gemma →
0.98+dfsg-2 →
armhf → 2018-10-27 06:44:13
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| gemma 0.98+dfsg-2 (armhf) Sat, 27 Oct 2018 06:12:16 +0000 |
+==============================================================================+
Package: gemma
Version: 0.98+dfsg-2
Source Version: 0.98+dfsg-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-61a28766-16ae-485c-9d82-ce2bad4aa2a7' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.9 MB]
Fetched 24.0 MB in 27s (883 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gemma' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/gemma.git
Please use:
git clone https://salsa.debian.org/med-team/gemma.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 49.1 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main gemma 0.98+dfsg-2 (dsc) [2093 B]
Get:2 http://172.17.0.1/private buster-staging/main gemma 0.98+dfsg-2 (tar) [49.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main gemma 0.98+dfsg-2 (diff) [4876 B]
Fetched 49.1 MB in 25s (2005 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gemma-1YQs9t/gemma-0.98+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gemma-1YQs9t' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-ukjSWh/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-ukjSWh/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ukjSWh/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (11.1 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 41 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15767 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2
Filtered Build-Depends: debhelper (>= 11~), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2
dpkg-deb: building package 'sbuild-build-depends-gemma-dummy' in '/<<BUILDDIR>>/resolver-ukjSWh/apt_archive/sbuild-build-depends-gemma-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gemma-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ Sources [532 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ Packages [613 B]
Fetched 2478 B in 0s (12.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gemma build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils catch cpp-8 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++-8 gcc-8 gcc-8-base
gettext gettext-base gfortran gfortran-8 groff-base intltool-debian
libarchive-zip-perl libasan5 libatomic1 libbsd0 libcc1-0 libcroco3
libeigen3-dev libelf1 libfile-stripnondeterminism-perl libfreetype6
libgcc-8-dev libgcc1 libgfortran-8-dev libgfortran5 libglib2.0-0 libgomp1
libgraphite2-3 libgsl-dev libgsl23 libgslcblas0 libharfbuzz0b libicu-le-hb0
libicu60 libmagic-mgc libmagic1 libopenblas-base libopenblas-dev
libpipeline1 libsigsegv2 libstdc++-8-dev libstdc++6 libtool libubsan1
libxml2 m4 man-db pkg-config po-debconf shunit2 zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-8-locales dh-make gcc-8-doc libstdc++6-8-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-8-doc
libgfortran5-dbg libcoarrays-dev groff libeigen3-doc libmpfrc++-dev
gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libstdc++-8-doc
libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils catch debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran
gfortran-8 groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3
libeigen3-dev libelf1 libfile-stripnondeterminism-perl libfreetype6
libgfortran-8-dev libgfortran5 libglib2.0-0 libgraphite2-3 libgsl-dev
libgsl23 libgslcblas0 libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc
libmagic1 libopenblas-base libopenblas-dev libpipeline1 libsigsegv2 libtool
libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-gemma-dummy
shunit2 zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libstdc++-8-dev libstdc++6 libubsan1
13 upgraded, 49 newly installed, 0 to remove and 28 not upgraded.
Need to get 43.7 MB/52.7 MB of archives.
After this operation, 130 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ukjSWh/apt_archive ./ sbuild-build-depends-gemma-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-8+rpi1 [30.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-8+rpi1 [187 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-8+rpi1 [36.5 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-8+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-8+rpi1 [8104 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-8+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-8+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-8+rpi1 [5940 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-8+rpi1 [1563 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-8+rpi1 [599 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-8+rpi1 [5844 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-8+rpi1 [5472 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-8+rpi1 [326 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2+b1 [1160 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-8 [117 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-2 [771 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-8 [434 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf catch armhf 1.12.1-1 [114 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.043-2 [20.2 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.043-2 [12.2 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-8 [1220 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.4.1 [989 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-8+rpi1 [205 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-8+rpi1 [248 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-8+rpi1 [5812 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:8.1.0-1+rpi1 [1424 B]
Get:49 http://172.17.0.1/private buster-staging/main armhf libeigen3-dev all 3.3.5-2 [848 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.5+dfsg-5 [78.8 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.5+dfsg-5 [703 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.5+dfsg-5 [894 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libopenblas-base armhf 0.3.3+ds-1+rpi1 [1969 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libopenblas-dev armhf 0.3.3+ds-1+rpi1 [1875 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf shunit2 all 2.1.6-1.1 [39.3 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libarchive-zip-perl (1.64-1) ...
