Tue Jul 6 11:45:45 UTC 2021 I: starting to build bolt-lmm/bullseye/i386 on jenkins on '2021-07-06 11:45' Tue Jul 6 11:45:45 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/12116/console.log Tue Jul 6 11:45:45 UTC 2021 I: Downloading source for bullseye/bolt-lmm=2.3.4+dfsg-3 --2021-07-06 11:45:45-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bolt-lmm/bolt-lmm_2.3.4+dfsg-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2254 (2.2K) Saving to: ‘bolt-lmm_2.3.4+dfsg-3.dsc’ 0K .. 100% 97.5M=0s 2021-07-06 11:45:45 (97.5 MB/s) - ‘bolt-lmm_2.3.4+dfsg-3.dsc’ saved [2254/2254] Tue Jul 6 11:45:45 UTC 2021 I: bolt-lmm_2.3.4+dfsg-3.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: 2.3.4+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ Standards-Version: 4.5.1 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, zlib1g-dev Package-List: bolt-lmm deb science optional arch=amd64,i386,ppc64el bolt-lmm-example deb science optional arch=all Checksums-Sha1: 67695812b0496904ddcc45869a3e3d2fd00b38f3 2804824 bolt-lmm_2.3.4+dfsg.orig.tar.xz e22bafabcd9f9b96582372d0179b8b7fd29312b6 8304 bolt-lmm_2.3.4+dfsg-3.debian.tar.xz Checksums-Sha256: 185ec510f80822357c04ca94ed3af8c482a7cafa6d561e8e5467089a759cba34 2804824 bolt-lmm_2.3.4+dfsg.orig.tar.xz 245afe793005a51c7a689d13d2d3acdc53c3da95330817a7502e84800e850164 8304 bolt-lmm_2.3.4+dfsg-3.debian.tar.xz Files: 43ae523b513377e46c3df6b45ee7e5c5 2804824 bolt-lmm_2.3.4+dfsg.orig.tar.xz 8445d549b44721a412f89940c4058004 8304 bolt-lmm_2.3.4+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/iCFcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEh1g//Xr/n97S7CV03HS31E6B5rBWKQqYTh1e0 WxmY10fqK7+bxBwnAcWpqJIt+kHt/QImAWX/HDJRbDLoJQERPHkI5/R37F9o2bR0 Ebl43sgJFJYQRSe9hW8kfkwvX7+jMlIn5spAw2KsfJA+v37OU8u+35M14J/7UkTN 7eWUTnNLqV7YdZcI+H8QJLLCp23gsn5/HTlnjVvlPe9j+tpLrrjf2CYfqyGUN938 gOwepkiwui3q4xVupZLJTTFkkFd3kzgIv2Jv8dj4bZtVBtzlwEjkOefq7AxAsNsf VYHx9vh0Z5Fi0+metvl2JqrEPi0VeEt24Z/dcqkpI2OHae+/IX+HZowmEPozlnjt XEcTbenj3tRZYP7Ps0tcQf4mBlbwMQ4CmKlJoP46vll4Lcha0bI4t7xbNSd0Z1NT Ybc8+XPfh7LI5wplvbROVw0iPxjRnBksmNonVW6kpDlUA++le0fQrw1r25H8lUW/ XybbUfWSxDQKAyMlK66OVbF2yh73HtXYBi6N/daQ3GRQGXOV1yvLfxJdfyy5E/I4 /9/p3IVBIOeP/1Qo4K4WuIDSKtvw0TnEQVs2q8NhM/OVNP5oj5QJyDwSBa7Nhux4 Cb9neK4cCxSrUwy7RpvDTsp/TKYd3mC1M3Y+22VKPjOUPv8wDUaucf6jrcA0pdSp XZ78VkjsuX0= =Z+/s -----END PGP SIGNATURE----- Tue Jul 6 11:45:45 UTC 2021 I: Checking whether the package is not for us Tue Jul 6 11:45:45 UTC 2021 I: Starting 1st build on remote node ionos16-i386.debian.net. Tue Jul 6 11:45:45 UTC 2021 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Tue Jul 6 11:46:35 UTC 2021 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 8 06:08:46 -12 2022 I: pbuilder-time-stamp: 1659982126 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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: using eatmydata during job I: Copying source file I: copying [bolt-lmm_2.3.4+dfsg-3.dsc] I: copying [./bolt-lmm_2.3.4+dfsg.orig.tar.xz] I: copying [./bolt-lmm_2.3.4+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.6qy9h7bO/trustedkeys.kbx': General error gpgv: Signature made Tue Dec 22 02:53:11 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bolt-lmm_2.3.4+dfsg-3.dsc dpkg-source: info: extracting bolt-lmm in bolt-lmm-2.3.4+dfsg dpkg-source: info: unpacking bolt-lmm_2.3.4+dfsg.orig.tar.xz dpkg-source: info: unpacking bolt-lmm_2.3.4+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix_makefile.patch dpkg-source: info: applying timer-for-other-arches.patch dpkg-source: info: applying dont-hardcode-glibc-version.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5796/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='534e8ef3ec064be2addffdfd21f2b119' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='5796' 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/tmp.WKQY91tlFC/pbuilderrc_1Fen --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WKQY91tlFC/b1 --logfile b1/build.log bolt-lmm_2.3.4+dfsg-3.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Jun 21 2021 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 2021 more -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 8 03:46 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 2021 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/5796/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: i386 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, 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 ... 