Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gemma/gemma_0.98.4+dfsg-4_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gemma-0.98.4+dfsg-4kisfrjip/gemma_0.98.4+dfsg-4_all.buildinfo Get source package info: gemma=0.98.4+dfsg-4 Source URL: http://snapshot.notset.fr/mr/package/gemma/0.98.4+dfsg-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11.1 base-passwd=3.5.51 bash=5.1-3+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-8 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 catch=1.12.1-1.1 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 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++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 gfortran=4:10.2.1-1 gfortran-10=10.2.1-6 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblkid1=2.36.1-7 libbz2-1.0=1.0.8-4 libc-bin=2.31-13 libc-dev-bin=2.31-13 libc6=2.31-13 libc6-dev=2.31-13 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.2-2 libcrypt-dev=1:4.4.18-4 libcrypt1=1:4.4.18-4 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.3.4 libdpkg-perl=1.20.9 libeigen3-dev=3.3.9-2 libelf1=0.183-3 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-6 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran-10-dev=10.2.1-6 libgfortran5=10.2.1-6 libglib2.0-0=2.66.8-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgsl-dev=2.6+dfsg-2 libgsl25=2.6+dfsg-2 libgslcblas0=2.6+dfsg-2 libgssapi-krb5-2=1.18.3-6 libicu67=67.1-7 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-6 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-6 libkrb5support0=1.18.3-6 liblsan0=10.2.1-6 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenblas-dev=0.3.13+ds-3 libopenblas-pthread-dev=0.3.13+ds-3 libopenblas0=0.3.13+ds-3 libopenblas0-pthread=0.3.13+ds-3 libpam-modules=1.4.0-9 libpam-modules-bin=1.4.0-9 libpam-runtime=1.4.0-9 libpam0g=1.4.0-9 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-4 libpipeline1=1.5.3-1 libquadmath0=10.2.1-6 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.36.1-7 libssl1.1=1.1.1k-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-6 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-6 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libxml2=2.9.10+dfsg-6.7 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.46-3 login=1:4.8.1-1 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=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.1-4 perl-base=5.32.1-4 perl-modules-5.32=5.32.1-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 sed=4.7-1 sensible-utils=0.0.14 shunit2=2.1.6-1.2 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 util-linux=2.36.1-7 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210820T090154Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210728T203306Z/ 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 gemma=0.98.4+dfsg-4 && mkdir -p /build/gemma-1fBlut && dpkg-source --no-check -x /*.dsc /build/gemma-1fBlut/gemma-0.98.4+dfsg && chown -R builduser:builduser /build/gemma-1fBlut" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gemma-1fBlut/gemma-0.98.4+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1627674837" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/gemma-1fBlut /tmp/gemma-0.98.4+dfsg-4kisfrjip bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210728T203306Z 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.JZNGGIwEyD 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.JZNGGIwEyD Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). 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/20210728T203306Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210728T203306Z 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 (928 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 ... 4668 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 (2.31-13) ... 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/20210820T090154Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210728T203306Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.JZNGGIwEyD Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210820T090154Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210728T203306Z 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/20210820T090154Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210820T090154Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210820T090154Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210820T090154Z unstable/main amd64 Packages [11.8 MB] Fetched 34.6 MB in 30s (1170 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.JZNGGIwEyD I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gemma=0.98.4+dfsg-4 && mkdir -p /build/gemma-1fBlut && dpkg-source --no-check -x /*.dsc /build/gemma-1fBlut/gemma-0.98.4+dfsg && chown -R builduser:builduser /build/gemma-1fBlut"' exec /tmp/mmdebstrap.JZNGGIwEyD Reading package lists... NOTICE: 'gemma' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gemma.git Please use: git clone https://salsa.debian.org/med-team/gemma.