I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 13 15:04:53 -12 2020 I: pbuilder-time-stamp: 1607915093 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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: Copying source file I: copying [bolt-lmm_2.3.2+dfsg-3.dsc] I: copying [./bolt-lmm_2.3.2+dfsg.orig.tar.xz] I: copying [./bolt-lmm_2.3.2+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Nov 15 18:59:28 2018 -12 gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 gpgv: issuer "daissi@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bolt-lmm_2.3.2+dfsg-3.dsc dpkg-source: info: extracting bolt-lmm in bolt-lmm-2.3.2+dfsg dpkg-source: info: unpacking bolt-lmm_2.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking bolt-lmm_2.3.2+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 Fix_compilation_error.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/46584/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='70f40575093c401da7093ac97fb422df' 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='46584' 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.RU5TutnBYx/pbuilderrc_fWPi --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RU5TutnBYx/b1 --logfile b1/build.log bolt-lmm_2.3.2+dfsg-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 4.19.0-13-amd64 #1 SMP Debian 4.19.160-2 (2020-11-28) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 6 20:24 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/46584/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 (>= 11), 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 ... 19195 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 (>= 11); however: Package debhelper 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-program-options-dev{a} libboost-program-options1.67-dev{a} libboost-program-options1.67.0{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libicu-dev{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libopenblas-base{a} libopenblas-dev{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 59.0 MB of archives. After unpacking 396 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u1 [117 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libgfortran-8-dev amd64 8.3.0-6 [616 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 gfortran-8 amd64 8.3.0-6 [9375 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 gfortran amd64 4:8.3.0-1 [1432 B] Get: 38 http://deb.debian.org/debian buster/main amd64 icu-devtools amd64 63.1-6+deb10u1 [189 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get: 41 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67.0 amd64 1.67.0-13+deb10u1 [485 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libicu-dev amd64 63.1-6+deb10u1 [9186 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67-dev amd64 1.67.0-13+deb10u1 [539 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libboost-iostreams1.67-dev amd64 1.67.0-13+deb10u1 [255 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libboost-iostreams-dev amd64 1.67.0.1 [3632 B] Get: 46 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67.0 amd64 1.67.0-13+deb10u1 [357 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67-dev amd64 1.67.0-13+deb10u1 [385 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libboost-program-options-dev amd64 1.67.0.1 [3656 B] Get: 49 http://deb.debian.org/debian buster/main amd64 libnlopt0 amd64 2.4.2+dfsg-8+b1 [165 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libnlopt-dev amd64 2.4.2+dfsg-8+b1 [170 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libnlopt-cxx0 amd64 2.4.2+dfsg-8+b1 [174 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libnlopt-cxx-dev amd64 2.4.2+dfsg-8+b1 [188 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libopenblas-base amd64 0.3.5+ds-3 [4290 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libopenblas-dev amd64 0.3.5+ds-3 [4390 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Fetched 59.0 MB in 1s (57.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../11-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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Setting up libopenblas-base:amd64 (0.3.5+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libgfortran-8-dev:amd64 (8.3.0-6) ... Setting up libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libboost-regex1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up gfortran-8 (8.3.0-6) ... Setting up m4 (1.4.18-2) ... 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/bolt-lmm-2.3.2+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 2.3.2+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j15 clean make[1]: Entering directory '/build/bolt-lmm-2.3.2+dfsg/src' rm -f *.o rm -f bolt make[1]: Leaving directory '/build/bolt-lmm-2.3.2+dfsg/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules build dh build --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 make[1]: Entering directory '/build/bolt-lmm-2.3.2+dfsg' dh_auto_build cd src && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/bolt-lmm-2.3.2+dfsg/src' g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltMain.o -c BoltMain.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Bolt.o -c Bolt.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParams.o -c BoltParams.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParEstCV.o -c BoltParEstCV.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltReml.o -c BoltReml.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o CovariateBasis.o -c CovariateBasis.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o DataMatrix.o -c DataMatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o FileUtils.o -c FileUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Jackknife.o -c Jackknife.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o LDscoreCalibration.o -c LDscoreCalibration.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MapInterpolater.o -c MapInterpolater.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MatrixUtils.o -c MatrixUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MemoryUtils.o -c MemoryUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o PhenoBuilder.o -c PhenoBuilder.