Mon Jun 15 06:01:37 UTC 2020 I: starting to build gemma/buster/armhf on jenkins on '2020-06-15 06:01'
Mon Jun 15 06:01:37 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_43/2466/console.log
Mon Jun 15 06:01:37 UTC 2020 I: Downloading source for buster/gemma=0.98.1+dfsg-1
--2020-06-15 06:01:37-- http://deb.debian.org/debian/pool/main/g/gemma/gemma_0.98.1+dfsg-1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2107 (2.1K)
Saving to: ‘gemma_0.98.1+dfsg-1.dsc’
0K .. 100% 15.6M=0s
2020-06-15 06:01:37 (15.6 MB/s) - ‘gemma_0.98.1+dfsg-1.dsc’ saved [2107/2107]
Mon Jun 15 06:01:37 UTC 2020 I: gemma_0.98.1+dfsg-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: gemma
Binary: gemma, gemma-doc
Architecture: any all
Version: 0.98.1+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Homepage: http://www.xzlab.org/software.html
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/gemma
Vcs-Git: https://salsa.debian.org/med-team/gemma.git
Testsuite: autopkgtest
Build-Depends: debhelper (>= 11~), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2
Package-List:
gemma deb science optional arch=any
gemma-doc deb doc optional arch=all
Checksums-Sha1:
cfaed159901aea7d455cf099584e250b58df7199 42613432 gemma_0.98.1+dfsg.orig.tar.xz
c985aeaf45d8e1d053e65d2d34abed71d1872ffe 4924 gemma_0.98.1+dfsg-1.debian.tar.xz
Checksums-Sha256:
da205d973dc0254a6a8d89eb47531d7ce93d2bd2c86c957e1d54ec0b711755d5 42613432 gemma_0.98.1+dfsg.orig.tar.xz
0b367ad85cddd5a5cae82caa9c122a0c95997ffb7fd16d6e411bf5ed7ef41e22 4924 gemma_0.98.1+dfsg-1.debian.tar.xz
Files:
db39fcee39851dd1c8e1f0201273eae4 42613432 gemma_0.98.1+dfsg.orig.tar.xz
b2f276fc8cd3b0f97cb5aba8a47e72fb 4924 gemma_0.98.1+dfsg-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=Bidc
-----END PGP SIGNATURE-----
Mon Jun 15 06:01:37 UTC 2020 I: Checking whether the package is not for us
Mon Jun 15 06:01:37 UTC 2020 I: Starting 1st build on remote node cbxi4b-armhf-rb.debian.net.
Mon Jun 15 06:01:37 UTC 2020 I: Preparing to do remote build '1' on cbxi4b-armhf-rb.debian.net.
Mon Jun 15 10:12:04 UTC 2020 I: Deleting $TMPDIR on cbxi4b-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 14 18:01:51 -12 2020
I: pbuilder-time-stamp: 1592200911
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz]
I: copying local configuration
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [gemma_0.98.1+dfsg-1.dsc]
I: copying [./gemma_0.98.1+dfsg.orig.tar.xz]
I: copying [./gemma_0.98.1+dfsg-1.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Dec 18 03:38:49 2018 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gemma_0.98.1+dfsg-1.dsc
dpkg-source: info: extracting gemma in gemma-0.98.1+dfsg
dpkg-source: info: unpacking gemma_0.98.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking gemma_0.98.1+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying Reproducible_builds.patch
dpkg-source: info: applying no-lquadmath.patch
dpkg-source: info: applying Makefile.patch
I: using fakeroot in build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/23038/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3'
DISTRIBUTION=''
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='84f22f34245c4bcbba759553ff6e406b'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='23038'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.objXwtn2CU/pbuilderrc_ha9y --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.objXwtn2CU/b1 --logfile b1/build.log gemma_0.98.1+dfsg-1.dsc'
SUDO_GID='116'
SUDO_UID='112'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:8000/'
I: uname -a
Linux cbxi4b 4.19.0-9-armmp #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux
I: ls -l /bin
total 3328
-rwxr-xr-x 1 root root 767656 Apr 17 2019 bash
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2
-rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore
-rwxr-xr-x 1 root root 22432 Feb 28 2019 cat
-rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp
-rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod
-rwxr-xr-x 1 root root 42972 Feb 28 2019 chown
-rwxr-xr-x 1 root root 88376 Feb 28 2019 cp
-rwxr-xr-x 1 root root 75516 Jan 17 2019 dash
-rwxr-xr-x 1 root root 71648 Feb 28 2019 date
-rwxr-xr-x 1 root root 51212 Feb 28 2019 dd
-rwxr-xr-x 1 root root 55672 Feb 28 2019 df
-rwxr-xr-x 1 root root 88444 Feb 28 2019 dir
-rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg
lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname
-rwxr-xr-x 1 root root 22364 Feb 28 2019 echo
-rwxr-xr-x 1 root root 28 Jan 7 2019 egrep
-rwxr-xr-x 1 root root 18260 Feb 28 2019 false
-rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep
-rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt
-rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount
-rwxr-xr-x 1 root root 124508 Jan 7 2019 grep
-rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip
-rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe
-rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip
-rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname
-rwxr-xr-x 1 root root 43044 Feb 28 2019 ln
-rwxr-xr-x 1 root root 34932 Jul 26 2018 login
-rwxr-xr-x 1 root root 88444 Feb 28 2019 ls
-rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk
-rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir
-rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod
-rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp
-rwxr-xr-x 1 root root 26024 Jan 9 2019 more
-rwsr-xr-x 1 root root 34268 Jan 9 2019 mount
-rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint
-rwxr-xr-x 1 root root 84284 Feb 28 2019 mv
lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd
lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash
-rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink
-rwxr-xr-x 1 root root 42968 Feb 28 2019 rm
-rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir
-rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts
-rwxr-xr-x 1 root root 76012 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Jun 12 20:27 sh -> dash
-rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep
-rwxr-xr-x 1 root root 51124 Feb 28 2019 stty
-rwsr-xr-x 1 root root 42472 Jan 9 2019 su
-rwxr-xr-x 1 root root 22392 Feb 28 2019 sync
-rwxr-xr-x 1 root root 283324 Apr 23 2019 tar
-rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile
-rwxr-xr-x 1 root root 63464 Feb 28 2019 touch
-rwxr-xr-x 1 root root 18260 Feb 28 2019 true
-rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server
-rwsr-xr-x 1 root root 21976 Jan 9 2019 umount
-rwxr-xr-x 1 root root 22380 Feb 28 2019 uname
-rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress
-rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir
-rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl
-rwxr-xr-x 1 root root 946 Jan 21 2019 which
lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat
-rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp
-rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff
-rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep
-rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep
-rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce
-rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep
-rwxr-xr-x 1 root root 2205 Jan 5 2019 zless
-rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore
-rwxr-xr-x 1 root root 4552 Jan 5 2019 znew
I: user script /srv/workspace/pbuilder/23038/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: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper (>= 11~), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 18932 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however:
Package debhelper is not installed.
pbuilder-satisfydepends-dummy depends on gfortran; however:
Package gfortran is not installed.
pbuilder-satisfydepends-dummy depends on libopenblas-dev; however:
Package libopenblas-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 zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on catch; however:
Package catch is not installed.
pbuilder-satisfydepends-dummy depends on shunit2; however:
Package shunit2 is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} catch{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libeigen3-dev{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libopenblas-base{a} libopenblas-dev{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} sensible-utils{a} shunit2{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs
0 packages upgraded, 47 newly installed, 0 to remove and 0 not upgraded.
Need to get 33.0 MB of archives. After unpacking 119 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB]
Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB]
Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB]
Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB]
Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB]
Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB]
Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB]
Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB]
Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB]
Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB]
Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB]
Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB]
Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB]
Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get: 18 http://deb.debian.org/debian buster/main armhf catch armhf 1.12.1-1 [114 kB]
Get: 19 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB]
Get: 20 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB]
Get: 21 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get: 22 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get: 23 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get: 24 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get: 25 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB]
Get: 26 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB]
Get: 27 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB]
Get: 28 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB]
Get: 29 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB]
Get: 30 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB]
Get: 31 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB]
Get: 32 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 33 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB]
Get: 34 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB]
Get: 35 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB]
Get: 36 http://deb.debian.org/debian buster/main armhf libgfortran-8-dev armhf 8.3.0-6 [260 kB]
Get: 37 http://deb.debian.org/debian buster/main armhf gfortran-8 armhf 8.3.0-6 [7219 kB]
Get: 38 http://deb.debian.org/debian buster/main armhf gfortran armhf 4:8.3.0-1 [1424 B]
Get: 39 http://deb.debian.org/debian buster/main armhf pkg-config armhf 0.29-6 [60.7 kB]
Get: 40 http://deb.debian.org/debian buster/main armhf libeigen3-dev all 3.3.7-1 [850 kB]
Get: 41 http://deb.debian.org/debian buster/main armhf libgslcblas0 armhf 2.5+dfsg-6 [79.1 kB]
Get: 42 http://deb.debian.org/debian buster/main armhf libgsl23 armhf 2.5+dfsg-6 [718 kB]
Get: 43 http://deb.debian.org/debian buster/main armhf libgsl-dev armhf 2.5+dfsg-6 [903 kB]
Get: 44 http://deb.debian.org/debian buster/main armhf libopenblas-base armhf 0.3.5+ds-3 [2116 kB]
Get: 45 http://deb.debian.org/debian buster/main armhf libopenblas-dev armhf 0.3.5+ds-3 [1992 kB]
Get: 46 http://deb.debian.org/debian buster/main armhf shunit2 all 2.1.6-1.1 [39.3 kB]
Get: 47 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB]
Fetched 33.0 MB in 7s (4721 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libbsd0:armhf.