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 42.5 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gemma 0.98.4+dfsg-4 (dsc) [2113 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gemma 0.98.4+dfsg-4 (tar) [42.5 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gemma 0.98.4+dfsg-4 (diff) [6412 B] Fetched 42.5 MB in 36s (1191 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gemma_0.98.4+dfsg-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gemma in /build/gemma-1fBlut/gemma-0.98.4+dfsg dpkg-source: info: unpacking gemma_0.98.4+dfsg.orig.tar.xz dpkg-source: info: unpacking gemma_0.98.4+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying exclude_assertions_failing_under_some_circumstances.patch dpkg-source: info: applying Reproducible_builds.patch dpkg-source: info: applying no-lquadmath.patch dpkg-source: info: applying Makefile.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gemma-1fBlut/gemma-0.98.4+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1627674837" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.JZNGGIwEyD dpkg-buildpackage: info: source package gemma dpkg-buildpackage: info: source version 0.98.4+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean dh_auto_clean install -d /build/gemma-1fBlut/gemma-0.98.4\+dfsg/debian/.debhelper/generated/_source/home make -j4 clean make[1]: Entering directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' rm -vf ./src/*.o rm -vf ./src/*~ rm -vf ./test/src/*.o rm -vf ./bin/gemma rm -vf ./bin/unittests-gemma make[1]: Leaving directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' debian/rules override_dh_clean make[1]: Entering directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/gemma.substvars debian/gemma-doc.substvars debian/files rm -fr -- debian/gemma/ debian/tmp/ debian/gemma-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *.log rm -rf test/output/ rm -f bin/gemma make[1]: Leaving directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i dh_auto_configure -i install -d /build/gemma-1fBlut/gemma-0.98.4\+dfsg/debian/.debhelper/generated/_source/home dh_auto_build -i make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmm.o src/bslmm.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmmdap.o src/bslmmdap.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/debug.o src/debug.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/fastblas.o src/fastblas.cpp src/debug.cpp:61:44: warning: extra ‘;’ [-Wpedantic] 61 | bool is_debug_mode() { return debug_mode; }; | ^ src/debug.cpp:62:54: warning: extra ‘;’ [-Wpedantic] 62 | bool is_debug_data_mode() { return debug_data_mode; }; | ^ src/debug.cpp:63:49: warning: extra ‘;’ [-Wpedantic] 63 | bool is_no_check_mode() { return !debug_check; }; | ^ src/debug.cpp:64:45: warning: extra ‘;’ [-Wpedantic] 64 | bool is_check_mode() { return debug_check; }; | ^ src/debug.cpp:65:53: warning: extra ‘;’ [-Wpedantic] 65 | bool is_fpe_check_mode() { return debug_fpe_check; }; | ^ src/debug.cpp:66:47: warning: extra ‘;’ [-Wpedantic] 66 | bool is_strict_mode() { return debug_strict; }; | ^ src/debug.cpp:67:45: warning: extra ‘;’ [-Wpedantic] 67 | bool is_quiet_mode() { return debug_quiet; }; | ^ src/debug.cpp:68:59: warning: extra ‘;’ [-Wpedantic] 68 | bool is_issue(uint issue) { return issue == debug_issue; }; | ^ src/debug.cpp:69:47: warning: extra ‘;’ [-Wpedantic] 69 | bool is_legacy_mode() { return debug_legacy; }; | ^ g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma.o src/gemma.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma_io.o src/gemma_io.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gzstream.o src/gzstream.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lapack.o src/lapack.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/ldr.o src/ldr.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lm.o src/lm.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lmm.o src/lmm.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/logistic.o src/logistic.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/main.o src/main.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/mathfunc.o src/mathfunc.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/mvlmm.o src/mvlmm.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/param.o src/param.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/prdt.o src/prdt.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/varcov.o src/varcov.