19675 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 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} gettext{a} gettext-base{a} gfortran{a} gfortran-10{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran-10-dev{a} libgfortran5{a} libicu-dev{a} libicu67{a} libmagic-mgc{a} libmagic1{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} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{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, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 59.9 MB of archives. After unpacking 369 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libgfortran-10-dev i386 10.2.1-6 [705 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 gfortran-10 i386 10.2.1-6 [9642 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 gfortran i386 4:10.2.1-1 [1436 B] Get: 36 http://deb.debian.org/debian bullseye/main i386 icu-devtools i386 67.1-7 [209 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 39 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74.0 i386 1.74.0-9 [542 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libicu-dev i386 67.1-7 [9801 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74-dev i386 1.74.0-9 [618 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams1.74-dev i386 1.74.0-9 [275 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 44 http://deb.debian.org/debian bullseye/main i386 libboost-program-options1.74.0 i386 1.74.0-9 [365 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libboost-program-options1.74-dev i386 1.74.0-9 [397 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libboost-program-options-dev i386 1.74.0.3 [4344 B] Get: 47 http://deb.debian.org/debian bullseye/main i386 libnlopt0 i386 2.7.0-4+b2 [170 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libnlopt-dev i386 2.7.0-4+b2 [29.8 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libnlopt-cxx0 i386 2.7.0-4+b2 [199 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libnlopt-cxx-dev i386 2.7.0-4+b2 [14.5 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libopenblas0-pthread i386 0.3.13+ds-3 [4761 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libopenblas0 i386 0.3.13+ds-3 [32.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libopenblas-pthread-dev i386 0.3.13+ds-3 [3162 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libopenblas-dev i386 0.3.13+ds-3 [44.1 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Fetched 59.9 MB in 1s (70.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../07-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../10-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../23-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../25-libicu67_67.1-7_i386.deb ... Unpacking libicu67:i386 (67.1-7) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_i386.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../31-libgfortran5_10.2.1-6_i386.deb ... Unpacking libgfortran5:i386 (10.2.1-6) ... Selecting previously unselected package libgfortran-10-dev:i386. Preparing to unpack .../32-libgfortran-10-dev_10.2.1-6_i386.deb ... Unpacking libgfortran-10-dev:i386 (10.2.1-6) ... Selecting previously unselected package gfortran-10. Preparing to unpack .../33-gfortran-10_10.2.1-6_i386.deb ... Unpacking gfortran-10 (10.2.1-6) ... Selecting previously unselected package gfortran. Preparing to unpack .../34-gfortran_4%3a10.2.1-1_i386.deb ... Unpacking gfortran (4:10.2.1-1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../35-icu-devtools_67.1-7_i386.deb ... Unpacking icu-devtools (67.1-7) ... Selecting previously unselected package libboost1.74-dev:i386. Preparing to unpack .../36-libboost1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-dev:i386. Preparing to unpack .../37-libboost-dev_1.74.0.3_i386.deb ... Unpacking libboost-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-regex1.74.0:i386. Preparing to unpack .../38-libboost-regex1.74.0_1.74.0-9_i386.deb ... Unpacking libboost-regex1.74.0:i386 (1.74.0-9) ... Selecting previously unselected package libicu-dev:i386. Preparing to unpack .../39-libicu-dev_67.1-7_i386.deb ... Unpacking libicu-dev:i386 (67.1-7) ... Selecting previously unselected package libboost-regex1.74-dev:i386. Preparing to unpack .../40-libboost-regex1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-regex1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-iostreams1.74-dev:i386. Preparing to unpack .../41-libboost-iostreams1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-iostreams1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-iostreams-dev:i386. Preparing to unpack .../42-libboost-iostreams-dev_1.74.0.3_i386.deb ... Unpacking libboost-iostreams-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-program-options1.74.0:i386. Preparing to unpack .../43-libboost-program-options1.74.0_1.74.0-9_i386.deb ... Unpacking libboost-program-options1.74.0:i386 (1.74.0-9) ... Selecting previously unselected package libboost-program-options1.74-dev:i386. Preparing to unpack .../44-libboost-program-options1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-program-options1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-program-options-dev:i386. Preparing to unpack .../45-libboost-program-options-dev_1.74.0.3_i386.deb ... Unpacking libboost-program-options-dev:i386 (1.74.0.3) ... Selecting previously unselected package libnlopt0:i386. Preparing to unpack .../46-libnlopt0_2.7.0-4+b2_i386.deb ... Unpacking libnlopt0:i386 (2.7.0-4+b2) ... Selecting previously unselected package libnlopt-dev:i386. Preparing to unpack .../47-libnlopt-dev_2.7.0-4+b2_i386.deb ... Unpacking