I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 28 02:03:13 +14 2024 I: pbuilder-time-stamp: 1714219393 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [qtltools_1.3.1+dfsg-4.dsc] I: copying [./qtltools_1.3.1+dfsg.orig.tar.xz] I: copying [./qtltools_1.3.1+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Dec 5 16:05:11 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting qtltools in qtltools-1.3.1+dfsg dpkg-source: info: unpacking qtltools_1.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking qtltools_1.3.1+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile_config.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2250399/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 27 12:03 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2250399/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2250399/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=8da9e99e4a504b15a151176e4a1c5dfb LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2250399 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tvEOKBfO/pbuilderrc_aNc4 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tvEOKBfO/b2 --logfile b2/build.log qtltools_1.3.1+dfsg-4.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:15 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2250399/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: arm64 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), libblas-dev, libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libeigen3-dev, libgsl-dev, libhts-dev, r-mathlib, 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 ... 19937 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 libblas-dev; however: Package libblas-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 libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on r-mathlib; however: Package r-mathlib 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} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libbz2-dev{a} libdebhelper-perl{a} libeigen3-dev{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpkgconf3{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} r-mathlib{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx r-base-core r-base-dev wget 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 47.9 MB of archives. After unpacking 328 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libhts-dev but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libssl3 [3.1.5-1 (now)] Install the following packages: 2) libbrotli1 [1.1.0-2+b3 (testing)] 3) libcurl3t64-gnutls [8.7.1-3 (testing)] 4) libcurl4-gnutls-dev [8.7.1-3 (testing)] 5) libdeflate-dev [1.20-1 (testing)] 6) libdeflate0 [1.20-1 (testing)] 7) libhts-dev [1.19+ds-1 (testing)] 8) libhts3 [1.19+ds-1 (testing)] 9) libhtscodecs2 [1.6.0-1+b1 (testing)] 10) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 11) liblzma-dev [5.6.1+really5.4.5-1 (testing)] 12) libnghttp2-14 [1.59.0-1 (testing)] 13) libpsl5t64 [0.21.2-1.1 (testing)] 14) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 15) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 16) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 17) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 18) libssl3t64 [3.2.1-3 (testing)] 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} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libbz2-dev{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libeigen3-dev{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssl3t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} r-mathlib{a} sensible-utils{a} zlib1g-dev{a} The following packages will be REMOVED: libssl3{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix r-base-core r-base-dev wget 0 packages upgraded, 70 newly installed, 1 to remove and 0 not upgraded. Need to get 54.8 MB of archives. After unpacking 344 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 72.1-4+b1 [194 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.0-3 [98.2 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-2+b2 [10.6 MB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libboost-regex1.83.0 arm64 1.83.0-2+b2 [311 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 72.1-4+b1 [10.2 MB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libboost-regex1.83-dev arm64 1.83.0-2+b2 [333 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-2+b2 [261 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 41 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2+b2 [332 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83-dev arm64 1.83.0-2+b2 [369 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 44 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-5.1 [31.8 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-3 [523 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libgslcblas0 arm64 2.7.1+dfsg-6+b1 [72.7 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libgsl27 arm64 2.7.1+dfsg-6+b1 [822 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libgsl-dev arm64 2.7.1+dfsg-6+b1 [1039 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libhts3 arm64 1.19+ds-1 [412 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.19+ds-1 [1603 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 r-mathlib arm64 4.3.2-1 [2429 kB] Fetched 54.8 MB in 1s (76.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19937 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:arm64. (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 ... 