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Unpacking libfile-stripnondeterminism-perl (0.043-2) ...
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Unpacking dh-strip-nondeterminism (0.043-2) ...
Selecting previously unselected package libelf1:armhf.
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Unpacking libelf1:armhf (0.170-0.5) ...
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Unpacking dwz (0.12-2) ...
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Unpacking libglib2.0-0:armhf (2.58.1-2) ...
Selecting previously unselected package libfreetype6:armhf.
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Unpacking libxml2:armhf (2.9.4+dfsg1-7) ...
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Unpacking libcroco3:armhf (0.6.12-2) ...
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Unpacking gettext (0.19.8.1-8) ...
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Unpacking sbuild-build-depends-gemma-dummy (0.invalid.0) ...
Setting up cpp-8 (8.2.0-8+rpi1) ...
Setting up libgomp1:armhf (8.2.0-8+rpi1) ...
Setting up libatomic1:armhf (8.2.0-8+rpi1) ...
Setting up libcc1-0:armhf (8.2.0-8+rpi1) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.58.1-2) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-8) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libgraphite2-3:armhf (1.3.12-1) ...
Setting up pkg-config (0.29-4) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up shunit2 (2.1.6-1.1) ...
Setting up bsdmainutils (11.1.2) ...
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 libgslcblas0:armhf (2.5+dfsg-5) ...
Setting up libasan5:armhf (8.2.0-8+rpi1) ...
Setting up libgfortran5:armhf (8.2.0-8+rpi1) ...
Setting up catch (1.12.1-1) ...
Setting up autopoint (0.19.8.1-8) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.043-2) ...
Setting up libubsan1:armhf (8.2.0-8+rpi1) ...
Setting up libopenblas-base:armhf (0.3.3+ds-1+rpi1) ...
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 libgsl23:armhf (2.5+dfsg-5) ...
Setting up libgsl-dev (2.5+dfsg-5) ...
Setting up libeigen3-dev (3.3.5-2) ...
Setting up libharfbuzz0b:armhf (1.9.0-1+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up automake (1:1.16.1-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.4-2+b1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libgcc-8-dev:armhf (8.2.0-8+rpi1) ...
Setting up libopenblas-dev:armhf (0.3.3+ds-1+rpi1) ...
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 libgfortran-8-dev:armhf (8.2.0-8+rpi1) ...
Setting up libtool (2.4.6-6) ...
Setting up libstdc++-8-dev:armhf (8.2.0-8+rpi1) ...
Setting up gcc-8 (8.2.0-8+rpi1) ...
Setting up g++-8 (8.2.0-8+rpi1) ...
Setting up gfortran-8 (8.2.0-8+rpi1) ...
Setting up gfortran (4:8.1.0-1+rpi1) ...
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 libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up gettext (0.19.8.1-8) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.4.1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (0.043-2) ...
Setting up sbuild-build-depends-gemma-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-6+rpi1 dpkg-dev_1.19.0.5 g++-8_8.2.0-8+rpi1 gcc-8_8.2.0-8+rpi1 libc6-dev_2.27-6+rpi1 libstdc++-8-dev_8.2.0-8+rpi1 libstdc++6_8.2.0-8+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.118 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-2 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-6+rpi1 binutils-arm-linux-gnueabihf_2.31.1-6+rpi1 binutils-common_2.31.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 catch_1.12.1-1 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.2.0-8+rpi1 dash_0.5.10.2-1 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.4.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.043-2 diffutils_1:3.6-1 dirmngr_2.2.10-3+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20180808-2 g++_4:8.1.0-1+rpi1 g++-8_8.2.0-8+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-8+rpi1 gcc-8-base_8.2.0-8+rpi1 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gfortran_4:8.1.0-1+rpi1 gfortran-8_8.2.0-8+rpi1 gnupg_2.2.10-3+rpi1 gnupg-agent_2.2.10-3+rpi1 gnupg-l10n_2.2.10-3+rpi1 gnupg-utils_2.2.10-3+rpi1 gpg_2.2.10-3+rpi1 gpg-agent_2.2.10-3+rpi1 gpg-wks-client_2.2.10-3+rpi1 gpg-wks-server_2.2.10-3+rpi1 gpgconf_2.2.10-3+rpi1 gpgsm_2.2.10-3+rpi1 gpgv_2.2.10-3+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.54 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-8+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-6+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.27-6+rpi1 libc-dev-bin_2.27-6+rpi1 libc6_2.27-6+rpi1 libc6-dev_2.27-6+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-8+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.94-1+rpi1 libdrm2_2.4.94-1+rpi1 libeigen3-dev_3.3.5-2 libelf1_0.170-0.5 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.043-2 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-8+rpi1 libgcc1_1:8.2.0-8+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.18-2 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgdbm6_1.18-2 libgfortran-8-dev_8.2.0-8+rpi1 libgfortran5_8.2.0-8+rpi1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.2.0-8+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libgsl-dev_2.5+dfsg-5 libgsl23_2.5+dfsg-5 libgslcblas0_2.5+dfsg-5 libgssapi-krb5-2_1.16.1-1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.6.2-1.1 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-10+rpi1 libopenblas-base_0.3.3+ds-1+rpi1 libopenblas-dev_0.3.3+ds-1+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-10+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27~rc8-1 libsasl2-modules_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.25.2-1 libss2_1.44.4-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-8+rpi1 libstdc++6_8.2.0-8+rpi1 libsystemd0_239-10+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-6 libubsan1_8.2.0-8+rpi1 libudev1_239-10+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-2+b1 mawk_1.3.3-17 mount_2.32.1-0.1 multiarch-support_2.27-6+rpi1 nano_3.1-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gemma-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 shunit2_2.1.6-1.1 systemd_239-10+rpi1 systemd-sysv_239-10+rpi1 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-10+rpi1 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 22 05:43:24 2018 UTC
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gemma_0.98+dfsg-2.dsc
dpkg-source: info: extracting gemma in /<<BUILDDIR>>/gemma-0.98+dfsg
dpkg-source: info: unpacking gemma_0.98+dfsg.orig.tar.gz
dpkg-source: info: unpacking gemma_0.98+dfsg-2.debian.tar.xz
dpkg-source: info: applying Reproducible_builds.patch
dpkg-source: info: applying no-lquadmath.patch
dpkg-source: info: applying Makefile.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-61a28766-16ae-485c-9d82-ce2bad4aa2a7
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gemma
dpkg-buildpackage: info: source version 0.98+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build gemma-0.98+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/gemma-0.98+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 '/<<BUILDDIR>>/gemma-0.98+dfsg'
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/gemma-0.98+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 '/<<BUILDDIR>>/gemma-0.98+dfsg'
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/gemma-0.98+dfsg'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
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; };
^
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