(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 ... 18932 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ...
Unpacking libbsd0:armhf (0.9.1-2) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ...
Unpacking bsdmainutils (11.1.2+b1) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.6-3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ...
Unpacking groff-base (1.22.4-3) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ...
Unpacking man-db (2.8.5-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ...
Unpacking sensible-utils (0.0.12) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ...
Unpacking libmagic-mgc (1:5.35-4+deb10u1) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ...
Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ...
Selecting previously unselected package file.
Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.deb ...
Unpacking file (1:5.35-4+deb10u1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../10-gettext-base_0.19.8.1-9_armhf.deb ...
Unpacking gettext-base (0.19.8.1-9) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../12-m4_1.4.18-2_armhf.deb ...
Unpacking m4 (1.4.18-2) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../13-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ...
Unpacking automake (1:1.16.1-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ...
Unpacking autopoint (0.19.8.1-9) ...
Selecting previously unselected package catch.
Preparing to unpack .../17-catch_1.12.1-1_armhf.deb ...
Unpacking catch (1.12.1-1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../18-libtool_2.4.6-9_all.deb ...
Unpacking libtool (2.4.6-9) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../19-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../20-libarchive-zip-perl_1.64-1_all.deb ...
Unpacking libarchive-zip-perl (1.64-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.1.2-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.1.2-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../23-libelf1_0.176-1.1_armhf.deb ...
Unpacking libelf1:armhf (0.176-1.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.12-3_armhf.deb ...
Unpacking dwz (0.12-3) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../25-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ...
Selecting previously unselected package libicu63:armhf.
Preparing to unpack .../26-libicu63_63.1-6+deb10u1_armhf.deb ...
Unpacking libicu63:armhf (63.1-6+deb10u1) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../27-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../28-libcroco3_0.6.12-3_armhf.deb ...
Unpacking libcroco3:armhf (0.6.12-3) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../29-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ...
Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../30-gettext_0.19.8.1-9_armhf.deb ...
Unpacking gettext (0.19.8.1-9) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../31-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../32-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../33-debhelper_12.1.1_all.deb ...
Unpacking debhelper (12.1.1) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../34-libgfortran5_8.3.0-6_armhf.deb ...
Unpacking libgfortran5:armhf (8.3.0-6) ...
Selecting previously unselected package libgfortran-8-dev:armhf.
Preparing to unpack .../35-libgfortran-8-dev_8.3.0-6_armhf.deb ...
Unpacking libgfortran-8-dev:armhf (8.3.0-6) ...
Selecting previously unselected package gfortran-8.
Preparing to unpack .../36-gfortran-8_8.3.0-6_armhf.deb ...
Unpacking gfortran-8 (8.3.0-6) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../37-gfortran_4%3a8.3.0-1_armhf.deb ...
Unpacking gfortran (4:8.3.0-1) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../38-pkg-config_0.29-6_armhf.deb ...
Unpacking pkg-config (0.29-6) ...
Selecting previously unselected package libeigen3-dev.
Preparing to unpack .../39-libeigen3-dev_3.3.7-1_all.deb ...
Unpacking libeigen3-dev (3.3.7-1) ...
Selecting previously unselected package libgslcblas0:armhf.
Preparing to unpack .../40-libgslcblas0_2.5+dfsg-6_armhf.deb ...
Unpacking libgslcblas0:armhf (2.5+dfsg-6) ...
Selecting previously unselected package libgsl23:armhf.
Preparing to unpack .../41-libgsl23_2.5+dfsg-6_armhf.deb ...
Unpacking libgsl23:armhf (2.5+dfsg-6) ...
Selecting previously unselected package libgsl-dev.
Preparing to unpack .../42-libgsl-dev_2.5+dfsg-6_armhf.deb ...
Unpacking libgsl-dev (2.5+dfsg-6) ...
Selecting previously unselected package libopenblas-base:armhf.
Preparing to unpack .../43-libopenblas-base_0.3.5+ds-3_armhf.deb ...
Unpacking libopenblas-base:armhf (0.3.5+ds-3) ...
Selecting previously unselected package libopenblas-dev:armhf.
Preparing to unpack .../44-libopenblas-dev_0.3.5+ds-3_armhf.deb ...
Unpacking libopenblas-dev:armhf (0.3.5+ds-3) ...
Selecting previously unselected package shunit2.
Preparing to unpack .../45-shunit2_2.1.6-1.1_all.deb ...
Unpacking shunit2 (2.1.6-1.1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../46-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up shunit2 (2.1.6-1.1) ...
Setting up libgslcblas0:armhf (2.5+dfsg-6) ...
Setting up libmagic-mgc (1:5.35-4+deb10u1) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ...
No schema files found: doing nothing.
Setting up libmagic1:armhf (1:5.35-4+deb10u1) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.35-4+deb10u1) ...
Setting up libicu63:armhf (63.1-6+deb10u1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libgsl23:armhf (2.5+dfsg-6) ...
Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up pkg-config (0.29-6) ...
Setting up libgfortran5:armhf (8.3.0-6) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up catch (1.12.1-1) ...
Setting up libbsd0:armhf (0.9.1-2) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ...
Setting up libfile-stripnondeterminism-perl (1.1.2-1) ...
Setting up libopenblas-base:armhf (0.3.5+ds-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openblas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openblas/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libgfortran-8-dev:armhf (8.3.0-6) ...
Setting up libgsl-dev (2.5+dfsg-6) ...
Setting up libtool (2.4.6-9) ...
Setting up gfortran-8 (8.3.0-6) ...
Setting up m4 (1.4.18-2) ...
Setting up gfortran (4:8.3.0-1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libopenblas-dev:armhf (0.3.5+ds-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openblas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openblas/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up bsdmainutils (11.1.2+b1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libeigen3-dev (3.3.7-1) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.12-3) ...
Setting up groff-base (1.22.4-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (12.1.1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.1.2-1) ...
Processing triggers for libc-bin (2.28-10) ...
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
Reading package lists...
Building dependency tree...
Reading state information...
fakeroot is already the newest version (1.23-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: Running cd /build/gemma-0.98.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
dpkg-buildpackage: info: source package gemma
dpkg-buildpackage: info: source version 0.98.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j3 clean
make[1]: Entering directory '/build/gemma-0.98.1+dfsg'
rm -vf ./src/*.o
rm -vf ./src/*~
rm -vf ./test/src/*.o
rm -vf ./bin/gemma
rm -vf ./bin/unittests-gemma
make[1]: Leaving directory '/build/gemma-0.98.1+dfsg'
debian/rules override_dh_clean
make[1]: Entering directory '/build/gemma-0.98.1+dfsg'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/gemma.substvars debian/gemma-doc.substvars debian/files
rm -fr -- debian/gemma/ debian/tmp/ debian/gemma-doc/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
rm -f *.log
rm -rf test/output/
rm -f bin/gemma
make[1]: Leaving directory '/build/gemma-0.98.1+dfsg'
debian/rules build
dh build
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j3 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/gemma-0.98.1+dfsg'
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmm.o src/bslmm.cpp
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmmdap.o src/bslmmdap.cpp
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/debug.o src/debug.cpp
src/debug.cpp:60:44: warning: extra ';' [-Wpedantic]
bool is_debug_mode() { return debug_mode; };
^
src/debug.cpp:61:54: warning: extra ';' [-Wpedantic]
bool is_debug_data_mode() { return debug_data_mode; };
^
src/debug.cpp:62:49: warning: extra ';' [-Wpedantic]
bool is_no_check_mode() { return !debug_check; };
^
src/debug.cpp:63:45: warning: extra ';' [-Wpedantic]
bool is_check_mode() { return debug_check; };
^
src/debug.cpp:64:53: warning: extra ';' [-Wpedantic]
bool is_fpe_check_mode() { return debug_fpe_check; };
^
src/debug.cpp:65:47: warning: extra ';' [-Wpedantic]
bool is_strict_mode() { return debug_strict; };
^
src/debug.cpp:66:45: warning: extra ';' [-Wpedantic]
bool is_quiet_mode() { return debug_quiet; };
^
src/debug.cpp:67:59: warning: extra ';' [-Wpedantic]
bool is_issue(uint issue) { return issue == debug_issue; };
^
src/debug.cpp:68:47: warning: extra ';' [-Wpedantic]
bool is_legacy_mode() { return debug_legacy; };
^
In file included from /usr/include/c++/8/map:60,
from src/param.h:27,
from src/bslmmdap.h:22,
from src/bslmmdap.cpp:41:
/usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from src/bslmm.cpp:23:
/usr/include/c++/8/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >]':
/usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__rotate(_RandomAccessIterator __first,
^~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/eigenlib.o src/eigenlib.cpp
In file included from /usr/include/c++/8/vector:69,
from src/param.h:29,
from src/bslmmdap.h:22,
from src/bslmmdap.cpp:41:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/param.h:29,
from src/bslmmdap.h:22,
from src/bslmmdap.cpp:41:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BSLMMDAP::DAP_CalcBF(const gsl_matrix*, const gsl_matrix*, const gsl_vector*, const gsl_vector*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from src/param.h:27,
from src/bslmmdap.h:22,
from src/bslmmdap.cpp:41:
/usr/include/c++/8/bits/stl_map.h: In function 'void single_ct_regression(const gsl_matrix_int*, const gsl_vector_int*, const gsl_vector*, gsl_vector*, gsl_vector*)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from src/bslmm.h:25,
from src/bslmm.cpp:41:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<double, double>}; _Tp = std::pair<double, double>; _Alloc = std::allocator<std::pair<double, double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<double, double> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:62,
from /usr/include/c++/8/algorithm:62,
from src/bslmm.cpp:23:
/usr/include/c++/8/bits/stl_tempbuf.h: In constructor 'std::_Temporary_buffer<_ForwardIterator, _Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Tp = std::pair<unsigned int, double>]':
/usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
_Temporary_buffer<_ForwardIterator, _Tp>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tempbuf.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from src/bslmm.h:25,
from src/bslmm.cpp:41:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/param.h:29,
from src/bslmmdap.h:22,
from src/bslmmdap.cpp:41:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BSLMMDAP::DAP_EstimateHyper(size_t, size_t, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::vector<std::vector<double> > >&, gsl_matrix*, gsl_matrix_int*, gsl_vector_int*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from src/bslmm.cpp:23:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__merge_without_buffer(_BidirectionalIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
return std::__rotate(__first, __middle, __last,
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__merge_without_buffer(__first, __first_cut, __new_middle,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len11, __len22, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__merge_without_buffer(__new_middle, __second_cut, __last,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len1 - __len11, __len2 - __len22, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__inplace_stable_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__inplace_stable_sort(__first, __middle, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__inplace_stable_sort(__middle, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__merge_without_buffer(__first, __middle, __last,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