libnlopt-dev:i386 (2.7.0-4+b2) ... Selecting previously unselected package libnlopt-cxx0:i386. Preparing to unpack .../48-libnlopt-cxx0_2.7.0-4+b2_i386.deb ... Unpacking libnlopt-cxx0:i386 (2.7.0-4+b2) ... Selecting previously unselected package libnlopt-cxx-dev:i386. Preparing to unpack .../49-libnlopt-cxx-dev_2.7.0-4+b2_i386.deb ... Unpacking libnlopt-cxx-dev:i386 (2.7.0-4+b2) ... Selecting previously unselected package libopenblas0-pthread:i386. Preparing to unpack .../50-libopenblas0-pthread_0.3.13+ds-3_i386.deb ... Unpacking libopenblas0-pthread:i386 (0.3.13+ds-3) ... Selecting previously unselected package libopenblas0:i386. Preparing to unpack .../51-libopenblas0_0.3.13+ds-3_i386.deb ... Unpacking libopenblas0:i386 (0.3.13+ds-3) ... Selecting previously unselected package libopenblas-pthread-dev:i386. Preparing to unpack .../52-libopenblas-pthread-dev_0.3.13+ds-3_i386.deb ... Unpacking libopenblas-pthread-dev:i386 (0.3.13+ds-3) ... Selecting previously unselected package libopenblas-dev:i386. Preparing to unpack .../53-libopenblas-dev_0.3.13+ds-3_i386.deb ... Unpacking libopenblas-dev:i386 (0.3.13+ds-3) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../54-zlib1g-dev_1%3a1.2.11.dfsg-2_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libboost1.74-dev:i386 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:i386 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-program-options1.74.0:i386 (1.74.0-9) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up libnlopt0:i386 (2.7.0-4+b2) ... Setting up file (1:5.39-3) ... Setting up libboost-program-options1.74-dev:i386 (1.74.0-9) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libboost-program-options-dev:i386 (1.74.0.3) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libboost-regex1.74.0:i386 (1.74.0-9) ... Setting up autopoint (0.21-4) ... Setting up icu-devtools (67.1-7) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libnlopt-cxx0:i386 (2.7.0-4+b2) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgfortran-10-dev:i386 (10.2.1-6) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libnlopt-dev:i386 (2.7.0-4+b2) ... Setting up libelf1:i386 (0.183-1) ... Setting up libicu-dev:i386 (67.1-7) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libopenblas0-pthread:i386 (0.3.13+ds-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/i386-linux-gnu/libopenblas.so.0 (libopenblas.so.0-i386-linux-gnu) in auto mode Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnlopt-cxx-dev:i386 (2.7.0-4+b2) ... Setting up gfortran-10 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libboost-regex1.74-dev:i386 (1.74.0-9) ... Setting up libopenblas0:i386 (0.3.13+ds-3) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libopenblas-pthread-dev:i386 (0.3.13+ds-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/i386-linux-gnu/libopenblas.so (libopenblas.so-i386-linux-gnu) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:10.2.1-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libboost-iostreams1.74-dev:i386 (1.74.0-9) ... Setting up dh-autoreconf (20) ... Setting up libopenblas-dev:i386 (0.3.13+ds-3) ... Setting up debhelper (13.3.4) ... Setting up libboost-iostreams-dev:i386 (1.74.0.3) ... Processing triggers for libc-bin (2.31-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/bolt-lmm-2.3.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package bolt-lmm dpkg-buildpackage: info: source version 2.3.4+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j18 clean make[1]: Entering directory '/build/bolt-lmm-2.3.4+dfsg/src' rm -f *.o rm -f bolt make[1]: Leaving directory '/build/bolt-lmm-2.3.4+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/bolt-lmm-2.3.4+dfsg' cd /build/bolt-lmm-2.3.4+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/bolt-lmm-2.3.4+dfsg' dh_auto_build -O--sourcedirectory=src -Nbolt-lmm-example cd src && make -j18 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bolt-lmm-2.3.4+dfsg/src' g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltMain.o -c BoltMain.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Bolt.o -c Bolt.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParams.o -c BoltParams.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParEstCV.o -c BoltParEstCV.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltReml.o -c BoltReml.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o CovariateBasis.o -c CovariateBasis.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o DataMatrix.o -c DataMatrix.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o FileUtils.o -c FileUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Jackknife.o -c Jackknife.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o LDscoreCalibration.o -c LDscoreCalibration.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MapInterpolater.o -c MapInterpolater.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MatrixUtils.o -c MatrixUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MemoryUtils.o -c MemoryUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o PhenoBuilder.o -c PhenoBuilder.