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>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_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: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/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/fstream:38,
from src/bslmm.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
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/fstream:38,
from src/bslmmdap.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
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
/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
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = 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<double*, std::vector<double> >' changed in GCC 7.1
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 member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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:2146:5: 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 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/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,
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
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::__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,
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included 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/fstream:38,
from src/bslmm.cpp:19:
/usr/include/c++/8/bits/stl_algobase.h: In function '_ForwardIterator std::__lower_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Tp = std::pair<unsigned int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(std::pair<unsigned int, double>, std::pair<unsigned int, double>)>]':
/usr/include/c++/8/bits/stl_algobase.h:946:5: 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
__lower_bound(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algobase.h:946:5: 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/algorithm:62,
from src/bslmm.cpp:23:
/usr/include/c++/8/bits/stl_algo.h: In function '_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _Tp = 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:2039:5: 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
__upper_bound(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2039:5: 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/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/fstream:38,
from src/bslmm.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = std::pair<unsigned int, double>*; _Container = std::vector<std::pair<unsigned int, double> >]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: 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
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
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::__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::__chunk_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Distance, _Compare) [with _RandomAccessIterator = __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:2689:5: 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
__chunk_insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2689:5: 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: 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
__move_merge(_InputIterator __first1, _InputIterator __last1,
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = std::pair<unsigned int, double>*; _RandomAccessIterator2 = __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:2665:5: 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_loop(_RandomAccessIterator1 __first,
^~~~~~~~~~~~~~~~~
/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: 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 'void std::__move_merge_adaptive(_InputIterator1, _InputIterator1, _InputIterator2, _InputIterator2, _OutputIterator, _Compare) [with _InputIterator1 = std::pair<unsigned int, double>*; _InputIterator2 = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<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:2304:5: 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(_InputIterator1 __first1, _InputIterator1 __last1,
^~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2304:5: 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:2304:5: 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 = __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: In function 'void std::__merge_sort_loop(_RandomAccessIterator1, _RandomAccessIterator1, _RandomAccessIterator2, _Distance, _Compare) [with _RandomAccessIterator1 = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _RandomAccessIterator2 = 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:2665:5: 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_loop(_RandomAccessIterator1 __first,
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2665:5: 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: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: 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:2716:34: 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::__chunk_insertion_sort(__first, __last, __step_size, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2720:26: 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_loop(__first, __last, __buffer,
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
__step_size, __comp);
~~~~~~~~~~~~~~~~~~~~
In file included 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/fstream:38,
from src/bslmm.cpp:19:
/usr/include/c++/8/bits/stl_algobase.h: In function '_ForwardIterator2 std::swap_ranges(_ForwardIterator1, _ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >; _ForwardIterator2 = __gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >]':
/usr/include/c++/8/bits/stl_algobase.h:166:5: 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
swap_ranges(_ForwardIterator1 __first1, _ForwardIterator1 __last1,
^~~~~~~~~~~
/usr/include/c++/8/bits/stl_algobase.h:166:5: 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_algobase.h:166:5: 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/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
/usr/include/c++/8/bits/stl_algo.h:1352:20: 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::swap_ranges(__first, __middle, __middle);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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:2501:26: 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::__lower_bound(__middle, __last, *__first_cut,
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__gnu_cxx::__ops::__iter_comp_val(__comp));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2510:26: 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::__upper_bound(__first, __middle, *__second_cut,
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__gnu_cxx::__ops::__val_comp_iter(__comp));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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::__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: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 '_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:2425:30: 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::__move_merge_adaptive(__buffer, __buffer_end, __middle, __last,
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__first, __comp);
~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2425:30: 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
/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:2445:23: 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::__lower_bound(__middle, __last, *__first_cut,
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__gnu_cxx::__ops::__iter_comp_val(__comp));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:2454:23: 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::__upper_bound(__first, __middle, *__second_cut,