__middle - __first,
~~~~~~~~~~~~~~~~~~~
__last - __middle,
~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__move_merge_adaptive_backward(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator2, _BidirectionalIterator2, _BidirectionalIterator3, _Compare) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _BidirectionalIterator2 = std::pair<unsigned int, double>*; _BidirectionalIterator3 = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__move_merge_adaptive_backward(_BidirectionalIterator1 __first1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _BidirectionalIterator2 = std::pair<unsigned int, double>*; _Distance = int]':
/usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__rotate_adaptive(_BidirectionalIterator1 __first,
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
return std::__rotate(__first, __middle, __last,
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Distance = int; _Pointer = std::pair<unsigned int, double>*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__merge_adaptive(_BidirectionalIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2431:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__move_merge_adaptive_backward(__first, __middle, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_end, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2431:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2460:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
= std::__rotate_adaptive(__first_cut, __middle, __second_cut,
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len1 - __len11, __len22, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_size);
~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2463:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__merge_adaptive(__first, __first_cut, __new_middle, __len11,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len22, __buffer, __buffer_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2465:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__merge_adaptive(__new_middle, __second_cut, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__len1 - __len11,
~~~~~~~~~~~~~~~~~
__len2 - __len22, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _OutputIterator = std::pair<unsigned int, double>*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__move_merge(_InputIterator __first1, _InputIterator __last1,
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = std::pair<unsigned int, double>*; _OutputIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Pointer = std::pair<unsigned int, double>*; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__merge_sort_with_buffer(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2695:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + __chunk_size, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__result = std::__move_merge(__first, __first + __step_size,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__first + __step_size,
~~~~~~~~~~~~~~~~~~~~~~
__first + __two_step,
~~~~~~~~~~~~~~~~~~~~~
__result, __comp);
~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__move_merge(__first, __first + __step_size,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__first + __step_size, __last, __result, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__result = std::__move_merge(__first, __first + __step_size,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__first + __step_size,
~~~~~~~~~~~~~~~~~~~~~~
__first + __two_step,
~~~~~~~~~~~~~~~~~~~~~
__result, __comp);
~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__move_merge(__first, __first + __step_size,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__first + __step_size, __last, __result, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Pointer = std::pair<unsigned int, double>*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
__stable_sort_adaptive(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:2741:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__stable_sort_adaptive(__first, __middle, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2743:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__stable_sort_adaptive(__middle, __last, __buffer,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2748:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2751:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__merge_adaptive(__first, __middle, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
_Distance(__middle - __first),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_Distance(__last - __middle),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__buffer, __buffer_size,
~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/bslmm.h:25,
from src/bslmm.cpp:41:
/usr/include/c++/8/bits/vector.tcc: In member function 'void BSLMM::MCMC(const gsl_matrix*, const gsl_matrix*, const gsl_vector*, const gsl_vector*, const gsl_vector*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from src/bslmm.cpp:23:
/usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
_TmpBuf __buf(__first, __last);
^~~~~
/usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__inplace_stable_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__stable_sort_adaptive(__first, __last, __buf.begin(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_DistanceType(__buf.size()), __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/bslmm.h:25,
from src/bslmm.cpp:41:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void BSLMM::MCMC(const gsl_matrix*, const gsl_vector*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from src/bslmm.cpp:23:
/usr/include/c++/8/bits/stl_algo.h:5001:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
_TmpBuf __buf(__first, __last);
^~~~~
/usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__inplace_stable_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
std::__stable_sort_adaptive(__first, __last, __buf.begin(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_DistanceType(__buf.size()), __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/fastblas.o src/fastblas.cpp
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma.o src/gemma.cpp
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma_io.o src/gemma_io.cpp
In file included from /usr/include/c++/8/vector:69,
from src/bslmm.h:25,
from src/gemma.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from src/bslmm.h:24,
from src/gemma.cpp:49:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/bslmm.h:25,
from src/gemma.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void GEMMA::BatchRun(PARAM&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/bslmm.h:25,
from src/gemma.cpp:49:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from src/bslmm.h:24,
from src/gemma.cpp:49:
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SNPINFO&}; _Tp = SNPINFO; _Alloc = std::allocator<SNPINFO>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<SNPINFO>::iterator' {aka '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/stl_vector.h: In function 'bool ReadFile_bim(const string&, std::vector<SNPINFO>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'bool ReadFile_cvt(const string&, std::vector<int>&, std::vector<std::vector<double> >&, size_t&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'bool ReadFile_column(const string&, std::vector<int>&, std::vector<double>&, const int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/vector.tcc: In function 'bool ReadFile_gene(const string&, std::vector<double>&, std::vector<SNPINFO>&, size_t&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/vector.tcc: In function 'void Calcq(size_t, const std::vector<unsigned int>&, const std::vector<unsigned int>&, const std::vector<double>&, const std::vector<double>&, gsl_matrix*, gsl_vector*, gsl_vector*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/gzstream.o src/gzstream.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'void ReadFile_beta(const string&, const std::map<std::__cxx11::basic_string<char>, unsigned int>&, const std::map<std::__cxx11::basic_string<char>, double>&, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<double>&, std::vector<double>&, size_t&, size_t&, size_t&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/lapack.o src/lapack.cpp
In file included from /usr/include/c++/8/map:60,
from src/gemma_io.cpp:29:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from src/gemma_io.cpp:29:
/usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/stl_vector.h: In function 'bool ReadFile_geno(const string&, const std::set<std::__cxx11::basic_string<char> >&, const gsl_matrix*, std::vector<int>&, std::vector<int>&, const double&, const double&, const double&, const double&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, long int>&, std::map<std::__cxx11::basic_string<char>, double>&, std::vector<SNPINFO>&, size_t&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from src/gemma_io.cpp:29:
/usr/include/c++/8/bits/stl_map.h: In function 'bool ReadFile_wsnp(const string&, std::map<std::__cxx11::basic_string<char>, double>&)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/ldr.o src/ldr.cpp
/usr/include/c++/8/bits/stl_map.h: In function 'bool ReadFile_anno(const string&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, long int>&, std::map<std::__cxx11::basic_string<char>, double>&)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/regex:51,
from src/gemma_io.cpp:30:
/usr/include/c++/8/bits/vector.tcc: In function 'bool ReadFile_pheno(const string&, std::vector<std::vector<int> >&, std::vector<std::vector<double> >&, const std::vector<unsigned int>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/lm.o src/lm.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'bool ReadFile_fam(const string&, std::vector<std::vector<int> >&, std::vector<std::vector<double> >&, std::map<std::__cxx11::basic_string<char>, int>&, const std::vector<unsigned int>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/lmm.o src/lmm.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'bool ReadFile_wsnp(const string&, size_t, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
src/lmm.cpp: In function 'void CalcPab(size_t, size_t, const gsl_vector*, const gsl_matrix*, const gsl_vector*, gsl_matrix*)':
src/lmm.cpp:281:10: warning: unused variable 'n_index' [-Wunused-variable]
size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; // result size
^~~~~~~
src/lmm.cpp:282:8: warning: unused variable 'ni_test' [-Wunused-variable]
auto ni_test = Uab->size1; // inds
^~~~~~~
src/lmm.cpp: In function 'double LogL_dev1(double, void*)':
src/lmm.cpp:596:8: warning: unused variable 'Uab' [-Wunused-variable]
auto Uab = p->Uab;
^~~
src/lmm.cpp:597:8: warning: unused variable 'ab' [-Wunused-variable]
auto ab = p->ab;
^~
In file included from /usr/include/c++/8/vector:69,
from src/lapack.h:22,
from src/lm.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SUMSTAT&}; _Tp = SUMSTAT; _Alloc = std::allocator<SUMSTAT>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<SUMSTAT>::iterator' {aka '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/lapack.h:22,
from src/lm.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void LM::AnalyzePlink(const gsl_matrix*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void LM::AnalyzeGene(const gsl_matrix*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void LM::AnalyzeBimbam(const gsl_matrix*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/lapack.h:22,
from src/lm.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<unsigned int, double>}; _Tp = std::pair<unsigned int, double>; _Alloc = std::allocator<std::pair<unsigned int, double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<unsigned int, double> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void MatrixCalcLmLR(const gsl_matrix*, const gsl_vector*, std::vector<std::pair<unsigned int, double> >&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/logistic.o src/logistic.cpp
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/main.o src/main.cpp
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/regex:51,