19924 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19939 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_arm64.deb ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-regex1.83.0:arm64 (1.83.0-2+b2) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libboost-program-options1.83-dev:arm64 (1.83.0-2+b2) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.59.0-1) ... Setting up libmagic1:arm64 (1:5.45-2+b1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:arm64 (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-4+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up libboost-program-options-dev:arm64 (1.83.0.2+b2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up autopoint (0.21-14) ... Setting up icu-devtools (72.1-4+b1) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:arm64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up r-mathlib (4.3.2-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libdeflate-dev:arm64 (1.20-1) ... Setting up libicu-dev:arm64 (72.1-4+b1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Setting up libblas-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libbz2-dev:arm64 (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libboost-regex1.83-dev:arm64 (1.83.0-2+b2) ... Setting up pkg-config:arm64 (1.8.1-1+b2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libboost-iostreams1.83-dev:arm64 (1.83.0-2+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up libboost-iostreams-dev:arm64 (1.83.0.2+b2) ... Setting up libcurl4-gnutls-dev:arm64 (8.7.1-3) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:arm64 (1.19+ds-1) ... Setting up libhts-dev:arm64 (1.19+ds-1) ... Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-18) ... 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: user script /srv/workspace/pbuilder/2250399/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2250399/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/qtltools-1.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../qtltools_1.3.1+dfsg-4_source.changes dpkg-buildpackage: info: source package qtltools dpkg-buildpackage: info: source version 1.3.1+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' rm -f debian/upstream.example/examples.tar.xz dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' rm -f obj/*.o bin/QTLtools make[2]: Leaving directory '/build/reproducible-path/qtltools-1.3.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/qtltools-1.3.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' mkdir -p /build/reproducible-path/qtltools-1.3.1+dfsg/obj/ mkdir -p /build/reproducible-path/qtltools-1.3.1+dfsg/bin/ dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' g++ -std=c++0x -o obj/QTLtools.o -c src/QTLtools.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/data.o -c src/common/data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_main.o -c src/mode_ase/ase_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_management.o -c src/mode_ase/ase_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_read_blacklist.o -c src/mode_ase/ase_read_blacklist.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_read_fasta.o -c src/mode_ase/ase_read_fasta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_read_genotypes.o -c src/mode_ase/ase_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_read_gtf.o -c src/mode_ase/ase_read_gtf.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_read_sequences.o -c src/mode_ase/ase_read_sequences.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/ase_run_analyses.o -c src/mode_ase/ase_run_analyses.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/bamstat_main.o -c src/mode_bamstat/bamstat_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/bamstat_read_annotations.o -c src/mode_bamstat/bamstat_read_annotations.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/bamstat_read_bam.o -c src/mode_bamstat/bamstat_read_bam.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/bamstat_write_output.o -c src/mode_bamstat/bamstat_write_output.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_chunking.o -c src/mode_cis/cis_chunking.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_collapse_phenotypes.o -c src/mode_cis/cis_collapse_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_conditionnal_pass.o -c src/mode_cis/cis_conditionnal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_initilization.o -c src/mode_cis/cis_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_learn_beta.o -c src/mode_cis/cis_learn_beta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_learn_dof.o -c src/mode_cis/cis_learn_dof.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_main.o -c src/mode_cis/cis_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_management.o -c src/mode_cis/cis_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_nominal_pass.o -c src/mode_cis/cis_nominal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_permutation_pass.o -c src/mode_cis/cis_permutation_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_read_covariates.o -c src/mode_cis/cis_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_read_genotypes.o -c src/mode_cis/cis_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_read_phenotypes.o -c src/mode_cis/cis_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/cis_read_thresholds.o -c src/mode_cis/cis_read_thresholds.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/correct_main.o -c src/mode_correct/correct_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/correct_management.o -c src/mode_correct/correct_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/correct_processing.o -c src/mode_correct/correct_processing.