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o RestrictSnpSet.o -c RestrictSnpSet.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpData.o -c SnpData.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpInfo.o -c SnpInfo.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SpectrumTools.o -c SpectrumTools.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StatsUtils.o -c StatsUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Timer.o -c Timer.cpp g++ -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bolt-lmm-2.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o memcpy.o -c memcpy.cpp NonlinearOptMulti.cpp: In function 'std::vector > NonlinearOptMulti::constrainedNR(double&, boost::numeric::ublas::vector&, const std::vector >&, const boost::numeric::ublas::vector&, const boost::numeric::ublas::matrix&, double)': NonlinearOptMulti.cpp:230:21: warning: catching polymorphic type 'class nlopt::roundoff_limited' by value [-Wcatch-value=] 230 | catch (nlopt::roundoff_limited) { | ^~~~~~~~~~~~~~~~ FileUtils.cpp: In function 'int FileUtils::checkBgenSample(const string&, const string&, int)': FileUtils.cpp:275:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 275 | uint offset; fread(&offset, 4, 1, fin); //cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:276:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 276 | uint L_H; fread(&L_H, 4, 1, fin); //cout << "L_H: " << L_H << endl; | ~~~~~^~~~~~~~~~~~~~~~~ FileUtils.cpp:277:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:279:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 279 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:284:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | char magic[5]; fread(magic, 1, 4, fin); magic[4] = '\0'; //cout << "magic bytes: " << string(magic) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:286:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | uint flags; fread(&flags, 4, 1, fin); //cout << "flags: " << flags << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:297:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 297 | uint Nrow; fread(&Nrow, 4, 1, fin); // cout << "Nrow: " << Nrow << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:304:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 304 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << endl; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:305:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; cout << "first snpID: " << string(snpID) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ FileUtils.cpp:307:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 307 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << endl; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:308:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 308 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; cout << "first rsID: " << string(rsID) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ FileUtils.cpp:313:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:314:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 314 | fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:323:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | uint bp; fread(&bp, 4, 1, fin); // cout << "bp: " << bp << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:325:28: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 325 | ushort Kheader; fread(&Kheader, 2, 1, fin); //cout << "K: " << K << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:331:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 331 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:332:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 332 | fread(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:334:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 334 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ FileUtils.cpp:335:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ FileUtils.cpp:337:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 337 | uint C; fread(&C, 4, 1, fin); //cout << "C: " << C << endl; | ~~~~~^~~~~~~~~~~~~~~ FileUtils.cpp:339:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 339 | uint D; fread(&D, 4, 1, fin); //cout << "D: " << D << endl; | ~~~~~^~~~~~~~~~~~~~~ FileUtils.cpp:341:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 341 | fread(zBuf, 1, C-4, fin); | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp: In member function 'void LMM::Bolt::streamBgen(const string&, int, const string&, const string&, double, double, const string&, bool, const std::vector&, bool) const': Bolt.cpp:2866:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2866 | uint offset; fread(&offset, 4, 1, fin); // cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2867:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2867 | uint H; fread(&H, 4, 1, fin); // cout << "H: " << H << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:2868:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2868 