stacks →
2.0Beta8c+dfsg-1 →
armhf → 2018-02-24 05:14:05
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| stacks 2.0Beta8c+dfsg-1 (armhf) Sat, 24 Feb 2018 05:05:00 +0000 |
+==============================================================================+
Package: stacks
Version: 2.0Beta8c+dfsg-1
Source Version: 2.0Beta8c+dfsg-1
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-364bf9e6-9023-46ee-9153-28ac31bbfe87' 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 [10.6 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.4 MB]
Fetched 23.0 MB in 8s (2838 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: 'stacks' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/stacks.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/stacks.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 6016 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main stacks 2.0Beta8c+dfsg-1 (dsc) [2164 B]
Get:2 http://172.17.0.1/private buster-staging/main stacks 2.0Beta8c+dfsg-1 (tar) [6005 kB]
Get:3 http://172.17.0.1/private buster-staging/main stacks 2.0Beta8c+dfsg-1 (diff) [9240 B]
Fetched 6016 kB in 1s (7469 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/stacks-I8Lk2P/stacks-2.0Beta8c+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/stacks-I8Lk2P' 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-VfMi48/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-VfMi48/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-VfMi48/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-VfMi48/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (10.5 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 e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 84 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-VfMi48/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15333 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~), python, zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0), samtools, libhts-dev
Filtered Build-Depends: debhelper (>= 11~), python, zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0), samtools, libhts-dev
dpkg-deb: building package 'sbuild-build-depends-stacks-dummy' in '/<<BUILDDIR>>/resolver-VfMi48/apt_archive/sbuild-build-depends-stacks-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-stacks-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-VfMi48/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ Sources [532 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ Packages [615 B]
Fetched 2480 B in 0s (12.4 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install stacks 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 e2fsprogs-l10n libsasl2-modules openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbam-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libgdbm5
libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu57 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libsparsehash-dev libssh2-1
libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
gdbm-l10n krb5-doc krb5-user liblzma-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl
cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbam-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libgdbm5
libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu57 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libsparsehash-dev libssh2-1
libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal samtools
sbuild-build-depends-stacks-dummy zlib1g-dev
0 upgraded, 57 newly installed, 0 to remove and 84 not upgraded.
Need to get 25.3 MB/25.4 MB of archives.
After this operation, 87.2 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VfMi48/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.7-1 [96.8 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 groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libgdbm5 armhf 1.14.1-3 [54.0 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.1-1+b1 [1143 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-6 [393 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-6 [1080 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.14-4 [41.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.14-6 [1841 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.14-6 [293 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.14-4 [20.4 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-4 [155 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-2 [225 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-2 [105 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-2 [63.8 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.2 [12.1 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20171216.1 [75.9 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 16 [16.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.3-2 [2651 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-6.1 [602 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.4 [1005 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.16-2 [59.0 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.16-2 [116 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.16-2 [265 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.16-2 [135 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.30.0-1 [70.6 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.19.1-4 [43.2 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.58.0-2 [275 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.2-1.3 [284 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libsparsehash-dev all 2.0.2-1 [76.9 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.7-1 [248 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package po-debconf.
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Unpacking po-debconf (1.0.20) ...
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Unpacking debhelper (11.1.4) ...
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Unpacking libbam-dev (0.1.19-2) ...
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Unpacking libkrb5support0:armhf (1.16-2) ...
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Unpacking libk5crypto3:armhf (1.16-2) ...
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Unpacking libkrb5-3:armhf (1.16-2) ...
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Unpacking libgssapi-krb5-2:armhf (1.16-2) ...
Selecting previously unselected package libnghttp2-14:armhf.
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Unpacking libnghttp2-14:armhf (1.30.0-1) ...
Selecting previously unselected package libpsl5:armhf.
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Unpacking libpsl5:armhf (0.19.1-4) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../33-librtmp1_2.4+20151223.gitfa8646d.1-1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../34-libssh2-1_1.8.0-1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-1) ...
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Unpacking libcurl3-gnutls:armhf (7.58.0-2) ...
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Unpacking libhts2:armhf (1.7-2) ...
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Unpacking liblzma-dev:armhf (5.2.2-1.3) ...
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Unpacking libsparsehash-dev (2.0.2-1) ...
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Unpacking samtools (1.7-1) ...
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Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
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Preparing to unpack .../42-sbuild-build-depends-stacks-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Setting up libsparsehash-dev (2.0.2-1) ...
Setting up libexpat1:armhf (2.2.5-3) ...
Setting up libarchive-zip-perl (1.60-1) ...