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__gnu_cxx::__ops::__val_comp_iter(__comp));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 '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: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/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/fstream:38,
from src/bslmmdap.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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_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/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 = {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/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);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BSLMM::MCMC(const gsl_matrix*, const gsl_vector*)':
/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/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/fstream:38,
from src/bslmm.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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 = {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/algorithm:62,
from src/bslmm.cpp:23:
/usr/include/c++/8/bits/stl_algo.h: 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/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:64,
from src/bslmm.h:25,
from src/bslmm.cpp:41:
/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 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
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::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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:2146:5: 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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/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/fstream:38,
from src/gemma.cpp:24:
/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)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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 = {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 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/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/fstream:38,
from src/ldr.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
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: In member function 'void GEMMA::BatchRun(PARAM&)':
/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,
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
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 member function 'void std::vector<_Tp, _Alloc>::emplace_back(_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: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/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/fstream:38,
from src/lm.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = SUMSTAT*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<SUMSTAT*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
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::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);
^~~~~~~~~~~~~~~~~
/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::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);
^~~~~~~~~~~~~~~~~
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::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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:2146:5: 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
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 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>::
^~~~~~~~~~~~~~~~~~~
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,
/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,
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 member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SNPINFO; _Alloc = std::allocator<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_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);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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/bits/stl_algobase.h:67,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/string:40,
from /usr/include/c++/8/bitset:47,
from src/gemma_io.cpp:22:
/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)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = 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<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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>::
^~~~~~~~~~~~~~~~~~~
/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/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_gene(const string&, std::vector<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: 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/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 'bool ReadFile_column(const string&, std::vector<int>&, std::vector<double>&, const 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: 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: 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);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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 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 member function 'void std::vector<_Tp, _Alloc>::emplace_back(_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: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)...);
^~~~~~~~~~~~~~~~~
/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>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_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: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/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/fstream:38,
from src/lmm.cpp:21:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = 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<double*, std::vector<double> >' changed in GCC 7.1
/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
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = SUMSTAT*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<SUMSTAT*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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>::
^~~~~~~~~~~~~~~~~~~
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 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 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 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);
^~~~~~~~~~~~~~~~~
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/fstream:38,
from src/lmm.cpp:21:
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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/string:40,
from /usr/include/c++/8/bitset:47,
from src/mathfunc.cpp:21:
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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 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)...);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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
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/string:40,
from /usr/include/c++/8/bitset:47,
from src/prdt.cpp:23:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
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::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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:2146:5: 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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::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,
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/fstream:38,
from src/mvlmm.cpp:19:
/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)
^~~~~~~~~~~~
