Wed Sep 17 20:05:56 UTC 2025 I: starting to build bolt-lmm/forky/amd64 on jenkins on '2025-09-17 20:05' Wed Sep 17 20:05:56 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/67884/console.log Wed Sep 17 20:05:56 UTC 2025 I: Downloading source for forky/bolt-lmm=2.4.1+dfsg-2 --2025-09-17 20:05:56-- http://deb.debian.org/debian/pool/main/b/bolt-lmm/bolt-lmm_2.4.1%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2267 (2.2K) [text/prs.lines.tag] Saving to: ‘bolt-lmm_2.4.1+dfsg-2.dsc’ 0K .. 100% 264M=0s 2025-09-17 20:05:56 (264 MB/s) - ‘bolt-lmm_2.4.1+dfsg-2.dsc’ saved [2267/2267] Wed Sep 17 20:05:56 UTC 2025 I: bolt-lmm_2.4.1+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bolt-lmm Binary: bolt-lmm, bolt-lmm-example Architecture: amd64 i386 ppc64el all Version: 2.4.1+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bolt-lmm Vcs-Git: https://salsa.debian.org/med-team/bolt-lmm.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gfortran, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libnlopt-dev, libnlopt-cxx-dev, libopenblas-dev, libzstd-dev, zlib1g-dev Package-List: bolt-lmm deb science optional arch=amd64,i386,ppc64el bolt-lmm-example deb science optional arch=all Checksums-Sha1: ca0c0601778384d95ae4c2d4a8729cc19a6738ed 2804564 bolt-lmm_2.4.1+dfsg.orig.tar.xz a2c345a414c055a24c2e769e824bcd06a931e9d9 8720 bolt-lmm_2.4.1+dfsg-2.debian.tar.xz Checksums-Sha256: 6bcd3f8a9585aaf3394636c416602a8cd684bd89cd3425e9a00131b330b74334 2804564 bolt-lmm_2.4.1+dfsg.orig.tar.xz 28f2aad7515e319fd2845a778526c0944168865970906d7106a71960b9b6d4fa 8720 bolt-lmm_2.4.1+dfsg-2.debian.tar.xz Files: 0916441b70d6f761d1129c27d193e309 2804564 bolt-lmm_2.4.1+dfsg.orig.tar.xz 6b58df1f617cc0a2c72bd3e75f84b6e7 8720 bolt-lmm_2.4.1+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW1hyURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE1oQ//YMslVcYoxb5r5BKHndEhPYm5bKrKFqqG t1f4rn+lj4arq3nYvr9FZGpC0gNtKPy8C351IeVZxNH0xZijdEBOqHHH1oq+nOxa Ri/FJJ6FgZrfcFv2cTKWqlmNwFYj2wHi6uhpQBRsEEaqvCKaESKmlkApY4CTpKBL NQ4H/IfStaKHnCJ4tKhQQfpi8mv2vOtzPXdmdup/pyk5nXoSZ1J2PO3rlFGI5MTP MD12X7x7hHJnkyvEjsaqSm7Pqjupk8Sx+LEqjacKW8oAzbOmq6XFqXrq0T32FsMm 9WrQVo9L774Vl4yl997QGBx8XEeH55DfcGw1bucF/tJ7IiNxZlckpa/gDSfqDxzg j21O2tsSQxt4L80XiC9BOxmVbw280HtZLT0Hymr07SWVNHeQ0yFkt08qm/fGlGMa zBXaFZ9x6OIpmCJTGbo/7mI+rn4ycY6YBmaKjGwh0oFPl4ZrQ8fDtWpXloBulr6C yqcGwbc3PuaMjyIs6Ir/0AF9bNQ36pLuGYjaG4hX1iwjVwBVtX7wE1r2OrSv7FaU 55FZnOrQLWMy72xpfbQwWEhpqCGKg/GqgYnXElE7YWmIHV0s43DhrC4vUonX+G/6 Wl4sw5N4SUaxQyx2BUdzNbMiBR+vMmNqjbs6/F38hasziAgnZ8sBG6Q3p4n8Igo4 zpvq11nfpXg= =61qg -----END PGP SIGNATURE----- Wed Sep 17 20:05:56 UTC 2025 I: Checking whether the package is not for us Wed Sep 17 20:05:56 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Wed Sep 17 20:05:56 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Wed Sep 17 20:12:35 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 17 08:05:58 -12 2025 I: pbuilder-time-stamp: 1758139558 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bolt-lmm_2.4.1+dfsg-2.dsc] I: copying [./bolt-lmm_2.4.1+dfsg.orig.tar.xz] I: copying [./bolt-lmm_2.4.1+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./bolt-lmm_2.4.1+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting bolt-lmm in bolt-lmm-2.4.1+dfsg dpkg-source: info: unpacking bolt-lmm_2.4.1+dfsg.orig.tar.xz dpkg-source: info: unpacking bolt-lmm_2.4.1+dfsg-2.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1422091/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='a379421140b14c82bc77889e72edace4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1422091' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jSmBUMqH/pbuilderrc_QUWM --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jSmBUMqH/b1 --logfile b1/build.log bolt-lmm_2.4.1+dfsg-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1422091/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gfortran, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libnlopt-dev, libnlopt-cxx-dev, libopenblas-dev, libzstd-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-dev; however: Package libnlopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-cxx-dev; however: Package libnlopt-cxx-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenblas-dev; however: Package libopenblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gcc-14-base{a} gettext{a} gettext-base{a} gfortran{a} gfortran-15{a} gfortran-15-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgcc-14-dev{a} libgfortran-15-dev{a} libgfortran5{a} libicu-dev{a} libicu76{a} libmagic-mgc{a} libmagic1t64{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libpipeline1{a} libstdc++-14-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 145 MB of archives. After unpacking 806 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-3 [894 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libgfortran-15-dev amd64 15.2.0-3 [918 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-3 [79.7 MB] Get: 34 http://deb.debian.org/debian forky/main amd64 gfortran-15 amd64 15.2.0-3 [17.8 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-1 [1276 B] Get: 36 http://deb.debian.org/debian forky/main amd64 gfortran amd64 4:15.2.0-1 [1436 B] Get: 37 http://deb.debian.org/debian forky/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 icu-devtools amd64 76.1-4 [215 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libgcc-14-dev amd64 14.3.0-8 [2670 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libstdc++-14-dev amd64 14.3.0-8 [2673 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get: 42 http://deb.debian.org/debian forky/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 43 http://deb.debian.org/debian forky/main amd64 libboost-regex1.83.0 amd64 1.83.0-4.2 [330 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libicu-dev amd64 76.1-4 [10.8 MB] Get: 45 http://deb.debian.org/debian forky/main amd64 libboost-regex1.83-dev amd64 1.83.0-4.2 [346 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4.2 [261 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 48 http://deb.debian.org/debian forky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.2 [347 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4.2 [375 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 51 http://deb.debian.org/debian forky/main amd64 libnlopt0 amd64 2.7.1-6+b4 [178 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libnlopt-dev amd64 2.7.1-6+b4 [46.8 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libnlopt-cxx0 amd64 2.7.1-6+b4 [205 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libnlopt-cxx-dev amd64 2.7.1-6+b4 [13.5 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libopenblas0-pthread amd64 0.3.29+ds-3 [6740 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libopenblas0 amd64 0.3.29+ds-3 [42.7 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libopenblas-pthread-dev amd64 0.3.29+ds-3 [5063 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libopenblas-dev amd64 0.3.29+ds-3 [57.0 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 145 MB in 14s (10.1 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bolt-lmm-2.4.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bolt-lmm_2.4.1+dfsg-2_source.changes dpkg-buildpackage: info: source package bolt-lmm dpkg-buildpackage: info: source version 2.4.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j40 clean make[1]: Entering directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg/src' rm -f *.o rm -f bolt make[1]: Leaving directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg' cd /build/reproducible-path/bolt-lmm-2.4.1+dfsg/example/ && \ tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner EUR_subset.bed EUR_subset.bim EUR_subset.dosage.chr17first100 EUR_subset.dosage.chr22last100.gz EUR_subset.dosage.indivs EUR_subset.dosage2.chr17first100.gz EUR_subset.dosage2.chr17first100.map EUR_subset.dosage2.chr17second100 EUR_subset.dosage2.chr17second100.map EUR_subset.dosage2.chr22last100.gz EUR_subset.dosage2.chr22last100.map EUR_subset.dosage2FileList.txt EUR_subset.exclude EUR_subset.exclude2 EUR_subset.fam