double, double*, bool, const std::vector&, double) const’: Bolt.cpp:2357:56: warning: ‘dotProd’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2357 | double beta = (stat==BAD_SNP_STAT) ? 0 : invNorm2*dotProd / retroData[0].VinvScaleFactors[0]; | ~~~~~~~~^~~~~~~~ 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-wSMza4/bolt-lmm-2.3.6+dfsg/src' dh: command-omitted: The call to "dh_auto_test -a -O--sourcedirectory=src" was omitted due to "DEB_BUILD_OPTIONS=nocheck" 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-wSMza4/bolt-lmm-2.3.6+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/bolt-lmm-wSMza4/bolt-lmm-2.3.6+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 -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -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' in '../bolt-lmm_2.3.6+dfsg-1_amd64.deb'. dpkg-deb: building package 'bolt-lmm-dbgsym' in '../bolt-lmm-dbgsym_2.3.6+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bolt-lmm_2.3.6+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/bolt-lmm-wSMza4 /tmp/bolt-lmm-2.3.6+dfsg-139464p7z I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.UhYuq5WwRW... I: success in 3176.9451 seconds md5: bolt-lmm-dbgsym_2.3.6+dfsg-1_amd64.deb: OK md5: bolt-lmm_2.3.6+dfsg-1_amd64.deb: OK sha1: bolt-lmm-dbgsym_2.3.6+dfsg-1_amd64.deb: OK sha1: bolt-lmm_2.3.6+dfsg-1_amd64.deb: OK sha256: bolt-lmm-dbgsym_2.3.6+dfsg-1_amd64.deb: OK sha256: bolt-lmm_2.3.6+dfsg-1_amd64.deb: OK Checksums: OK