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/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/fstream:38,
from src/mvlmm.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = 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<double*, std::vector<double> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/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,
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: 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_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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)...);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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/bits/stl_algobase.h:67,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/string:40,
from /usr/include/c++/8/bitset:47,
from src/varcov.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
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 = {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>::
^~~~~~~~~~~~~~~~~~~
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/string:40,
from /usr/include/c++/8/bitset:47,
from src/varcov.cpp:19:
/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)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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 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 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/varcov.cpp:31:
/usr/include/c++/8/bits/stl_vector.h: In function 'void Calc_Cor(std::vector<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: In member function 'void VARCOV::AnalyzeBimbam()':
/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 member function 'void VARCOV::AnalyzePlink()':
/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::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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:2146:5: 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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/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/ostream:38,
from /usr/include/c++/8/iostream:39,
from src/param.cpp:21:
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = SNPINFO*; _Container = std::vector<SNPINFO>]':
/usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SNPINFO*, std::vector<SNPINFO> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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>::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/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/ostream:38,
from /usr/include/c++/8/iostream:39,
from src/param.cpp:21:
/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)
^~~~~~~~~~~~
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/fstream:38,
from src/vc.cpp:19:
/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)
^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = 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<double*, std::vector<double> >' changed in GCC 7.1
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::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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:2146:5: 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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/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/fstream:38,
from src/vc.cpp:19:
/usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
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);
^~~~~~~~~~~~~~~~~
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/map:61,
from src/vc.cpp:28:
/usr/include/c++/8/bits/stl_map.h: 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/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++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -g -Og -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 -lgfortran -o ./bin/gemma
make[1]: Leaving directory '/<<BUILDDIR>>/gemma-0.98+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/gemma-0.98+dfsg'
dh_auto_test --no-parallel
make -j1 check
make[2]: Entering directory '/<<BUILDDIR>>/gemma-0.98+dfsg'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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 -fdebug-prefix-map=/<<BUILDDIR>>/gemma-0.98+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 -g -Og -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 -g -Og -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 -lgfortran -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
* RowMajor 101 transA 111 transB 111 m 2000 n 1000 k 200
* lda 200 ldb 1000 ldc 1000 alpha 1.000e+00 beta 0.000e+00
* A03 4.000e+00 B03 -4.000e+00 C03 0.000e+00 Asum 8.000e+10 Bsum -2.000e+10
Csum 0.000e+00
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
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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
**** DEBUG: entering in src/lm.cpp at line 383 in AnalyzeBimbam
0%
==== 8%
======== 16%
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================ 33%
==================== 41%
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================================ 65%
==================================== 74%
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============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
## total computation time = 0.309703 min
testBXDStandardRelatednessMatrixKSingularError
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
**** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt
Reading Files ...
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
GSL ERROR: matrix is singular in lu.c at line 266 errno 1
testBXDStandardRelatednessMatrixK
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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 ...
**** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin
0%
====== 14%
============= 27%
==================== 41%
=========================== 55%
================================== 68%
======================================== 82%
=============================================== 96%
================================================== 100%
**** INFO: Done.
testBXDLMLikelihoodRatio
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## number of total individuals = 198
**** DEBUG: entering in src/lm.cpp at line 383 in AnalyzeBimbam
## 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 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin
Start Eigen-Decomposition...
pve estimate =0.00100086
se(pve) =0.204166
**** DEBUG: ../example/BXD_geno.txt.gz in src/lmm.cpp at line 1649 in AnalyzeBimbam
0%
====== 14%
============= 27%
==================== 41%
=========================== 55%
================================== 68%
======================================== 82%
=============================================== 96%
================================================== 100%
================================================== 100%
**** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles
**** INFO: Done.
testCenteredRelatednessMatrixKLOCO1
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
**** DEBUG: entered in src/gemma_io.cpp at line 153 in ReadFile_snps
Reading Files ...
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** TEST MODE: trim individuals from 1940 to 400
**** TEST MODE: trim individuals from 1940 to 400
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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 ...
**** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
## total computation time = 0.23781 min
testUnivariateLinearMixedModelLOCO1
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
**** DEBUG: entered in src/gemma_io.cpp at line 153 in ReadFile_snps
Reading Files ...