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, from src/mode_cis/cis_conditionnal_pass.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, from src/mode_cis/cis_collapse_phenotypes.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/correct_read_covariates.o -c src/mode_correct/correct_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_cis/../common/data.h:19, from src/mode_cis/cis_data.h:33, from src/mode_cis/cis_initilization.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/extract_main.o -c src/mode_extract/extract_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/extract_managment.o -c src/mode_extract/extract_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/extract_read_data.o -c src/mode_extract/extract_read_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/extract_write.o -c src/mode_extract/extract_write.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fdensity_main.o -c src/mode_fdensity/fdensity_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_correct/correct_processing.cpp: In member function 'void correct_data::processVCF(std::string, std::string)': src/mode_correct/correct_processing.cpp:127:22: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 127 | bcf_hdr_write(fp, hdr_new); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ g++ -std=c++0x -o obj/fdensity_process.o -c src/mode_fdensity/fdensity_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fdensity_read_annotation.o -c src/mode_fdensity/fdensity_read_annotation.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fdensity_read_qtl.o -c src/mode_fdensity/fdensity_read_qtl.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_main.o -c src/mode_fenrich/fenrich_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_management.o -c src/mode_fenrich/fenrich_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_process.o -c src/mode_fenrich/fenrich_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_read_annotation.o -c src/mode_fenrich/fenrich_read_annotation.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_correct/../common/data.h:19, from src/mode_correct/correct_data.h:24, from src/mode_correct/correct_processing.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/fenrich_read_qtl.o -c src/mode_fenrich/fenrich_read_qtl.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/fenrich_read_tss.o -c src/mode_fenrich/fenrich_read_tss.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_binning_process.o -c src/mode_genrich/genrich_binning_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_main.o -c src/mode_genrich/genrich_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_process.o -c src/mode_genrich/genrich_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_read_auxillliary_data.o -c src/mode_genrich/genrich_read_auxillliary_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_read_phenotypes.o -c src/mode_genrich/genrich_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_read_reference_genotypes.o -c src/mode_genrich/genrich_read_reference_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/genrich_routines.o -c src/mode_genrich/genrich_routines.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/gwas_analysis_pass.o -c src/mode_gwas/gwas_analysis_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/gwas_initilization.o -c src/mode_gwas/gwas_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/gwas_main.o -c src/mode_gwas/gwas_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/gwas_managment.o -c src/mode_gwas/gwas_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/gwas_read_covariates.o -c src/mode_gwas/gwas_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/gwas_read_phenotypes.o -c src/mode_gwas/gwas_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/match_main.o -c src/mode_match/match_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib src/mode_gwas/gwas_analysis_pass.cpp: In member function 'void gwas_data::runGwasPassOnVCF(std::string, std::string)': src/mode_gwas/gwas_analysis_pass.cpp:28:28: warning: ignoring return value of 'int bcf_hdr_set_samples(bcf_hdr_t*, const char*, int)' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | bcf_hdr_set_samples(hdr, concat_id.c_str(), 0); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/match_managment.o -c src/mode_match/match_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/match_process.o -c src/mode_match/match_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/match_read_genotypes.o -c src/mode_match/match_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/match_read_sequences.o -c src/mode_match/match_read_sequences.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/pca_main.o -c src/mode_pca/pca_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/pca_management.o -c src/mode_pca/pca_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/pca_pca.o -c src/mode_pca/pca_pca.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/pca_read_data.o -c src/mode_pca/pca_read_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_gwas/../common/data.h:19, from src/mode_gwas/gwas_data.h:20, from src/mode_gwas/gwas_managment.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/quan_main.o -c src/mode_quan/quan_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_readBAM.o -c src/mode_quan/quan_readBAM.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_readGTF.o -c src/mode_quan/quan_readGTF.