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "BGEN snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2869:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2869 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "BGEN samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2884:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2884 | uint Nrow; fread(&Nrow, 4, 1, fin); // cout << "Nrow: " << Nrow << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2889:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2889 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2890:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2890 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; // cout << "snpID: " << string(snpID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:2891:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2891 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2892:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2892 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2893:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2893 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2894:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2894 | fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2901:26: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2901 | uint physpos; fread(&physpos, 4, 1, fin); // cout << "physpos: " << physpos << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2903:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2903 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2909:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2909 | fread(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2910:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2910 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:2916:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2916 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:2917:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2917 | uint zLen; fread(&zLen, 4, 1, fin); // cout << "zLen: " << zLen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:2918:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2918 | fread(zBuf, 1, zLen, fin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp: In member function 'void LMM::Bolt::streamBgen2(const string&, int, const string&, const string&, double, double, const string&, bool, const std::vector&, bool, int) const': Bolt.cpp:3188:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3188 | uint offset; fread(&offset, 4, 1, fin); //cout << "offset: " << offset << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3189:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3189 | uint L_H; fread(&L_H, 4, 1, fin); //cout << "L_H: " << L_H << endl; | ~~~~~^~~~~~~~~~~~~~~~~ Bolt.cpp:3190:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3190 | uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "snpBlocks (Mbgen): " << Mbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3192:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3192 | uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "samples (Nbgen): " << Nbgen << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3197:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3197 | char magic[5]; fread(magic, 1, 4, fin); magic[4] = '\0'; //cout << "magic bytes: " << string(magic) << endl; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:3199:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3199 | uint flags; fread(&flags, 4, 1, fin); //cout << "flags: " << flags << endl; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3231:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3231 | ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3232:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3232 | fread(snpID, 1, LS, fin); snpID[LS] = '\0'; // cout << "snpID: " << string(snpID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3233:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3233 | ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3234:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3234 | fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:3237:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3237 | ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3238:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3238 | fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3247:26: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3247 | uint physpos; fread(&physpos, 4, 1, fin); // cout << "physpos: " << physpos << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3253:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3253 | ushort K; fread(&K, 2, 1, fin); //cout << "K: " << K << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3259:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3259 | uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3265:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3265 | fread(allele1, 