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** TEST MODE: trim individuals from 1940 to 400
**** TEST MODE: trim individuals from 1940 to 400
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin
Start Eigen-Decomposition...
pve estimate =0.678775
se(pve) =0.0717914
**** DEBUG: ../example/mouse_hs1940.geno.txt.gz in src/lmm.cpp at line 1649 in AnalyzeBimbam
**** DEBUG: Analyze subset of SNPs (LOCO) in src/lmm.cpp at line 1471 in Analyze
0%
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==================== 41%
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================================ 65%
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============================================ 90%
================================================= 98%
================================================== 100%
================================================== 100%
**** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles
**** INFO: Done.
## total computation time = 0.117644 min
testPlinkCenteredRelatednessMatrixKLOCO1
testPlinkUnivariateLinearMixedModelLOCO1
testCorrelatedPhenotypesMvLLM
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-10583-rs58108140 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-10611-rs189107123 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-13302-rs180734498 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-13327-rs144762171 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-13980-rs151276478 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-30923-rs140337953 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-51479-rs116400033 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-52058-rs62637813 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-52238-rs150021059 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for 1-54421-rs146477069 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Skipping similar warnings in src/gemma_io.cpp at line 721 in ReadFile_geno
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1299 in ReadFile_eigenU
**** DEBUG: entered in src/gemma_io.cpp at line 1348 in ReadFile_eigenD
**** DEBUG: entering in src/mvlmm.cpp at line 2973 in AnalyzeBimbam
**** DEBUG: MphInitial in src/mvlmm.cpp at line 2770 in MphInitial
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 10 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/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 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1689 in ReadFile_geno
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 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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 ...
**** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin
0%
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================================================= 98%
================================================== 100%
**** INFO: Done.
testBslmm3
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1689 in ReadFile_geno
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 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 2170 in ReadFile_est
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 2236 in CountFileLines
**** DEBUG: entered in src/gemma_io.cpp at line 342 in ReadFile_column
**** DEBUG: ReadFile_log in src/gemma_io.cpp at line 239 in ReadFile_log
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
Adding Breeding Values ...
**** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin
Start Eigen-Decomposition...
**** DEBUG: entering in src/prdt.cpp at line 208 in AnalyzeBimbam
0%
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==================== 41%
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======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testBslmm5
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 2170 in ReadFile_est
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 2236 in CountFileLines
**** DEBUG: ReadFile_log in src/gemma_io.cpp at line 239 in ReadFile_log
## number of total individuals = 1940
## number of analyzed individuals = 757
## number of covariates = 1
## number of phenotypes = 1
**** DEBUG: entering in src/prdt.cpp at line 208 in AnalyzeBimbam
0%
==== 8%
======== 16%
============ 25%
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==================== 41%
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================================ 65%
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======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testCenteredRelatednessMatrixKFullLOCO1
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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 ...
**** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin
0%
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======== 16%
============ 25%
================ 33%
==================== 41%
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================================================= 98%
================================================== 100%
**** INFO: Done.
testUnivariateLinearMixedModelFullLOCO1
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin
Start Eigen-Decomposition...
pve estimate =0.593114
se(pve) =0.0332587
**** DEBUG: ../example/mouse_hs1940.geno.txt.gz in src/lmm.cpp at line 1649 in AnalyzeBimbam
**** DEBUG: Analyze subset of SNPs (LOCO) in src/lmm.cpp at line 1471 in Analyze
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
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============================================ 90%
================================================= 98%
================================================== 100%
================================================== 100%
**** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles
**** INFO: Done.
## total computation time = 0.920269 min
testCenteredRelatednessMatrixK
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
**** DEBUG: Can't figure out position for rs3683945 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs3707673 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs6269442 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs6336442 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs13475699 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs13475700 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs3658242 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs6243160 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs13475701 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Can't figure out position for rs6198069 in src/gemma_io.cpp at line 719 in ReadFile_geno
**** DEBUG: Skipping similar warnings in src/gemma_io.cpp at line 721 in ReadFile_geno
## 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 ...
**** DEBUG: entered in src/gemma_io.cpp at line 1397 in BimbamKin
0%
==== 8%
======== 16%
============ 25%
================ 33%
==================== 41%
======================== 49%
============================ 57%
================================ 65%
==================================== 74%
======================================== 82%
============================================ 90%
================================================= 98%
================================================== 100%
**** INFO: Done.
testUnivariateLinearMixedModel
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin
Start Eigen-Decomposition...