EUR_subset.impute2.chr17first100.gz EUR_subset.impute2.chr17second100 EUR_subset.impute2.chr22last100.gz EUR_subset.impute2.indivs EUR_subset.impute2FileList.txt EUR_subset.modelSnps EUR_subset.modelSnps2 EUR_subset.pheno.covars EUR_subset.pheno2.covars EUR_subset.remove example.dosage2Snps.stats example.dosageSnps.stats example.impute2Snps.stats example.log example.stats example_reml2.log run_example.sh run_example_reml2.sh make[1]: Leaving directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg' dh_auto_build -O--sourcedirectory=src -Nbolt-lmm-example cd src && make -j40 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg/src' g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o BoltMain.o -c BoltMain.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o Bolt.o -c Bolt.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o BoltParams.o -c BoltParams.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o BoltParEstCV.o -c BoltParEstCV.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o BoltReml.o -c BoltReml.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o CovariateBasis.o -c CovariateBasis.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o DataMatrix.o -c DataMatrix.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o FileUtils.o -c FileUtils.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o Jackknife.o -c Jackknife.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o LDscoreCalibration.o -c LDscoreCalibration.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o MapInterpolater.o -c MapInterpolater.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o MatrixUtils.o -c MatrixUtils.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o MemoryUtils.o -c MemoryUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o PhenoBuilder.o -c PhenoBuilder.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o RestrictSnpSet.o -c RestrictSnpSet.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o SnpData.o -c SnpData.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o SnpInfo.o -c SnpInfo.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o SpectrumTools.o -c SpectrumTools.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o StatsUtils.o -c StatsUtils.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o Timer.o -c Timer.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o memcpy.o -c memcpy.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ FileUtils.cpp: In function 'int FileUtils::checkBgenSample(const std::string&, const std::string&, int)': FileUtils.cpp:338:14: warning: unused variable 'destLen' [-Wunused-variable] 338 | uLongf destLen = D, bufLen = D, zBufLen = C-4; | ^~~~~~~ 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 'std::vector > LMM::Bolt::computeSnpChunkEnds(const std::vector&) const': Bolt.cpp:268:11: warning: ignoring return value of '_FIter std::unique(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator*, vector > >]', declared with attribute 'nodiscard' [-Wunused-result] 268 | unique(snpChunkEnds.begin(), snpChunkEnds.end()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/algorithm:63, from Bolt.cpp:29: /usr/include/c++/15/bits/stl_algo.h:875:5: note: declared here 875 | unique(_ForwardIterator __first, _ForwardIterator __last) | ^~~~~~ In file included from Bolt.cpp:56: 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:2219:16: 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:2188:19: note: 'nextVCs' declared here 2188 | VarCompData nextVCs; | ^~~~~~~ Bolt.cpp: In member function 'std::string LMM::Bolt::getSnpStats(const std::string&, int, int, double, const std::string&, const std::string&, double, double, double*, bool, const std::vector&, double) const': Bolt.cpp:2358:56: warning: 'dotProd' may be used uninitialized [-Wmaybe-uninitialized] 2358 | double beta = (stat==BAD_SNP_STAT) ? 