from src/lmm.cpp:31:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SUMSTAT&}; _Tp = SUMSTAT; _Alloc = std::allocator<SUMSTAT>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<SUMSTAT>::iterator' {aka '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<unsigned int, double>}; _Tp = std::pair<unsigned int, double>; _Alloc = std::allocator<std::pair<unsigned int, double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<unsigned int, double> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<double, double>}; _Tp = std::pair<double, double>; _Alloc = std::allocator<std::pair<double, double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<double, double> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function 'void CalcLambda(char, FUNC_PARAM&, double, double, size_t, double&, double&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void CalcLambda(char, FUNC_PARAM&, double, double, size_t, double&, double&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void CalcLambda(char, FUNC_PARAM&, double, double, size_t, double&, double&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, double>*, std::vector<std::pair<double, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/regex:51,
from src/lmm.cpp:31:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void LMM::AnalyzeGene(const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In lambda function:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'LMM::Analyze(std::function<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<double, std::allocator<double> > >(unsigned int)>&, const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, std::set<std::__cxx11::basic_string<char> >)::<lambda(size_t)>':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void LMM::AnalyzePlink(const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, std::set<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/mathfunc.o src/mathfunc.cpp
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/regex:51,
from src/lmm.cpp:31:
/usr/include/c++/8/bits/vector.tcc: In function 'void MatrixCalcLR(const gsl_matrix*, const gsl_matrix*, const gsl_vector*, const gsl_vector*, double, double, size_t, std::vector<std::pair<unsigned int, double> >&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/regex:51,
from src/lmm.cpp:31:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void LMM::AnalyzeBimbamGXE(const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void LMM::AnalyzePlinkGXE(const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_vector*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SUMSTAT*, std::vector<SUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
src/mathfunc.cpp: In function 'bool isMatrixIllConditioned(const gsl_vector*, double)':
src/mathfunc.cpp:390:8: warning: unused variable 'absmin' [-Wunused-variable]
auto absmin = get<0>(t);
^~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/mvlmm.o src/mvlmm.cpp
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/regex:51,
from src/mathfunc.cpp:29:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void StandardizeMatrix(gsl_matrix*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/gemma_io.h:28,
from src/mvlmm.cpp:42:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MPHSUMSTAT&}; _Tp = MPHSUMSTAT; _Alloc = std::allocator<MPHSUMSTAT>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<MPHSUMSTAT>::iterator' {aka '__gnu_cxx::__normal_iterator<MPHSUMSTAT*, std::vector<MPHSUMSTAT> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/gemma_io.h:28,
from src/mvlmm.cpp:42:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MPHSUMSTAT; _Alloc = std::allocator<MPHSUMSTAT>]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MPHSUMSTAT*, std::vector<MPHSUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/gemma_io.h:28,
from src/mvlmm.cpp:42:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/gemma_io.h:28,
from src/mvlmm.cpp:42:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void MVLMM::AnalyzePlink(const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_matrix*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MPHSUMSTAT*, std::vector<MPHSUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/param.o src/param.cpp
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/prdt.o src/prdt.cpp
In file included from /usr/include/c++/8/vector:69,
from src/gemma_io.h:28,
from src/mvlmm.cpp:42:
/usr/include/c++/8/bits/vector.tcc: In member function 'void MVLMM::AnalyzeBimbam(const gsl_matrix*, const gsl_vector*, const gsl_matrix*, const gsl_matrix*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/gemma_io.h:28,
from src/mvlmm.cpp:42:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MPHSUMSTAT*, std::vector<MPHSUMSTAT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from src/gemma_io.h:27,
from src/prdt.cpp:35:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from src/gemma_io.h:27,
from src/prdt.cpp:35:
/usr/include/c++/8/bits/stl_map.h: In member function 'void PRDT::AnalyzePlink(gsl_vector*)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/varcov.o src/varcov.cpp
/usr/include/c++/8/bits/stl_map.h: In member function 'void PRDT::AnalyzeBimbam(gsl_vector*)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o src/vc.o src/vc.cpp
In file included from /usr/include/c++/8/vector:69,
from src/varcov.cpp:31:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void Calc_Cor(std::vector<std::vector<double> >&, std::vector<double>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/param.h:29,
from src/gemma.h:24,
from src/param.cpp:38:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SNPINFO&}; _Tp = SNPINFO; _Alloc = std::allocator<SNPINFO>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<SNPINFO>::iterator' {aka '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<SNPINFO>::iterator' {aka '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function 'void JackknifeAKtoS(const gsl_matrix*, const gsl_matrix*, const gsl_matrix*, gsl_matrix*, gsl_matrix*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void VARCOV::AnalyzePlink()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/varcov.cpp:31:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void PARAM::CheckCvt()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void PARAM::ProcessCvtPhen()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/varcov.cpp:31:
/usr/include/c++/8/bits/vector.tcc: In member function 'void VARCOV::AnalyzeBimbam()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/varcov.cpp:31:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from src/param.h:27,
from src/gemma.h:24,
from src/param.cpp:38:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from src/param.h:27,
from src/gemma.h:24,
from src/param.cpp:38:
/usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from src/param.h:29,
from src/gemma.h:24,
from src/param.cpp:38:
/usr/include/c++/8/bits/vector.tcc: In member function 'void PARAM::UpdateWeight(size_t, const std::map<std::__cxx11::basic_string<char>, double>&, size_t, const gsl_vector*, std::map<std::__cxx11::basic_string<char>, double>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/vc.cpp:33:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/vc.cpp:33:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'void CalcVCss(const gsl_matrix*, const gsl_matrix*, const gsl_matrix*, const gsl_vector*, const gsl_vector*, double, std::vector<double>&, std::vector<double>&, double&, double&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:63,
from src/param.h:29,
from src/gemma.h:24,
from src/param.cpp:38:
/usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >; _ForwardIterator = SNPINFO*; bool _TrivialValueTypes = false]':
/usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_uninitialized.h: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = SNPINFO; _Alloc = std::allocator<SNPINFO>]':
/usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
return std::__uninitialized_copy<__is_trivial(_ValueType1)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& __is_trivial(_ValueType2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&& __assignable>::
~~~~~~~~~~~~~~~~~~
__uninit_copy(__first, __last, __result);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/param.h:29,
from src/gemma.h:24,
from src/param.cpp:38:
/usr/include/c++/8/bits/vector.tcc: In member function 'void PARAM::ObtainWeight(const std::set<std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, double>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from src/vc.cpp:33:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from src/vc.cpp:33:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void VC::CalcVChe(const gsl_matrix*, const gsl_matrix*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void VC::CalcVCreml(bool, const gsl_matrix*, const gsl_matrix*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void VC::CalcVCacl(const gsl_matrix*, const gsl_matrix*, const gsl_vector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'void CalcCIss(const gsl_matrix*, const gsl_matrix*, const gsl_matrix*, const gsl_matrix*, const gsl_matrix*, const gsl_vector*, const gsl_vector*, const gsl_vector*, const std::vector<unsigned int>&, const std::vector<double>&, std::vector<double>&, double&, double&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from src/vc.cpp:28:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from src/vc.cpp:28:
/usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from src/vc.cpp:33:
/usr/include/c++/8/bits/vector.tcc: In function 'void ReadFile_beta(bool, const string&, const std::map<std::__cxx11::basic_string<char>, unsigned int>&, std::map<std::__cxx11::basic_string<char>, unsigned int>&, std::map<std::__cxx11::basic_string<char>, double>&, std::map<std::__cxx11::basic_string<char>, unsigned int>&, gsl_vector*, gsl_vector*, gsl_vector*, size_t&, size_t&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from src/vc.cpp:28:
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from src/vc.cpp:33:
/usr/include/c++/8/bits/vector.tcc: In function 'void ReadFile_cor(const string&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<unsigned int>&, const std::vector<double>&, const std::vector<double>&, const std::map<std::__cxx11::basic_string<char>, unsigned int>&, const std::map<std::__cxx11::basic_string<char>, unsigned int>&, const std::map<std::__cxx11::basic_string<char>, double>&, const std::map<std::__cxx11::basic_string<char>, unsigned int>&, size_t, const double&, const double&, const double&, gsl_matrix*, gsl_matrix*, gsl_vector*, size_t&, size_t&, size_t&, size_t&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc src/bslmm.o src/bslmmdap.o src/debug.o src/eigenlib.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/main.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -o ./bin/gemma
make[1]: Leaving directory '/build/gemma-0.98.1+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/gemma-0.98.1+dfsg'
dh_auto_test --no-parallel
make -j1 check
make[2]: Entering directory '/build/gemma-0.98.1+dfsg'
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-main.o test/src/unittests-main.cpp
In file included from /usr/include/c++/8/vector:69,
from /usr/include/catch/catch.hpp:677,
from test/src/unittests-main.cpp:2:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator<Catch::SectionEndInfo>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<Catch::SectionEndInfo>::iterator' {aka '__gnu_cxx::__normal_iterator<Catch::SectionEndInfo*, std::vector<Catch::SectionEndInfo> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/catch/catch.hpp:677,
from test/src/unittests-main.cpp:2:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Catch::SectionEndInfo*, std::vector<Catch::SectionEndInfo> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/gemma-0.98.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-math.o test/src/unittests-math.cpp
In file included from /usr/include/c++/8/bits/stl_algobase.h:67,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/istream:38,
from /usr/include/c++/8/sstream:38,
from /usr/include/catch/catch.hpp:384,
from test/src/unittests-math.cpp:1:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector<double>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc -Og -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -isystem/usr/include/eigen3 -Icontrib/catch-1.9.7 -Isrc ./test/src/unittests-main.o ./test/src/unittests-math.o src/bslmm.o src/bslmmdap.o src/debug.o src/eigenlib.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -o ./bin/unittests-gemma
./bin/unittests-gemma
Mismatch coordinates (1,0)0:3!