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_writeResults.o -c src/mode_quan/quan_writeResults.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/quan_xxhash.o -c src/mode_quan/quan_xxhash.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_initilization.o -c src/mode_rep/rep_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_main.o -c src/mode_rep/rep_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_management.o -c src/mode_rep/rep_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_nominal_pass.o -c src/mode_rep/rep_nominal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_read_covariates.o -c src/mode_rep/rep_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_read_genotypes.o -c src/mode_rep/rep_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_read_phenotypes.o -c src/mode_rep/rep_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rep_read_qtls.o -c src/mode_rep/rep_read_qtls.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from src/mode_pca/pca_pca.h:21, from src/mode_pca/pca_pca.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/rtc_chunking.o -c src/mode_rtc/rtc_chunking.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_collapse_phenotypes.o -c src/mode_rtc/rtc_collapse_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_common.o -c src/mode_rtc/rtc_common.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_gwas_cis.o -c src/mode_rtc/rtc_gwas_cis.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_rep/../common/data.h:19, from src/mode_rep/rep_data.h:31, from src/mode_rep/rep_initilization.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/rtc_gwas_trans.o -c src/mode_rtc/rtc_gwas_trans.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_initilization.o -c src/mode_rtc/rtc_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_main.o -c src/mode_rtc/rtc_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_management.o -c src/mode_rtc/rtc_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_mergeQTL_cis.o -c src/mode_rtc/rtc_mergeQTL_cis.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_mergeQTL_trans.o -c src/mode_rtc/rtc_mergeQTL_trans.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_read_covariates.o -c src/mode_rtc/rtc_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_read_genotypes.o -c src/mode_rtc/rtc_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_read_get_hotspots.o -c src/mode_rtc/rtc_read_get_hotspots.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/rtc_read_phenotypes.o -c src/mode_rtc/rtc_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_collapse_phenotypes.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_common.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/rtc_sampling.o -c src/mode_rtc/rtc_sampling.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_rtc/../common/data.h:19, from src/mode_rtc/rtc_data.h:36, from src/mode_rtc/rtc_initilization.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x -o obj/trans_adjust.o -c src/mode_trans/trans_adjust.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_analysis_pass.o -c src/mode_trans/trans_analysis_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_chunking.o -c src/mode_trans/trans_chunking.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_initilization.o -c src/mode_trans/trans_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_learn_beta.o -c src/mode_trans/trans_learn_beta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_main.o -c src/mode_trans/trans_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_managment.o -c src/mode_trans/trans_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_read_covariates.o -c src/mode_trans/trans_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_read_phenotypes.o -c src/mode_trans/trans_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/trans_read_samples.o -c src/mode_trans/trans_read_samples.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_initilization.o -c src/mode_union/union_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_main.o -c src/mode_union/union_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_management.o -c src/mode_union/union_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_read_covariates.o -c src/mode_union/union_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_read_genotypes.o -c src/mode_union/union_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_read_get_hotspots.o -c src/mode_union/union_read_get_hotspots.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_read_phenotypes.o -c src/mode_union/union_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib g++ -std=c++0x -o obj/union_union.o -c src/mode_union/union_union.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -ffile-prefix-map=/build/reproducible-path/qtltools-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_trans/../common/data.h:19, from src/mode_trans/trans_data.h:26, from src/mode_trans/trans_managment.