0 : invNorm2*dotProd / retroData[0].VinvScaleFactors[0]; | ~~~~~~~~^~~~~~~~ Bolt.cpp:2315:12: note: 'dotProd' was declared here 2315 | double dotProd, stat; | ^~~~~~~ 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 -L/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -lboost_program_options -lboost_iostreams -lzstd -lz -lnlopt -lopenblas -llapack -lgfortran -lpthread -lm make[1]: Leaving directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg/src' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg' dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -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 -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'bolt-lmm' in '../bolt-lmm_2.4.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'bolt-lmm-example' in '../bolt-lmm-example_2.4.1+dfsg-2_all.deb'. dpkg-deb: building package 'bolt-lmm-dbgsym' in '../bolt-lmm-dbgsym_2.4.1+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bolt-lmm_2.4.1+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../bolt-lmm_2.4.1+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1422091 and its subdirectories I: Current time: Wed Sep 17 08:12:35 -12 2025 I: pbuilder-time-stamp: 1758139955 Wed Sep 17 20:12:36 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed Sep 17 20:12:36 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed Sep 17 20:18:49 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed Sep 17 20:18:49 UTC 2025 I: bolt-lmm_2.4.1+dfsg-2_amd64.changes: Format: 1.8 Date: Sat, 27 Jan 2024 21:05:33 +0100 Source: bolt-lmm Binary: bolt-lmm bolt-lmm-dbgsym bolt-lmm-example Architecture: amd64 all Version: 2.4.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bolt-lmm - Efficient large cohorts genome-wide Bayesian mixed-model associat bolt-lmm-example - Examples for bolt-lmm Closes: 1043783 1049735 Changes: bolt-lmm (2.4.1+dfsg-2) unstable; urgency=medium . * Team upload. * Fix clean target Closes: #1043783, #1049735 Remove patch simde.patch that is missing from debian/patches/series. Checksums-Sha1: f3246450195ac29e4426b948aed42aa1b887870c 4922440 bolt-lmm-dbgsym_2.4.1+dfsg-2_amd64.deb 87a14efcf24a6474fc61df02fadcfbae2a416222 2708188 bolt-lmm-example_2.4.1+dfsg-2_all.deb 1834facde2379f0291f5b040d92593f93b7f21a2 6327 bolt-lmm_2.4.1+dfsg-2_amd64.buildinfo b515ba9e10aff9e8df13f6d29cc838816f424378 383468 bolt-lmm_2.4.1+dfsg-2_amd64.deb Checksums-Sha256: 8e885e69ec1c2f68b3ff2fe8629ef4b6be077b08092ba727261cd2a531e64fba 4922440 bolt-lmm-dbgsym_2.4.1+dfsg-2_amd64.deb 6d7cdd3d7d8f114e446ad3f3c8c6b0e08891d6702d1ecc4e1acadb66ebacb3fd 2708188 bolt-lmm-example_2.4.1+dfsg-2_all.deb c277fde66e774b0a3a80347048dbb1f75775f991e1f74f5cc4b275b13059d473 6327 bolt-lmm_2.4.1+dfsg-2_amd64.buildinfo 2b5e5cd270f71447426b1e006a26b172f1dc965d0ae51cc94ab6a46bbf9afbe2 383468 bolt-lmm_2.4.1+dfsg-2_amd64.deb Files: 258464600c629d76154b9dcf80c83e7d 4922440 debug optional bolt-lmm-dbgsym_2.4.1+dfsg-2_amd64.deb 48723e2300ceb82f8f830035f3dee13a 2708188 science optional bolt-lmm-example_2.4.1+dfsg-2_all.deb 7a533b540e39fb0c832fbb1e541e002e 6327 science optional bolt-lmm_2.4.1+dfsg-2_amd64.buildinfo 018e9f3f65ec2ce55d0de8879d772c8c 383468 science optional bolt-lmm_2.4.1+dfsg-2_amd64.deb Wed Sep 17 20:18:50 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_11-67884.service; invocation ID: 3318f2b75cee483eab8a3a97cfde46b7 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.jSmBUMqH/bolt-lmm_2.4.1+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.jSmBUMqH/bolt-lmm_2.4.1+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.jSmBUMqH/bolt-lmm_2.4.1+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.jSmBUMqH/b1/bolt-lmm_2.4.1+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.jSmBUMqH/b2/bolt-lmm_2.4.1+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 168ms CPU time consumed: 169ms Memory peak: 17.9M (swap: 0B) Wed Sep 17 20:18:50 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Wed Sep 17 20:18:50 UTC 2025 I: bolt-lmm from forky built successfully and reproducibly on amd64. Wed Sep 17 20:18:51 UTC 2025 I: Removing signed bolt-lmm_2.4.1+dfsg-2_amd64.buildinfo.asc files: removed './b1/bolt-lmm_2.4.1+dfsg-2_amd64.buildinfo.asc' removed './b2/bolt-lmm_2.4.1+dfsg-2_amd64.buildinfo.asc'