pve estimate =0.608801
se(pve) =0.032774
**** DEBUG: ../example/mouse_hs1940.geno.txt.gz in src/lmm.cpp at line 1649 in AnalyzeBimbam
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**** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles
**** INFO: Done.
## total computation time = 1.95767 min
testLinearMixedModelPhenotypes
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: ReadFile_anno in src/gemma_io.cpp at line 282 in ReadFile_anno
**** DEBUG: entered in src/gemma_io.cpp at line 386 in ReadFile_pheno
**** DEBUG: entered in src/gemma_io.cpp at line 643 in ReadFile_geno
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin
Start Eigen-Decomposition...
**** DEBUG: entering in src/mvlmm.cpp at line 2973 in AnalyzeBimbam
**** DEBUG: MphInitial in src/mvlmm.cpp at line 2770 in MphInitial
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
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**** INFO: Done.
testPlinkStandardRelatednessMatrixK
**** DEBUG: entered in src/gemma_io.cpp at line 511 in ReadFile_bim
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 558 in ReadFile_fam
**** DEBUG: entered in src/gemma_io.cpp at line 857 in ReadFile_bed
## number of total individuals = 427
## number of analyzed individuals = 427
**** DEBUG: entered in src/gemma_io.cpp at line 1546 in PlinkKin
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var = 358499
## number of analyzed SNPs = 273349
Calculating Relatedness Matrix ...
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**** INFO: Done.
testPlinkLinearMixedModelCovariates
GEMMA 0.98 (2018-09-28) by Xiang Zhou and team (C) 2012-2018
**** DEBUG: entered in src/gemma_io.cpp at line 444 in ReadFile_cvt
Reading Files ...
**** DEBUG: entered in src/gemma_io.cpp at line 511 in ReadFile_bim
**** DEBUG: entered in src/gemma_io.cpp at line 558 in ReadFile_fam
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
**** DEBUG: entered in src/gemma_io.cpp at line 857 in ReadFile_bed
## 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
**** DEBUG: entered in src/gemma_io.cpp at line 1164 in ReadFile_kin
Start Eigen-Decomposition...
pve estimate =0.365545
se(pve) =0.47481
**** DEBUG: ../example/HLC.bed in src/lmm.cpp at line 1698 in AnalyzePlink
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**** DEBUG: LMM::WriteFiles in src/lmm.cpp at line 100 in WriteFiles
**** INFO: Done.
Ran 12 tests.
OK
tail -n 1 test.log | grep -q 'OK' test.log
make[2]: Leaving directory '/<<BUILDDIR>>/gemma-0.98+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/gemma-0.98+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f -- debian/gemma.substvars
rm -fr -- debian/.debhelper/generated/gemma/ debian/gemma/ debian/tmp/
dh_auto_install -a
install -d /<<BUILDDIR>>/gemma-0.98\+dfsg/debian/tmp
dh_install -a
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 -a
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
dh_installchangelogs -a
install -p -m0644 debian/changelog debian/gemma/usr/share/doc/gemma/changelog.Debian
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
cd debian/gemma
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 '/<<BUILDDIR>>/gemma-0.98+dfsg'
dh_fixperms -a
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/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/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/gemma -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/gemma/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing -a
dh_strip -a
install -d debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/b5
objcopy --only-keep-debug --compress-debug-sections debian/gemma/usr/bin/gemma debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/b5/092aae4f9d91f74dcd5287da83af23d5271086.debug
chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/b5/092aae4f9d91f74dcd5287da83af23d5271086.debug
chown 0:0 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/b5/092aae4f9d91f74dcd5287da83af23d5271086.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/b5/092aae4f9d91f74dcd5287da83af23d5271086.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 -a
rm -f debian/gemma/DEBIAN/shlibs
dh_shlibdeps -a
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
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gemma/usr/bin/gemma was not linked against libgfortran.so.5 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gemma/usr/bin/gemma was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
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=b5092aae4f9d91f74dcd5287da83af23d5271086 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
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 -a
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
dh_builddeb -a
dpkg-deb --build debian/gemma ..
dpkg-deb --build debian/.debhelper/gemma/dbgsym-root ..
dpkg-deb: building package 'gemma-dbgsym' in '../gemma-dbgsym_0.98+dfsg-2_armhf.deb'.
dpkg-deb: building package 'gemma' in '../gemma_0.98+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../gemma_0.98+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build gemma-0.98+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-10-27T06:44:10Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
gemma_0.98+dfsg-2_armhf.changes:
--------------------------------
Format: 1.8
Date: Mon, 22 Oct 2018 07:32:31 +0200
Source: gemma
Binary: gemma gemma-doc
Architecture: armhf
Version: 0.98+dfsg-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
gemma - Genome-wide Efficient Mixed Model Association
gemma-doc - Example folder for GEMMA
Closes: 907406
Changes:
gemma (0.98+dfsg-2) unstable; urgency=medium
.