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/vc.o src/vc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc src/bslmm.o src/bslmmdap.o src/debug.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/main.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -o ./bin/gemma make[1]: Leaving directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' dh_auto_test --no-parallel make -j1 check make[2]: Entering directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-main.o test/src/unittests-main.cpp g++ -g -O2 -ffile-prefix-map=/build/gemma-1fBlut/gemma-0.98.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-math.o test/src/unittests-math.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc ./test/src/unittests-main.o ./test/src/unittests-math.o src/bslmm.o src/bslmmdap.o src/debug.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -o ./bin/unittests-gemma ./bin/unittests-gemma Mismatch coordinates (1,0)0:3! This example computes real matrix C=alpha*A*B+beta*C using Intel(R) MKL function dgemm, where A, B, and C are matrices and alpha and beta are double precision scalars Initializing data for matrix multiplication C=A*B for matrix A(2000x200) and matrix B(200x1000) Allocating memory for matrices aligned on 64-byte boundary for better performance Intializing matrix data Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface This example computes real matrix C=alpha*A*B+beta*C using Intel(R) MKL function dgemm, where A, B, and C are matrices and alpha and beta are double precision scalars Initializing data for matrix multiplication C=A*B for matrix A(2000x200) and matrix B(200x1000) Allocating memory for matrices aligned on 64-byte boundary for better performance Intializing matrix data Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface Computations completed. =============================================================================== All tests passed (23 assertions in 4 test cases) rm -vf test/output/* cd test && ./dev_test_suite.sh | tee ../dev_test.log run system shunit2 testLinearModel GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. ## total computation time = 0.100404 min testBXDStandardRelatednessMatrixKSingularError GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. GSL ERROR: matrix is singular in lu.c at line 449 errno 1 testBXDStandardRelatednessMatrixK GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 Calculating Relatedness Matrix ... 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. testBXDLMLikelihoodRatio GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. testBXDLMMLikelihoodRatio GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 Start Eigen-Decomposition... pve estimate =0.00100086 se(pve) =0.204165 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. testBXDLMM9LikelihoodRatio GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 Start Eigen-Decomposition... pve estimate =0.00100086 se(pve) =0.204165 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixissue188 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... ## number of total individuals = 1008 ## number of analyzed individuals = 876 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 2000 ## number of analyzed SNPs = 1850 Calculating Relatedness Matrix ... 0% ========================= 50% ================================================== 100% **** WARNING: K has 75 eigenvalues close to zero in src/gemma.cpp at line 1912 **** WARNING: K is ill conditioned! in src/gemma.cpp at line 1912 **** INFO: Done. testLMMissue188 GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... ## number of total individuals = 1008 ## number of analyzed individuals = 876 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 2000 ## number of analyzed SNPs = 1850 **** WARNING: K has 3 eigenvalues close to zero in src/gemma.cpp at line 2590 **** WARNING: K is ill conditioned! in src/gemma.cpp at line 2590 Start Eigen-Decomposition... **** WARNING: Matrix G has 3 eigenvalues close to zero pve estimate =0.631857 se(pve) =0.0548406 0% ========================= 50% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKLOCO1 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** TEST MODE: trim individuals from 1940 to 400 **** TEST MODE: trim individuals from 1940 to 400 ## number of total individuals = 400 ## number of analyzed individuals = 247 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of considered SNPS = 1000 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 889 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. ## total computation time = 1.19538 min testUnivariateLinearMixedModelLOCO1 GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** TEST MODE: trim individuals from 1940 to 400 **** TEST MODE: trim individuals from 1940 to 400 ## number of total individuals = 400 ## number of