1, LA, fin); allele1[LA] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3267:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3267 | uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; | ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3273:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3273 | fread(allele0, 1, LB, fin); allele0[LB] = '\0'; | ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3276:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3276 | uint C; fread(&C, 4, 1, fin); //cout << "C: " << C << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3278:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3278 | uint D; fread(&D, 4, 1, fin); //cout << "D: " << D << endl; | ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3280:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3280 | fread(&zBufs[B][0], 1, C-4, fin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -fopenmp -Wl,-z,relro -Wl,-z,now -o bolt BoltMain.o Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o memcpy.o -lboost_program_options -lboost_iostreams -lz -lnlopt -lopenblas -llapack -lgfortran -lpthread -lm make[1]: Leaving directory '/build/bolt-lmm-2.3.4+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/bolt-lmm-2.3.4+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/bolt-lmm-2.3.4+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_2.3.4+dfsg-3_i386.deb'. dpkg-deb: building package 'bolt-lmm-dbgsym' in '../bolt-lmm-dbgsym_2.3.4+dfsg-3_i386.deb'. dpkg-deb: building package 'bolt-lmm-example' in '../bolt-lmm-example_2.3.4+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bolt-lmm_2.3.4+dfsg-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/5796 and its subdirectories I: Current time: Mon Aug 8 06:09:34 -12 2022 I: pbuilder-time-stamp: 1659982174 Tue Jul 6 11:46:36 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Tue Jul 6 11:46:36 UTC 2021 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Tue Jul 6 11:53:28 UTC 2021 I: Deleting $TMPDIR on ionos2-i386.debian.net. Tue Jul 6 11:53:28 UTC 2021 I: bolt-lmm_2.3.4+dfsg-3_i386.changes: Format: 1.8 Date: Tue, 22 Dec 2020 15:48:38 +0100 Source: bolt-lmm Binary: bolt-lmm bolt-lmm-dbgsym bolt-lmm-example Architecture: i386 all Version: 2.3.4+dfsg-3 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: 976527 Changes: bolt-lmm (2.3.4+dfsg-3) unstable; urgency=medium . * Team upload. * Enable architecture all builds on arm64 Closes: #976527 * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright). Checksums-Sha1: bcaa68983cecc8e4626dcb232c9bfda228ee3824 4528160 bolt-lmm-dbgsym_2.3.4+dfsg-3_i386.deb 348c2748befdc4434b0f34380b5023363d434094 2707352 bolt-lmm-example_2.3.4+dfsg-3_all.deb bb43b9710a64083d25691522777dcde3e9f99cfe 6037 bolt-lmm_2.3.4+dfsg-3_i386.buildinfo ac58ebe8017125b0c59f5ae1a4770882355cff5d 355104 bolt-lmm_2.3.4+dfsg-3_i386.deb Checksums-Sha256: d29c2340816c5e657692ab0706b28c575225c0c10ec6ba9e85fed227bfa6013b 4528160 bolt-lmm-dbgsym_2.3.4+dfsg-3_i386.deb 374e7436148783051afeb9837548c718fee1067d588be5b923ce4e6b6b218c84 2707352 bolt-lmm-example_2.3.4+dfsg-3_all.deb f86459bcde6dcaec95e9d67fe9ef2f03a0a9838ba4af9cb388de6c397ad87fa6 6037 bolt-lmm_2.3.4+dfsg-3_i386.buildinfo 8b712ac3f76c906182c52cde60c2ab8c3df7c3947f1b40c67a69031c532f7f75 355104 bolt-lmm_2.3.4+dfsg-3_i386.deb Files: 45a1e9f6eac88a759b04c4c8f077ce80 4528160 debug optional bolt-lmm-dbgsym_2.3.4+dfsg-3_i386.deb 0eb041ad2b0962062c9e954254a73fd6 2707352 science optional bolt-lmm-example_2.3.4+dfsg-3_all.deb addd220bacb750485f33b5a946fc9499 6037 science optional bolt-lmm_2.3.4+dfsg-3_i386.buildinfo 3b613a48804ced3020cdb1ecff64295d 355104 science optional bolt-lmm_2.3.4+dfsg-3_i386.deb Tue Jul 6 11:53:29 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.WKQY91tlFC/bolt-lmm_2.3.4+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.WKQY91tlFC/bolt-lmm_2.3.4+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.WKQY91tlFC/bolt-lmm_2.3.4+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.WKQY91tlFC/b1/bolt-lmm_2.3.4+dfsg-3_i386.changes /srv/reproducible-results/rbuild-debian/tmp.WKQY91tlFC/b2/bolt-lmm_2.3.4+dfsg-3_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.297s) 0.297s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.086s) 0.086s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 6 11:53:31 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 6 11:53:31 UTC 2021 I: bolt-lmm from bullseye built successfully and reproducibly on i386. Tue Jul 6 11:53:33 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Jul 6 11:53:33 UTC 2021 I: Submitting 8.0K b1/bolt-lmm_2.3.4+dfsg-3_i386.buildinfo.asc Tue Jul 6 11:53:34 UTC 2021 I: Submitting 8.0K b2/bolt-lmm_2.3.4+dfsg-3_i386.buildinfo.asc Tue Jul 6 11:53:35 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 6 11:53:35 UTC 2021 I: Done submitting .buildinfo files. Tue Jul 6 11:53:35 UTC 2021 I: Removing signed bolt-lmm_2.3.4+dfsg-3_i386.buildinfo.asc files: removed './b1/bolt-lmm_2.3.4+dfsg-3_i386.buildinfo.asc' removed './b2/bolt-lmm_2.3.4+dfsg-3_i386.buildinfo.asc'