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o RestrictSnpSet.o -c RestrictSnpSet.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpData.o -c SnpData.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpInfo.o -c SnpInfo.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=] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] fread(zBuf, 1, C-4, fin); ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SpectrumTools.o -c SpectrumTools.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StatsUtils.o -c StatsUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Timer.o -c Timer.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o memcpy.o -c memcpy.cpp Bolt.cpp: In member function 'void LMM::Bolt::streamBgen(const string&, int, const string&, const string&, double, double, const string&, bool, const std::vector&, bool) const': Bolt.cpp:2866:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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:3176:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint offset; fread(&offset, 4, 1, fin); //cout << "offset: " << offset << endl; ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3177:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint L_H; fread(&L_H, 4, 1, fin); //cout << "L_H: " << L_H << endl; ~~~~~^~~~~~~~~~~~~~~~~ Bolt.cpp:3178:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint Mbgen; fread(&Mbgen, 4, 1, fin); cout << "snpBlocks (Mbgen): " << Mbgen << endl; ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3180:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint Nbgen; fread(&Nbgen, 4, 1, fin); cout << "samples (Nbgen): " << Nbgen << endl; ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3185:25: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] char magic[5]; fread(magic, 1, 4, fin); magic[4] = '\0'; //cout << "magic bytes: " << string(magic) << endl; ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:3187:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint flags; fread(&flags, 4, 1, fin); //cout << "flags: " << flags << endl; ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3219:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] ushort LS; fread(&LS, 2, 1, fin); // cout << "LS: " << LS << " " << std::flush; ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3220:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(snpID, 1, LS, fin); snpID[LS] = '\0'; // cout << "snpID: " << string(snpID) << " " << std::flush; ~~~~~^~~~~~~~~~~~~~~~~~~ Bolt.cpp:3221:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] ushort LR; fread(&LR, 2, 1, fin); // cout << "LR: " << LR << " " << std::flush; ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3222:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; ~~~~~^~~~~~~~~~~~~~~~~~ Bolt.cpp:3225:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] ushort LC; fread(&LC, 2, 1, fin); // cout << "LC: " << LC << " " << std::flush; ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3226:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(chrStr, 1, LC, fin); chrStr[LC] = '\0'; ~~~~~^~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3235:26: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint physpos; fread(&physpos, 4, 1, fin); // cout << "physpos: " << physpos << " " << std::flush; ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3241:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] ushort K; fread(&K, 2, 1, fin); //cout << "K: " << K << endl; ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3247:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint LA; fread(&LA, 4, 1, fin); // cout << "LA: " << LA << " " << std::flush; ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3253:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(allele1, 1, LA, fin); allele1[LA] = '\0'; ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3255:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint LB; fread(&LB, 4, 1, fin); // cout << "LB: " << LB << " " << std::flush; ~~~~~^~~~~~~~~~~~~~~~ Bolt.cpp:3261:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(allele0, 1, LB, fin); allele0[LB] = '\0'; ~~~~~^~~~~~~~~~~~~~~~~~~~~ Bolt.cpp:3264:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint C; fread(&C, 4, 1, fin); //cout << "C: " << C << endl; ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3266:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] uint D; fread(&D, 4, 1, fin); //cout << "D: " << D << endl; ~~~~~^~~~~~~~~~~~~~~ Bolt.cpp:3268:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] 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[2]: Leaving directory '/build/bolt-lmm-2.3.2+dfsg/src' cd /build/bolt-lmm-2.3.2+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-2.3.2+dfsg' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=src 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-2.3.2+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/bolt-lmm-2.3.2+dfsg' dh_installman -O--sourcedirectory=src dh_installinit -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_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bolt-lmm/usr/bin/bolt was not linked against liblapack.so.3 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bolt-lmm/usr/bin/bolt was not linked against libpthread.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bolt-lmm/usr/bin/bolt was not linked against libgfortran.so.5 (it uses none of the library's symbols) 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-dbgsym' in '../bolt-lmm-dbgsym_2.3.2+dfsg-3_amd64.deb'. dpkg-deb: building package 'bolt-lmm' in '../bolt-lmm_2.3.2+dfsg-3_amd64.deb'. dpkg-deb: building package 'bolt-lmm-example' in '../bolt-lmm-example_2.3.2+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bolt-lmm_2.3.2+dfsg-3_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) 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/46584 and its subdirectories I: Current time: Sun Dec 13 15:06:05 -12 2020 I: pbuilder-time-stamp: 1607915165