analyzed individuals = 247 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of considered SNPS = 1000 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 889 Start Eigen-Decomposition... pve estimate =0.678775 se(pve) =0.0717914 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 0.521553 min testPlinkCenteredRelatednessMatrixKLOCO1 testPlinkUnivariateLinearMixedModelLOCO1 testCorrelatedPhenotypesMvLLM GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... ## number of total individuals = 1000 ## number of analyzed individuals = 1000 ## number of covariates = 1 ## number of phenotypes = 5 ## number of total SNPs/var = 100 ## number of analyzed SNPs = 100 REMLE estimate for Vg in the null model: 0.8091 0.1435 0.0660 -0.1456 -0.0664 0.1165 0.0907 0.0362 -0.0830 0.0639 -0.5533 -0.0985 0.1171 -0.0765 0.4131 se(Vg): 0.0736 0.0355 0.0299 0.0421 0.0264 0.0422 0.0444 0.0279 0.0430 0.0479 0.0516 0.0254 0.0295 0.0313 0.0389 REMLE estimate for Ve in the null model: 0.0334 0.0267 0.4502 -0.0529 -0.0883 0.6004 0.0683 0.1413 -0.6502 0.8400 -0.0128 -0.0041 -0.0706 0.0880 0.0419 se(Ve): 0.0378 0.0252 0.0329 0.0299 0.0281 0.0456 0.0332 0.0319 0.0494 0.0583 0.0266 0.0186 0.0215 0.0242 0.0208 REMLE likelihood = -3813.3258 MLE estimate for Vg in the null model: 0.8082 0.1434 0.0660 -0.1455 -0.0664 0.1165 0.0906 0.0362 -0.0830 0.0639 -0.5528 -0.0984 0.1170 -0.0764 0.4127 se(Vg): 0.0735 0.0355 0.0298 0.0420 0.0264 0.0421 0.0443 0.0278 0.0430 0.0478 0.0515 0.0254 0.0295 0.0313 0.0388 MLE estimate for Ve in the null model: 0.0334 0.0267 0.4497 -0.0529 -0.0882 0.5997 0.0682 0.1412 -0.6495 0.8391 -0.0128 -0.0040 -0.0705 0.0879 0.0418 se(Ve): 0.0378 0.0252 0.0329 0.0298 0.0281 0.0455 0.0331 0.0318 0.0493 0.0582 0.0265 0.0185 0.0215 0.0242 0.0207 MLE likelihood = -3814.3913 0% ================================================== 100% **** INFO: Done. Ran 13 tests. OK tail -n 1 dev_test.log | grep -q 'OK' rm -vf test/output/* removed 'test/output/BXD.cXX.txt' removed 'test/output/BXD.log.txt' removed 'test/output/BXD_LMM_LR.assoc.txt' removed 'test/output/BXD_LMM_LR.log.txt' removed 'test/output/BXD_LM_LR.assoc.txt' removed 'test/output/BXD_LM_LR.log.txt' removed 'test/output/corrpheno.assoc.txt' removed 'test/output/corrpheno.log.txt' removed 'test/output/issue188.assoc.txt' removed 'test/output/issue188.cXX.txt' removed 'test/output/issue188.log.txt' removed 'test/output/mouse_hs1940_CD8_LOCO1_lmm.assoc.txt' removed 'test/output/mouse_hs1940_CD8_LOCO1_lmm.log.txt' removed 'test/output/mouse_hs1940_CD8_lm.assoc.txt' removed 'test/output/mouse_hs1940_CD8_lm.log.txt' removed 'test/output/mouse_hs1940_LOCO1.cXX.txt' removed 'test/output/mouse_hs1940_LOCO1.log.txt' cd test && ./test_suite.sh | tee ../test.log run system shunit2 testBslmm1 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 1 (option 1); first value = 1791095845 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 Start Eigen-Decomposition... pve estimate =0.590431 se(pve) =0.0480392 Calculating UtX... initial value of h = 0.590431 initial value of rho = 0.41375 initial value of pi = 0.00269142 initial value of |gamma| = 29 0% 0.00 ==== 9% 0.18 ========= 18% 0.18 ============= 27% 0.18 ================== 36% 0.18 ====================== 45% 0.17 =========================== 55% 0.17 =============================== 64% 0.17 ==================================== 73% 0.16 ======================================== 82% 0.16 ============================================= 91% 0.16 ================================================== 100% 0.16 **** INFO: Done. testBslmm2 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm3 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 1 (option 1); first value = 1791095845 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 Start Eigen-Decomposition... pve estimate =0.372151 se(pve) =0.0522377 Calculating UtX... initial value of h = 0.372151 initial value of rho = 0.393216 initial value of pi = 0.00194896 initial value of |gamma| = 21 0% 0.00 ==== 9% 0.22 ========= 18% 0.22 ============= 27% 0.21 ================== 36% 0.21 ====================== 45% 0.21 =========================== 55% 0.21 =============================== 64% 0.21 ==================================== 73% 0.21 ======================================== 82% 0.21 ============================================= 91% 0.21 ================================================== 100% 0.21 **** INFO: Done. testBslmm4 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 Adding Breeding Values ... Start Eigen-Decomposition... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm5 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option 100); first value = 2333906440 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKFullLOCO1 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModelFullLOCO1 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 10768 Start Eigen-Decomposition... pve estimate =0.593114 se(pve) =0.0332587 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 8.01929 min testCenteredRelatednessMatrixK GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModel GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 Start Eigen-Decomposition... pve estimate =0.608801 se(pve) =0.032774 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 8.67009 min testLinearMixedModelPhenotypes GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1197 ## number of covariates = 1 ## number of phenotypes = 2 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10758 Start Eigen-Decomposition... REMLE estimate for Vg in the null model: 1.3940 -0.2267 2.0817 se(Vg): 0.1567 0.1363 0.2359 REMLE estimate for Ve in the null model: 0.3489 0.0491 0.4144 se(Ve): 0.0206 0.0166 0.0267 REMLE likelihood = -2855.1664 MLE estimate for Vg in the null model: 1.3959 -0.2267 2.0854 se(Vg): 0.1568 0.1365 0.2361 MLE estimate for Ve in the null model: 0.3483 0.0490 0.4136 se(Ve): 0.0206 0.0166 0.0266 MLE likelihood = -2856.0280 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testPlinkStandardRelatednessMatrixK GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random 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================================================== 100% **** INFO: Done. testPlinkLinearMixedModelCovariates GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 427 ## number of analyzed individuals = 427 ## number of covariates = 2 ## number of phenotypes = 1 ## number of total SNPs/var = 358499 ## number of analyzed SNPs = 223242 Start Eigen-Decomposition... pve estimate =0.365545 se(pve) =0.47481 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% 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Ran 12 tests. OK tail -n 1 test.log | grep -q 'OK' test.log make[2]: Leaving directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' rm -fr -- /tmp/dh-xdg-rundir-eznX6yCz make[1]: Leaving directory '/build/gemma-1fBlut/gemma-0.98.4+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -i rm -f -- debian/gemma-doc.substvars rm -fr -- debian/.debhelper/generated/gemma-doc/ debian/gemma-doc/ debian/tmp/ dh_auto_install -i install -d /build/gemma-1fBlut/gemma-0.98.4\+dfsg/debian/tmp dh_install -i install -d debian/.debhelper/generated/gemma install -d debian/.debhelper/generated/gemma-doc dh_installdocs -i install -d debian/gemma-doc/usr/share/doc/gemma-doc install -d debian/gemma-doc/usr/share/doc/gemma cd './example/..' && find 'example' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/gemma-1fBlut/gemma-0.98.4+dfsg/debian/gemma-doc/usr/share/doc/gemma chmod -R u\+rw,go=rX debian/gemma-doc/usr/share/doc install -p -m0644 debian/copyright debian/gemma-doc/usr/share/doc/gemma-doc/copyright dh_installchangelogs -i install -p -m0644 debian/changelog debian/gemma-doc/usr/share/doc/gemma-doc/changelog.Debian dh_perl -i dh_link -i dh_strip_nondeterminism -i Using 1627674837 as canonical time Normalizing debian/gemma-doc/usr/share/doc/gemma/example/BXD_geno.txt.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/gemma-doc/usr/share/doc/gemma/example/mouse_hs1940.geno.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress -i cd debian/gemma-doc chmod a-x usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt gzip -9nf usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt cd '/build/gemma-1fBlut/gemma-0.98.4+dfsg' dh_fixperms -i find debian/gemma-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/gemma-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/gemma-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -i dh_installdeb -i install -d debian/gemma-doc/DEBIAN dh_gencontrol -i echo misc:Depends= >> debian/gemma-doc.substvars echo misc:Pre-Depends= >> debian/gemma-doc.substvars dpkg-gencontrol -pgemma-doc -ldebian/changelog -Tdebian/gemma-doc.substvars -Pdebian/gemma-doc chmod 0644 -- debian/gemma-doc/DEBIAN/control dh_md5sums -i cd debian/gemma-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/gemma-doc/DEBIAN/md5sums dh_builddeb -i dpkg-deb --root-owner-group --build debian/gemma-doc .. dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.4+dfsg-4_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../gemma_0.98.4+dfsg-4_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/gemma-1fBlut /tmp/gemma-0.98.4+dfsg-4kisfrjip I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.JZNGGIwEyD... I: success in 28118.8798 seconds md5: gemma-doc_0.98.4+dfsg-4_all.deb: OK sha1: gemma-doc_0.98.4+dfsg-4_all.deb: OK sha256: gemma-doc_0.98.4+dfsg-4_all.deb: OK Checksums: OK