This example computes real matrix C=alpha*A*B+beta*C using
Intel(R) MKL function dgemm, where A, B, and C are matrices and
alpha and beta are double precision scalars
Initializing data for matrix multiplication C=A*B for matrix
A(2000x200) and matrix B(200x1000)
Allocating memory for matrices aligned on 64-byte boundary for better
performance
Intializing matrix data
Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface
This example computes real matrix C=alpha*A*B+beta*C using
Intel(R) MKL function dgemm, where A, B, and C are matrices and
alpha and beta are double precision scalars
Initializing data for matrix multiplication C=A*B for matrix
A(2000x200) and matrix B(200x1000)
Allocating memory for matrices aligned on 64-byte boundary for better
performance
Intializing matrix data
Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface
Computations completed.
===============================================================================
All tests passed (24 assertions in 4 test cases)
rm -vf test/output/*
cd test && ./dev_test_suite.sh | tee ../dev_test.log
run system shunit2
testLinearModel
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10768
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
## total computation time = 0.74771 min
testBXDStandardRelatednessMatrixKSingularError
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
GSL ERROR: matrix is singular in lu.c at line 266 errno 1
testBXDStandardRelatednessMatrixK
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
## number of total individuals = 198
## number of analyzed individuals = 67
## number of covariates = 3
## number of phenotypes = 1
## number of total SNPs/var = 7320
## number of analyzed SNPs = 7317
Calculating Relatedness Matrix ...
0%
====== 14%
============= 27%
==================== 41%
=========================== 55%
================================== 68%
======================================== 82%
=============================================== 96%
================================================== 100%
**** INFO: Done.
testBXDLMLikelihoodRatio
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
## number of total individuals = 198
## number of analyzed individuals = 67
## number of covariates = 3
## number of phenotypes = 1
## number of total SNPs/var = 7320
## number of analyzed SNPs = 7317
0%
====== 14%
============= 27%
==================== 41%
=========================== 55%
================================== 68%
======================================== 82%
=============================================== 96%
================================================== 100%
**** INFO: Done.
testBXDLMMLikelihoodRatio
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
## number of total individuals = 198
## number of analyzed individuals = 67
## number of covariates = 3
## number of phenotypes = 1
## number of total SNPs/var = 7320
## number of analyzed SNPs = 7317
Start Eigen-Decomposition...
pve estimate =0.00100086
se(pve) =0.204165
0%
====== 14%
============= 27%
==================== 41%
=========================== 55%
================================== 68%
======================================== 82%
=============================================== 96%
================================================== 100%
================================================== 100%
**** INFO: Done.
testCenteredRelatednessMatrixissue188
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1008
## number of analyzed individuals = 876
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 2000
## number of analyzed SNPs = 1850
Calculating Relatedness Matrix ...
0%
========================= 50%
================================================== 100%
**** WARNING: K has 75 eigenvalues close to zero in src/gemma.cpp at line 1912
**** WARNING: K is ill conditioned! in src/gemma.cpp at line 1912
**** INFO: Done.
testLMMissue188
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1008
## number of analyzed individuals = 876
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 2000
## number of analyzed SNPs = 1850
**** WARNING: K has 3 eigenvalues close to zero in src/gemma.cpp at line 2588
**** WARNING: K is ill conditioned! in src/gemma.cpp at line 2588
Start Eigen-Decomposition...
**** WARNING: Matrix G has 3 eigenvalues close to zero
pve estimate =0.631857
se(pve) =0.0548406
0%
========================= 50%
================================================== 100%
**** INFO: Done.
testCenteredRelatednessMatrixKLOCO1
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** TEST MODE: trim individuals from 1940 to 400
**** TEST MODE: trim individuals from 1940 to 400
## number of total individuals = 400
## number of analyzed individuals = 247
## number of covariates = 1
## number of phenotypes = 1
## leave one chromosome out (LOCO) = 1
## number of total SNPs/var = 12226
## number of considered SNPS = 1000
## number of SNPS for K = 11182
## number of SNPS for GWAS = 1044
## number of analyzed SNPs = 889
Calculating Relatedness Matrix ...
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
## total computation time = 0.684685 min
testUnivariateLinearMixedModelLOCO1
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** TEST MODE: trim individuals from 1940 to 400
**** TEST MODE: trim individuals from 1940 to 400
## number of total individuals = 400
## number of analyzed individuals = 247
## number of covariates = 1
## number of phenotypes = 1
## leave one chromosome out (LOCO) = 1
## number of total SNPs/var = 12226
## number of considered SNPS = 1000
## number of SNPS for K = 11182
## number of SNPS for GWAS = 1044
## number of analyzed SNPs = 889
Start Eigen-Decomposition...
pve estimate =0.678775
se(pve) =0.0717914
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
================================================== 100%
**** INFO: Done.
## total computation time = 0.310882 min
testPlinkCenteredRelatednessMatrixKLOCO1
testPlinkUnivariateLinearMixedModelLOCO1
testCorrelatedPhenotypesMvLLM
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1000
## number of analyzed individuals = 1000
## number of covariates = 1
## number of phenotypes = 5
## number of total SNPs/var = 100
## number of analyzed SNPs = 100
REMLE estimate for Vg in the null model:
0.8091
0.1435 0.0660
-0.1456 -0.0664 0.1165
0.0907 0.0362 -0.0830 0.0639
-0.5533 -0.0985 0.1171 -0.0765 0.4131
se(Vg):
0.0736
0.0355 0.0299
0.0421 0.0264 0.0422
0.0444 0.0279 0.0430 0.0479
0.0516 0.0254 0.0295 0.0313 0.0389
REMLE estimate for Ve in the null model:
0.0334
0.0267 0.4502
-0.0529 -0.0883 0.6004
0.0683 0.1413 -0.6502 0.8400
-0.0128 -0.0041 -0.0706 0.0880 0.0419
se(Ve):
0.0378
0.0252 0.0329
0.0299 0.0281 0.0456
0.0332 0.0319 0.0494 0.0583
0.0266 0.0186 0.0215 0.0242 0.0208
REMLE likelihood = -3813.3258
MLE estimate for Vg in the null model:
0.8082
0.1434 0.0660
-0.1455 -0.0664 0.1165
0.0906 0.0362 -0.0830 0.0639
-0.5528 -0.0984 0.1170 -0.0764 0.4127
se(Vg):
0.0735
0.0355 0.0298
0.0420 0.0264 0.0421
0.0443 0.0278 0.0430 0.0478
0.0515 0.0254 0.0295 0.0313 0.0388
MLE estimate for Ve in the null model:
0.0334
0.0267 0.4497
-0.0529 -0.0882 0.5997
0.0682 0.1412 -0.6495 0.8391
-0.0128 -0.0040 -0.0705 0.0879 0.0418
se(Ve):
0.0378
0.0252 0.0329
0.0298 0.0281 0.0455
0.0331 0.0318 0.0493 0.0582
0.0265 0.0185 0.0215 0.0242 0.0207
MLE likelihood = -3814.3913
0%
================================================== 100%
**** INFO: Done.
Ran 12 tests.