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from lib/OTools/residualizer.h:36, from lib/OTools/otools.h:60, from src/mode_union/../common/data.h:19, from src/mode_union/union_data.h:20, from src/mode_union/union_initilization.cpp:16: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++0x obj/QTLtools.o obj/data.o obj/ase_main.o obj/ase_management.o obj/ase_read_blacklist.o obj/ase_read_fasta.o obj/ase_read_genotypes.o obj/ase_read_gtf.o obj/ase_read_sequences.o obj/ase_run_analyses.o obj/bamstat_main.o obj/bamstat_read_annotations.o obj/bamstat_read_bam.o obj/bamstat_write_output.o obj/cis_chunking.o obj/cis_collapse_phenotypes.o obj/cis_conditionnal_pass.o obj/cis_initilization.o obj/cis_learn_beta.o obj/cis_learn_dof.o obj/cis_main.o obj/cis_management.o obj/cis_nominal_pass.o obj/cis_permutation_pass.o obj/cis_read_covariates.o obj/cis_read_genotypes.o obj/cis_read_phenotypes.o obj/cis_read_thresholds.o obj/correct_main.o obj/correct_management.o obj/correct_processing.o obj/correct_read_covariates.o obj/extract_main.o obj/extract_managment.o obj/extract_read_data.o obj/extract_write.o obj/fdensity_main.o obj/fdensity_process.o obj/fdensity_read_annotation.o obj/fdensity_read_qtl.o obj/fenrich_main.o obj/fenrich_management.o obj/fenrich_process.o obj/fenrich_read_annotation.o obj/fenrich_read_qtl.o obj/fenrich_read_tss.o obj/genrich_binning_process.o obj/genrich_main.o obj/genrich_process.o obj/genrich_read_auxillliary_data.o obj/genrich_read_phenotypes.o obj/genrich_read_reference_genotypes.o obj/genrich_routines.o obj/gwas_analysis_pass.o obj/gwas_initilization.o obj/gwas_main.o obj/gwas_managment.o obj/gwas_read_covariates.o obj/gwas_read_phenotypes.o obj/match_main.o obj/match_managment.o obj/match_process.o obj/match_read_genotypes.o obj/match_read_sequences.o obj/pca_main.o obj/pca_management.o obj/pca_pca.o obj/pca_read_data.o obj/quan_main.o obj/quan_readBAM.o obj/quan_readGTF.o obj/quan_writeResults.o obj/quan_xxhash.o obj/rep_initilization.o obj/rep_main.o obj/rep_management.o obj/rep_nominal_pass.o obj/rep_read_covariates.o obj/rep_read_genotypes.o obj/rep_read_phenotypes.o obj/rep_read_qtls.o obj/rtc_chunking.o obj/rtc_collapse_phenotypes.o obj/rtc_common.o obj/rtc_gwas_cis.o obj/rtc_gwas_trans.o obj/rtc_initilization.o obj/rtc_main.o obj/rtc_management.o obj/rtc_mergeQTL_cis.o obj/rtc_mergeQTL_trans.o obj/rtc_read_covariates.o obj/rtc_read_genotypes.o obj/rtc_read_get_hotspots.o obj/rtc_read_phenotypes.o obj/rtc_sampling.o obj/trans_adjust.o obj/trans_analysis_pass.o obj/trans_chunking.o obj/trans_initilization.o obj/trans_learn_beta.o obj/trans_main.o obj/trans_managment.o obj/trans_read_covariates.o obj/trans_read_phenotypes.o obj/trans_read_samples.o obj/union_initilization.o obj/union_main.o obj/union_management.o obj/union_read_covariates.o obj/union_read_genotypes.o obj/union_read_get_hotspots.o obj/union_read_phenotypes.o obj/union_union.o -lRmath -lhts -lboost_iostreams -lboost_program_options -o bin/QTLtools -lz -lgsl -lblas -lbz2 -lm -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/qtltools-1.3.1+dfsg' make[1]: Leaving directory '/build/reproducible-path/qtltools-1.3.1+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/qtltools-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' mkdir -p -m 755 /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/bin /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/share/man/man1 /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/etc/bash_completion.d install --strip-program=true bin/QTLtools /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/bin install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -m 755 scripts/qtltools_runFDR_atrans.R scripts/qtltools_plotTrans.R scripts/qtltools_runFDR_ftrans.R scripts/qtltools_runFDR_cis.R /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/bin install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -m 644 doc/QTLtools-gwas.1 doc/QTLtools-bamstat.1 doc/QTLtools-pca.1 doc/QTLtools-cis.1 doc/QTLtools-quan.1 doc/QTLtools-fdensity.1 doc/QTLtools-rtc.1 doc/QTLtools-trans.1 doc/QTLtools-mbv.1 doc/QTLtools-rep.1 doc/QTLtools-fenrich.1 doc/QTLtools-extract.1 doc/QTLtools.1 doc/QTLtools-correct.1 doc/QTLtools-rtc-union.1 doc/QTLtools-ase.1 /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/usr/local/share/man/man1 install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -m 644 doc/QTLtools_bash_autocomplete.bash /build/reproducible-path/qtltools-1.3.1+dfsg/debian/tmp/etc/bash_completion.d install: WARNING: ignoring --strip-program option as -s option was not specified make[1]: Leaving directory '/build/reproducible-path/qtltools-1.3.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/qtltools-1.3.1+dfsg' cd debian/upstream.example && find -type f | LC_ALL=C sort | grep -v examples.tar.xz | \ tar -T - --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner -Jcvf examples.tar.xz ./genes.50percent.chr22.bed.gz ./genes.50percent.chr22.bed.gz.tbi ./genes.covariates.pc50.txt.gz ./genes.simulated.chr22.bed.gz ./genes.simulated.chr22.bed.gz.tbi ./genotypes.chr22.vcf.gz ./genotypes.chr22.vcf.gz.tbi dh_install make[1]: Leaving directory '/build/reproducible-path/qtltools-1.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/qtltools/usr/bin/QTLtools was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'qtltools' in '../qtltools_1.3.1+dfsg-4_arm64.deb'. dpkg-deb: building package 'qtltools-dbgsym' in '../qtltools-dbgsym_1.3.1+dfsg-4_arm64.deb'. dpkg-deb: building package 'qtltools-example' in '../qtltools-example_1.3.1+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../qtltools_1.3.1+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../qtltools_1.3.1+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2250399/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2250399/tmp/hooks/B01_cleanup finished 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/2250399 and its subdirectories I: Current time: Sun Apr 28 02:30:35 +14 2024 I: pbuilder-time-stamp: 1714221035