* Team upload.
* Fix folder of examples files in autopkgtest (Closes: #907406)
* Set Multi-Arch: foreign for gemma-doc
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2abc6598b3ca274d717e885b806a696923de3c8e 262584 gemma_0.98+dfsg-2_armhf.deb
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Files:
18a36ad350f141145ce43d5ed7d1eb6f 7471360 debug optional gemma-dbgsym_0.98+dfsg-2_armhf.deb
5bebc39e12fa5225c4f987c2677a92c5 5037 science optional gemma_0.98+dfsg-2_armhf.buildinfo
d4ab6d3aec3c1c5029bcc383fc4a33ff 262584 science optional gemma_0.98+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
gemma-dbgsym_0.98+dfsg-2_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 7471360 bytes: control archive=536 bytes.
371 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: gemma-dbgsym
Source: gemma
Version: 0.98+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7628
Depends: gemma (= 0.98+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for gemma
Build-Ids: b5092aae4f9d91f74dcd5287da83af23d5271086
drwxr-xr-x root/root 0 2018-10-22 05:32 ./
drwxr-xr-x root/root 0 2018-10-22 05:32 ./usr/
drwxr-xr-x root/root 0 2018-10-22 05:32 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-22 05:32 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-22 05:32 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-22 05:32 ./usr/lib/debug/.build-id/b5/
-rw-r--r-- root/root 7800304 2018-10-22 05:32 ./usr/lib/debug/.build-id/b5/092aae4f9d91f74dcd5287da83af23d5271086.debug
drwxr-xr-x root/root 0 2018-10-22 05:32 ./usr/share/
drwxr-xr-x root/root 0 2018-10-22 05:32 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-22 05:32 ./usr/share/doc/gemma-dbgsym -> gemma
gemma_0.98+dfsg-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 262584 bytes: control archive=1372 bytes.
1958 bytes, 34 lines control
327 bytes, 5 lines md5sums
Package: gemma
Version: 0.98+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 971
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgfortran5 (>= 8), libgsl23 (>= 2.5), libopenblas-base, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: http://www.xzlab.org/software.html
Description: Genome-wide Efficient Mixed Model Association
GEMMA is the software implementing the Genome-wide Efficient Mixed
Model Association algorithm for a standard linear mixed model and some
of its close relatives for genome-wide association studies (GWAS):
.
* It fits a univariate linear mixed model (LMM) for marker association
tests with a single phenotype to account for population stratification
and sample structure, and for estimating the proportion of variance in
phenotypes explained (PVE) by typed genotypes (i.e. "chip heritability").
* It fits a multivariate linear mixed model (mvLMM) for testing marker
associations with multiple phenotypes simultaneously while controlling
for population stratification, and for estimating genetic correlations
among complex phenotypes.
* It fits a Bayesian sparse linear mixed model (BSLMM) using Markov
chain Monte Carlo (MCMC) for estimating PVE by typed genotypes,
predicting phenotypes, and identifying associated markers by jointly
modeling all markers while controlling for population structure.
* It estimates variance component/chip heritability, and partitions
it by different SNP functional categories. In particular, it uses HE
regression or REML AI algorithm to estimate variance components when
individual-level data are available. It uses MQS to estimate variance
components when only summary statisics are available.
.
GEMMA is computationally efficient for large scale GWAS and uses freely
available open-source numerical libraries.
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Build Architecture: armhf
Build-Space: 422752
Build-Time: 1645
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 208
Job: gemma_0.98+dfsg-2
Machine Architecture: armhf
Package: gemma
Package-Time: 1914
Source-Version: 0.98+dfsg-2
Space: 422752
Status: successful
Version: 0.98+dfsg-2
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Finished at 2018-10-27T06:44:10Z
Build needed 00:31:54, 422752k disk space