OK
tail -n 1 dev_test.log | grep -q 'OK'
rm -vf test/output/*
removed 'test/output/BXD.cXX.txt'
removed 'test/output/BXD.log.txt'
removed 'test/output/BXD_LMM_LR.assoc.txt'
removed 'test/output/BXD_LMM_LR.log.txt'
removed 'test/output/BXD_LM_LR.assoc.txt'
removed 'test/output/BXD_LM_LR.log.txt'
removed 'test/output/corrpheno.assoc.txt'
removed 'test/output/corrpheno.log.txt'
removed 'test/output/issue188.assoc.txt'
removed 'test/output/issue188.cXX.txt'
removed 'test/output/issue188.log.txt'
removed 'test/output/mouse_hs1940_CD8_LOCO1_lmm.assoc.txt'
removed 'test/output/mouse_hs1940_CD8_LOCO1_lmm.log.txt'
removed 'test/output/mouse_hs1940_CD8_lm.assoc.txt'
removed 'test/output/mouse_hs1940_CD8_lm.log.txt'
removed 'test/output/mouse_hs1940_LOCO1.cXX.txt'
removed 'test/output/mouse_hs1940_LOCO1.log.txt'
cd test && ./test_suite.sh | tee ../test.log
run system shunit2
testBslmm1
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10775
Start Eigen-Decomposition...
pve estimate =0.590431
se(pve) =0.0480392
Calculating UtX...
initial value of h = 0.590431
initial value of rho = 0.41375
initial value of pi = 0.00269142
initial value of |gamma| = 29
0% 0.00
==== 9% 0.16
========= 18% 0.17
============= 27% 0.17
================== 36% 0.17
====================== 45% 0.17
=========================== 55% 0.16
=============================== 64% 0.16
==================================== 73% 0.16
======================================== 82% 0.16
============================================= 91% 0.16
================================================== 100% 0.16
**** INFO: Done.
testBslmm2
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10775
Calculating Relatedness Matrix ...
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testBslmm3
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10775
Start Eigen-Decomposition...
pve estimate =0.372151
se(pve) =0.0522377
Calculating UtX...
initial value of h = 0.372151
initial value of rho = 0.393216
initial value of pi = 0.00194896
initial value of |gamma| = 21
0% 0.00
==== 9% 0.26
========= 18% 0.25
============= 27% 0.24
================== 36% 0.23
====================== 45% 0.23
=========================== 55% 0.23
=============================== 64% 0.23
==================================== 73% 0.23
======================================== 82% 0.22
============================================= 91% 0.22
================================================== 100% 0.22
**** INFO: Done.
testBslmm4
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
Adding Breeding Values ...
Start Eigen-Decomposition...
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testBslmm5
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testCenteredRelatednessMatrixKFullLOCO1
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## leave one chromosome out (LOCO) = 1
## number of total SNPs/var = 12226
## number of SNPS for K = 11182
## number of SNPS for GWAS = 1044
## number of analyzed SNPs = 10768
Calculating Relatedness Matrix ...
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testUnivariateLinearMixedModelFullLOCO1
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## leave one chromosome out (LOCO) = 1
## number of total SNPs/var = 12226
## number of SNPS for K = 11182
## number of SNPS for GWAS = 1044
## number of analyzed SNPs = 10768
Start Eigen-Decomposition...
pve estimate =0.593114
se(pve) =0.0332587
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
================================================== 100%
**** INFO: Done.
## total computation time = 5.36339 min
testCenteredRelatednessMatrixK
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10768
Calculating Relatedness Matrix ...
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testUnivariateLinearMixedModel
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10768
Start Eigen-Decomposition...
pve estimate =0.608801
se(pve) =0.032774
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
================================================== 100%
**** INFO: Done.
## total computation time = 11.7249 min
testLinearMixedModelPhenotypes
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1197
## number of covariates = 1
## number of phenotypes = 2
## number of total SNPs/var = 12226
## number of analyzed SNPs = 10758
Start Eigen-Decomposition...
REMLE estimate for Vg in the null model:
1.3940
-0.2267 2.0817
se(Vg):
0.1567
0.1363 0.2359
REMLE estimate for Ve in the null model:
0.3489
0.0491 0.4144
se(Ve):
0.0206
0.0166 0.0267
REMLE likelihood = -2855.1664
MLE estimate for Vg in the null model:
1.3959
-0.2267 2.0854
se(Vg):
0.1568
0.1365 0.2361
MLE estimate for Ve in the null model:
0.3483
0.0490 0.4136
se(Ve):
0.0206
0.0166 0.0266
MLE likelihood = -2856.0280
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testPlinkStandardRelatednessMatrixK
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 427
## number of analyzed individuals = 427
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 358499
## number of analyzed SNPs = 273349
Calculating Relatedness Matrix ...
0%
0%
1%
1%
1%
1%
2%
2%
= 2%
= 3%
= 3%
= 3%
= 3%
= 4%
= 4%
== 4%
== 4%
== 5%
== 5%
== 5%
== 6%
== 6%
=== 6%
=== 6%
=== 7%
=== 7%
=== 7%
=== 8%
=== 8%
==== 8%
==== 8%
==== 9%
==== 9%
==== 9%
==== 9%
==== 10%
===== 10%
===== 10%
===== 11%
===== 11%
===== 11%
===== 11%
===== 12%
===== 12%
====== 12%
====== 13%
====== 13%
====== 13%
====== 13%
====== 14%
====== 14%
======= 14%
======= 15%
======= 15%
======= 15%
======= 15%
======= 16%
======= 16%
======== 16%
======== 16%
======== 17%
======== 17%
======== 17%
======== 18%
======== 18%
========= 18%
========= 18%
========= 19%
========= 19%
========= 19%
========= 20%
========= 20%
========== 20%
========== 20%
========== 21%
========== 21%
========== 21%
========== 21%
========== 22%
=========== 22%
=========== 22%
=========== 23%
=========== 23%
=========== 23%
=========== 23%
=========== 24%
=========== 24%
============ 24%
============ 25%
============ 25%
============ 25%
============ 25%
============ 26%
============ 26%
============= 26%
============= 26%
============= 27%
============= 27%
============= 27%
============= 28%
============= 28%
============== 28%
============== 28%
============== 29%
============== 29%
============== 29%
============== 30%
============== 30%
=============== 30%
=============== 30%
=============== 31%
=============== 31%
=============== 31%
=============== 32%
=============== 32%
================ 32%
================ 32%
================ 33%
================ 33%
================ 33%
================ 33%
================ 34%
================= 34%
================= 34%
================= 35%
================= 35%
================= 35%
================= 35%
================= 36%
================= 36%
================== 36%
================== 37%
================== 37%
================== 37%
================== 37%
================== 38%
================== 38%
=================== 38%
=================== 38%
=================== 39%
=================== 39%
=================== 39%
=================== 40%
=================== 40%
==================== 40%
==================== 40%
==================== 41%
==================== 41%
==================== 41%
==================== 42%
==================== 42%
===================== 42%
===================== 42%
===================== 43%
===================== 43%
===================== 43%
===================== 44%
===================== 44%
====================== 44%
====================== 44%
====================== 45%
====================== 45%
====================== 45%
====================== 45%
====================== 46%
======================= 46%
======================= 46%
======================= 47%
======================= 47%
======================= 47%
======================= 47%
======================= 48%
======================= 48%
======================== 48%
======================== 49%
======================== 49%
======================== 49%
======================== 49%
======================== 50%
======================== 50%
========================= 50%
========================= 50%
========================= 51%
========================= 51%
========================= 51%
========================= 52%
========================= 52%
========================== 52%
========================== 52%
========================== 53%
========================== 53%
========================== 53%
========================== 54%
========================== 54%
=========================== 54%
=========================== 54%
=========================== 55%
=========================== 55%
=========================== 55%
=========================== 56%
=========================== 56%
============================ 56%
============================ 56%
============================ 57%
============================ 57%
============================ 57%
============================ 57%
============================ 58%
============================= 58%
============================= 58%
============================= 59%
============================= 59%
============================= 59%
============================= 59%
============================= 60%
============================= 60%
============================== 60%
============================== 61%
============================== 61%
============================== 61%
============================== 61%
============================== 62%
============================== 62%
=============================== 62%
=============================== 62%
=============================== 63%
=============================== 63%
=============================== 63%
=============================== 64%
=============================== 64%
================================ 64%
================================ 64%
================================ 65%
================================ 65%
================================ 65%
================================ 66%
================================ 66%
================================= 66%
================================= 66%
================================= 67%
================================= 67%
================================= 67%
================================= 68%
================================= 68%
================================== 68%
================================== 68%
================================== 69%
================================== 69%
================================== 69%
================================== 69%
================================== 70%
=================================== 70%
=================================== 70%
=================================== 71%
=================================== 71%
=================================== 71%
=================================== 71%
=================================== 72%
=================================== 72%
==================================== 72%
==================================== 73%
==================================== 73%
==================================== 73%
==================================== 73%
==================================== 74%
==================================== 74%
===================================== 74%
===================================== 74%
===================================== 75%
===================================== 75%
===================================== 75%
===================================== 76%
===================================== 76%
====================================== 76%
====================================== 76%
====================================== 77%
====================================== 77%
====================================== 77%
====================================== 78%
====================================== 78%
======================================= 78%
======================================= 78%
======================================= 79%
======================================= 79%
======================================= 79%
======================================= 79%
======================================= 80%
======================================== 80%
======================================== 80%
======================================== 81%
======================================== 81%
======================================== 81%
======================================== 81%
======================================== 82%
========================================= 82%
========================================= 82%
========================================= 83%
========================================= 83%
========================================= 83%
========================================= 83%
========================================= 84%
========================================= 84%
========================================== 84%
========================================== 85%
========================================== 85%
========================================== 85%
========================================== 85%
========================================== 86%
========================================== 86%
=========================================== 86%
=========================================== 86%
=========================================== 87%
=========================================== 87%
=========================================== 87%
=========================================== 88%
=========================================== 88%
============================================ 88%
============================================ 88%
============================================ 89%
============================================ 89%
============================================ 89%
============================================ 90%
============================================ 90%
============================================= 90%
============================================= 90%
============================================= 91%
============================================= 91%
============================================= 91%
============================================= 91%
============================================= 92%
============================================== 92%
============================================== 92%
============================================== 93%
============================================== 93%
============================================== 93%
============================================== 93%
============================================== 94%
=============================================== 94%
=============================================== 94%
=============================================== 95%
=============================================== 95%
=============================================== 95%
=============================================== 95%
=============================================== 96%
=============================================== 96%
================================================ 96%
================================================ 97%
================================================ 97%
================================================ 97%
================================================ 97%
================================================ 98%
================================================ 98%
================================================= 98%
================================================= 98%
================================================= 99%
================================================= 99%
================================================= 99%
================================================= 100%
================================================= 100%
================================================== 100%
**** INFO: Done.
testPlinkLinearMixedModelCovariates
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
## number of total individuals = 427
## number of analyzed individuals = 427
## number of covariates = 2
## number of phenotypes = 1
## number of total SNPs/var = 358499
## number of analyzed SNPs = 223242
Start Eigen-Decomposition...
pve estimate =0.365545
se(pve) =0.47481
0%
0%
1%
1%
1%
1%
2%
2%
= 2%
= 3%
= 3%
= 3%
= 3%
= 4%
= 4%
== 4%
== 4%
== 5%
== 5%
== 5%
== 6%
== 6%
=== 6%
=== 6%
=== 7%
=== 7%
=== 7%
=== 8%
=== 8%
==== 8%
==== 8%
==== 9%
==== 9%
==== 9%
==== 9%
==== 10%
===== 10%
===== 10%
===== 11%
===== 11%
===== 11%
===== 11%
===== 12%
===== 12%
====== 12%
====== 13%
====== 13%
====== 13%
====== 13%
====== 14%
====== 14%
======= 14%
======= 15%
======= 15%
======= 15%
======= 15%
======= 16%
======= 16%
======== 16%
======== 16%
======== 17%
======== 17%
======== 17%
======== 18%
======== 18%
========= 18%
========= 18%
========= 19%
========= 19%
========= 19%
========= 20%
========= 20%
========== 20%
========== 20%
========== 21%
========== 21%
========== 21%
========== 21%
========== 22%
=========== 22%
=========== 22%
=========== 23%
=========== 23%
=========== 23%
=========== 23%
=========== 24%
=========== 24%
============ 24%
============ 25%
============ 25%
============ 25%
============ 25%
============ 26%
============ 26%
============= 26%
============= 26%
============= 27%
============= 27%
============= 27%
============= 28%
============= 28%
============== 28%
============== 28%
============== 29%
============== 29%
============== 29%
============== 30%
============== 30%
=============== 30%
=============== 30%
=============== 31%
=============== 31%
=============== 31%
=============== 32%
=============== 32%
================ 32%
================ 32%
================ 33%
================ 33%
================ 33%
================ 33%
================ 34%
================= 34%
================= 34%
================= 35%
================= 35%
================= 35%
================= 35%
================= 36%
================= 36%
================== 36%
================== 37%
================== 37%
================== 37%
================== 37%
================== 38%
================== 38%
=================== 38%
=================== 38%
=================== 39%
=================== 39%
=================== 39%
=================== 40%
=================== 40%
==================== 40%
==================== 40%
==================== 41%
==================== 41%
==================== 41%
==================== 42%
==================== 42%
===================== 42%
===================== 42%
===================== 43%
===================== 43%
===================== 43%
===================== 44%
===================== 44%
====================== 44%
====================== 44%
====================== 45%
====================== 45%
====================== 45%
====================== 45%
====================== 46%
======================= 46%
======================= 46%
======================= 47%
======================= 47%
======================= 47%
======================= 47%
======================= 48%
======================= 48%
======================== 48%
======================== 49%
======================== 49%
======================== 49%
======================== 49%
======================== 50%
======================== 50%
========================= 50%
========================= 50%
========================= 51%
========================= 51%
========================= 51%
========================= 52%
========================= 52%
========================== 52%
========================== 52%
========================== 53%
========================== 53%
========================== 53%
========================== 54%
========================== 54%
=========================== 54%
=========================== 54%
=========================== 55%
=========================== 55%
=========================== 55%
=========================== 56%
=========================== 56%
============================ 56%
============================ 56%
============================ 57%
============================ 57%
============================ 57%
============================ 57%
============================ 58%
============================= 58%
============================= 58%
============================= 59%
============================= 59%
============================= 59%
============================= 59%
============================= 60%
============================= 60%
============================== 60%
============================== 61%
============================== 61%
============================== 61%
============================== 61%
============================== 62%
============================== 62%
=============================== 62%
=============================== 62%
=============================== 63%
=============================== 63%
=============================== 63%
=============================== 64%
=============================== 64%
================================ 64%
================================ 64%
================================ 65%
================================ 65%
================================ 65%
================================ 66%
================================ 66%
================================= 66%
================================= 66%
================================= 67%
================================= 67%
================================= 67%
================================= 68%
================================= 68%
================================== 68%
================================== 68%
================================== 69%
================================== 69%
================================== 69%
================================== 69%
================================== 70%
=================================== 70%
=================================== 70%
=================================== 71%
=================================== 71%
=================================== 71%
=================================== 71%
=================================== 72%
=================================== 72%
==================================== 72%
==================================== 73%
==================================== 73%
==================================== 73%
==================================== 73%
==================================== 74%
==================================== 74%
===================================== 74%
===================================== 74%
===================================== 75%
===================================== 75%
===================================== 75%
===================================== 76%
===================================== 76%
====================================== 76%
====================================== 76%
====================================== 77%
====================================== 77%
====================================== 77%
====================================== 78%
====================================== 78%
======================================= 78%
======================================= 78%
======================================= 79%
======================================= 79%
======================================= 79%
======================================= 79%
======================================= 80%
======================================== 80%
======================================== 80%
======================================== 81%
======================================== 81%
======================================== 81%
======================================== 81%
======================================== 82%
========================================= 82%
========================================= 82%
========================================= 83%
========================================= 83%
========================================= 83%
========================================= 83%
========================================= 84%
========================================= 84%
========================================== 84%
========================================== 85%
========================================== 85%
========================================== 85%
========================================== 85%
========================================== 86%
========================================== 86%
=========================================== 86%
=========================================== 86%
=========================================== 87%
=========================================== 87%
=========================================== 87%
=========================================== 88%
=========================================== 88%
============================================ 88%
============================================ 88%
============================================ 89%
============================================ 89%
============================================ 89%
============================================ 90%
============================================ 90%
============================================= 90%
============================================= 90%
============================================= 91%
============================================= 91%
============================================= 91%
============================================= 91%
============================================= 92%
============================================== 92%
============================================== 92%
============================================== 93%
============================================== 93%
============================================== 93%
============================================== 93%
============================================== 94%
=============================================== 94%
=============================================== 94%
=============================================== 95%
=============================================== 95%
=============================================== 95%
=============================================== 95%
=============================================== 96%
=============================================== 96%
================================================ 96%
================================================ 97%
================================================ 97%
================================================ 97%
================================================ 97%
================================================ 98%
================================================ 98%
================================================= 98%
================================================= 98%
================================================= 99%
================================================= 99%
================================================= 99%
================================================= 100%
================================================= 100%
================================================== 100%
**** INFO: Done.
Ran 12 tests.
OK
tail -n 1 test.log | grep -q 'OK' test.log
make[2]: Leaving directory '/build/gemma-0.98.1+dfsg'
make[1]: Leaving directory '/build/gemma-0.98.1+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
rm -f -- debian/gemma.substvars debian/gemma-doc.substvars
rm -fr -- debian/.debhelper/generated/gemma/ debian/gemma/ debian/tmp/ debian/.debhelper/generated/gemma-doc/ debian/gemma-doc/
dh_auto_install
install -d /build/gemma-0.98.1\+dfsg/debian/tmp
dh_install
install -d debian/gemma/usr/bin
cp --reflink=auto -a ./bin/gemma debian/gemma/usr/bin/
install -d debian/.debhelper/generated/gemma
install -d debian/.debhelper/generated/gemma-doc
dh_installdocs
install -d debian/gemma/usr/share/doc/gemma
cp --reflink=auto -a ./RELEASE-NOTES.md debian/gemma/usr/share/doc/gemma
cp --reflink=auto -a ./README.md debian/gemma/usr/share/doc/gemma
chown -R 0:0 debian/gemma/usr/share/doc
chmod -R u\+rw,go=rX debian/gemma/usr/share/doc
install -p -m0644 debian/copyright debian/gemma/usr/share/doc/gemma/copyright
install -d debian/gemma-doc/usr/share/doc/gemma-doc
install -d debian/gemma-doc/usr/share/doc/gemma
cd './example/..' && find 'example' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/gemma-0.98.1+dfsg/debian/gemma-doc/usr/share/doc/gemma
chown -R 0:0 debian/gemma-doc/usr/share/doc
chmod -R u\+rw,go=rX debian/gemma-doc/usr/share/doc
install -p -m0644 debian/copyright debian/gemma-doc/usr/share/doc/gemma-doc/copyright
dh_installchangelogs
install -p -m0644 debian/changelog debian/gemma-doc/usr/share/doc/gemma-doc/changelog.Debian
install -p -m0644 debian/changelog debian/gemma/usr/share/doc/gemma/changelog.Debian
dh_perl
dh_link
dh_strip_nondeterminism
Using 1545146165 as canonical time
Normalizing debian/gemma-doc/usr/share/doc/gemma/example/BXD_geno.txt.gz using File::StripNondeterminism::handlers::gzip
Normalizing debian/gemma-doc/usr/share/doc/gemma/example/mouse_hs1940.geno.txt.gz using File::StripNondeterminism::handlers::gzip
dh_compress
cd debian/gemma
cd debian/gemma-doc
chmod a-x usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian
gzip -9nf usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian
cd '/build/gemma-0.98.1+dfsg'
chmod a-x usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt
gzip -9nf usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt
cd '/build/gemma-0.98.1+dfsg'
dh_fixperms
find debian/gemma-doc -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/gemma -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/gemma ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/gemma-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/gemma/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/gemma-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/gemma/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/gemma -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/gemma-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/gemma/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/gemma-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
dh_missing
dh_strip
install -d debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/74
objcopy --only-keep-debug --compress-debug-sections debian/gemma/usr/bin/gemma debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/74/711641e5fbdb1f0e9c7567e65712d432979e13.debug
chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/74/711641e5fbdb1f0e9c7567e65712d432979e13.debug
chown 0:0 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/74/711641e5fbdb1f0e9c7567e65712d432979e13.debug
strip --remove-section=.comment --remove-section=.note debian/gemma/usr/bin/gemma
objcopy --add-gnu-debuglink debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/74/711641e5fbdb1f0e9c7567e65712d432979e13.debug debian/gemma/usr/bin/gemma
install -d debian/.debhelper/gemma/dbgsym-root/usr/share/doc
ln -s gemma debian/.debhelper/gemma/dbgsym-root/usr/share/doc/gemma-dbgsym
dh_makeshlibs
rm -f debian/gemma/DEBIAN/shlibs
rm -f debian/gemma-doc/DEBIAN/shlibs
dh_shlibdeps
install -d debian/gemma/DEBIAN
dpkg-shlibdeps -Tdebian/gemma.substvars debian/gemma/usr/bin/gemma
dpkg-shlibdeps: warning: debian/gemma/usr/bin/gemma contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb
install -d debian/gemma-doc/DEBIAN
dh_gencontrol
echo misc:Depends= >> debian/gemma-doc.substvars
echo misc:Pre-Depends= >> debian/gemma-doc.substvars
dpkg-gencontrol -pgemma-doc -ldebian/changelog -Tdebian/gemma-doc.substvars -Pdebian/gemma-doc
echo misc:Depends= >> debian/gemma.substvars
echo misc:Pre-Depends= >> debian/gemma.substvars
install -d debian/.debhelper/gemma/dbgsym-root/DEBIAN
dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/.debhelper/gemma/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=gemma-dbgsym "-DDepends=gemma (= \${binary:Version})" "-DDescription=debug symbols for gemma" -DBuild-Ids=74711641e5fbdb1f0e9c7567e65712d432979e13 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/gemma-doc/DEBIAN/control
chown 0:0 -- debian/gemma-doc/DEBIAN/control
chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/gemma -UMulti-Arch
chmod 0644 -- debian/gemma/DEBIAN/control
chown 0:0 -- debian/gemma/DEBIAN/control
dh_md5sums
cd debian/gemma-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/gemma >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/gemma/DEBIAN/md5sums
chown 0:0 -- debian/gemma/DEBIAN/md5sums
cd debian/.debhelper/gemma/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/gemma-doc/DEBIAN/md5sums
chown 0:0 -- debian/gemma-doc/DEBIAN/md5sums
dh_builddeb
dpkg-deb --build debian/.debhelper/gemma/dbgsym-root ..
dpkg-deb --build debian/gemma ..
dpkg-deb --build debian/gemma-doc ..
dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.1+dfsg-1_all.deb'.
dpkg-deb: building package 'gemma-dbgsym' in '../gemma-dbgsym_0.98.1+dfsg-1_armhf.deb'.
dpkg-deb: building package 'gemma' in '../gemma_0.98.1+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../gemma_0.98.1+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/23038 and its subdirectories
I: Current time: Sun Jun 14 22:10:59 -12 2020
I: pbuilder-time-stamp: 1592215859
Mon Jun 15 10:12:07 UTC 2020 I: 1st build successful. Starting 2nd build on remote node cb3a-armhf-rb.debian.net.
Mon Jun 15 10:12:07 UTC 2020 I: Preparing to do remote build '2' on cb3a-armhf-rb.debian.net.
Mon Jun 15 12:52:53 UTC 2020 I: Deleting $TMPDIR on cb3a-armhf-rb.debian.net.
Mon Jun 15 12:52:56 UTC 2020 I: gemma_0.98.1+dfsg-1_armhf.changes:
Format: 1.8
Date: Tue, 18 Dec 2018 16:16:05 +0100
Source: gemma
Binary: gemma gemma-dbgsym gemma-doc
Architecture: armhf all
Version: 0.98.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
gemma - Genome-wide Efficient Mixed Model Association
gemma-doc - Example folder for GEMMA
Changes:
gemma (0.98.1+dfsg-1) unstable; urgency=medium
.
* Team upload.
* Simplify watch file
Checksums-Sha1:
d4aa72b15db904e315270efe0e0815315a55cd69 7377184 gemma-dbgsym_0.98.1+dfsg-1_armhf.deb
be502067f315fa7e743611c20f2b7fd92e9ba57e 33410876 gemma-doc_0.98.1+dfsg-1_all.deb
336dbd2d2ed1a0fad754c1d616906e8594257c6d 5179 gemma_0.98.1+dfsg-1_armhf.buildinfo
1b49a5b14792f5a1120b5be23836faa762202e3f 331744 gemma_0.98.1+dfsg-1_armhf.deb
Checksums-Sha256:
ff0dffef0bf09a4d0007d48fdba640d8d6e2343aadf4decf6036c8cfcb5a60eb 7377184 gemma-dbgsym_0.98.1+dfsg-1_armhf.deb
cebb7991111f4bf47676913285bf2acef45fa9ec2abe32ff0b094097d7e9e340 33410876 gemma-doc_0.98.1+dfsg-1_all.deb
5ccf4d5b8e6835ddddbe499ab3f456e2967d56e74c78ed4b8cdc75cdc16041e0 5179 gemma_0.98.1+dfsg-1_armhf.buildinfo
6f0e1ec6a4e93c61506a4d30700904a7972874d8703ed84348a0380918a2bb75 331744 gemma_0.98.1+dfsg-1_armhf.deb
Files:
e239008e5229f91943ae70040ca5bb34 7377184 debug optional gemma-dbgsym_0.98.1+dfsg-1_armhf.deb
c3b929554bb7162fe0e57ebe665b05f9 33410876 doc optional gemma-doc_0.98.1+dfsg-1_all.deb
72530e3e7a7b8b434d26878da11bc531 5179 science optional gemma_0.98.1+dfsg-1_armhf.buildinfo
c88111d93891c84759046ee004501fff 331744 science optional gemma_0.98.1+dfsg-1_armhf.deb
Mon Jun 15 12:52:57 UTC 2020 I: diffoscope 147 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.objXwtn2CU/gemma_0.98.1+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.objXwtn2CU/gemma_0.98.1+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.objXwtn2CU/gemma_0.98.1+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.objXwtn2CU/b1/gemma_0.98.1+dfsg-1_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.objXwtn2CU/b2/gemma_0.98.1+dfsg-1_armhf.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.558s)
0.558s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.372s)
0.372s 10 calls diffoscope.comparators.binary.FilesystemFile
0.000s 8 calls abc.DotChangesFile
Mon Jun 15 12:53:00 UTC 2020 I: diffoscope 147 found no differences in the changes files, and a .buildinfo file also exists.
Mon Jun 15 12:53:00 UTC 2020 I: gemma from buster built successfully and reproducibly on armhf.
Mon Jun 15 12:53:01 UTC 2020 I: Submitting .buildinfo files to external archives:
Mon Jun 15 12:53:01 UTC 2020 I: Submitting 8.0K b1/gemma_0.98.1+dfsg-1_armhf.buildinfo.asc
Mon Jun 15 12:53:02 UTC 2020 I: Submitting 8.0K b2/gemma_0.98.1+dfsg-1_armhf.buildinfo.asc
Mon Jun 15 12:53:03 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon Jun 15 12:53:03 UTC 2020 I: Done submitting .buildinfo files.
Mon Jun 15 12:53:03 UTC 2020 I: Removing signed gemma_0.98.1+dfsg-1_armhf.buildinfo.asc files:
removed './b1/gemma_0.98.1+dfsg-1_armhf.buildinfo.asc'
removed './b2/gemma_0.98.1+dfsg-1_armhf.buildinfo.asc'