Setting up libnghttp2-14:armhf (1.30.0-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-1) ...
Setting up libpsl5:armhf (0.19.1-4) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.54.3-2) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libgdbm5:armhf (1.14.1-3) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libmagic-mgc (1:5.32-2) ...
Setting up libmagic1:armhf (1:5.32-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.26-4+rpi1) ...
Setting up autotools-dev (20171216.1) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
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 libpython2.7-stdlib:armhf (2.7.14-6) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up gettext (0.19.8.1-4) ...
Setting up python2.7 (2.7.14-6) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-2) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up libpython-stdlib:armhf (2.7.14-4) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.1-1+b1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python (2.7.14-4) ...
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up libcurl3-gnutls:armhf (7.58.0-2) ...
Setting up libhts2:armhf (1.7-2) ...
Setting up libhts-dev:armhf (1.7-2) ...
Setting up samtools (1.7-1) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (11.1.4) ...
Setting up dh-autoreconf (16) ...
Setting up sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.26-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-13+rpi1 dpkg-dev_1.19.0.5 g++-7_7.2.0-19+b1 gcc-7_7.2.0-19+b1 libc6-dev_2.26-4+rpi1 libstdc++-7-dev_7.2.0-19+b1 libstdc++6_7.2.0-19+b1 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha6 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20171216.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-13+rpi1 binutils-arm-linux-gnueabihf_2.29.1-13+rpi1 binutils-common_2.29.1-13+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.30.2-0.3 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-19+b1 dash_0.5.8-2.10 debconf_1.5.65 debhelper_11.1.4 debianutils_4.8.4 dh-autoreconf_16 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.4-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.43.8-2 e2fsprogs_1.43.8-2 e2fsprogs-l10n_1.43.8-2 fakeroot_1.22-2 fdisk_2.30.2-0.3 file_1:5.32-2 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1d1 g++-7_7.2.0-19+b1 gcc_4:7.2.0-1d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-19+b1 gcc-7-base_7.2.0-19+b1 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.4-1 gnupg-agent_2.2.4-1 gnupg-l10n_2.2.4-1 gnupg-utils_2.2.4-1 gpg_2.2.4-1 gpg-agent_2.2.4-1 gpg-wks-client_2.2.4-1 gpg-wks-server_2.2.4-1 gpgconf_2.2.4-1 gpgsm_2.2.4-1 gpgv_2.2.4-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-2 libapt-pkg5.0_1.6~alpha6 libarchive-zip-perl_1.60-1 libasan4_7.2.0-19+b1 libassuan0_2.5.1-1 libatomic1_7.2.0-19+b1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbam-dev_0.1.19-2 libbinutils_2.29.1-13+rpi1 libblkid1_2.30.2-0.3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-4+rpi1 libc-dev-bin_2.26-4+rpi1 libc6_2.26-4+rpi1 libc6-dev_2.26-4+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_7.2.0-19+b1 libcilkrts5_7.2.0-19+b1 libcomerr2_1.43.8-2 libcroco3_0.6.12-2 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.58.0-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.2-1 libdebconfclient0_0.239 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.89-1+rpi1 libdrm2_2.4.89-1+rpi1 libexpat1_2.2.5-3 libfakeroot_1.22-2 libfdisk1_2.30.2-0.3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-19+b1 libgcc1_1:7.2.0-19+b1 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libgdbm5_1.14.1-3 libglib2.0-0_2.54.3-2 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.17-1 libgomp1_7.2.0-19+b1 libgpg-error0_1.27-5 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu57_57.1-8 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.30.2-0.3 libmpc3_1.1.0-1 libmpfr6_4.0.0-7 libncurses5_6.0+20171125-1 libncursesw5_6.0+20171125-1 libnettle6_3.4-1 libnghttp2-14_1.30.0-1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-8 libperl5.24_5.24.1-7 libperl5.26_5.26.1-4 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpsl5_0.19.1-4 libpython-stdlib_2.7.14-4 libpython2.7-minimal_2.7.14-6 libpython2.7-stdlib_2.7.14-6 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-1 libsmartcols1_2.30.2-0.3 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.22.0-1 libss2_1.43.8-2 libssh2-1_1.8.0-1 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-19+b1 libstdc++6_7.2.0-19+b1 libsystemd0_236-2 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20171125-1 libtool_2.4.6-2 libubsan0_7.2.0-19+b1 libudev1_236-2 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.3 libxml2_2.9.4+dfsg1-6.1 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.1-1+b1 mawk_1.3.3-17 mime-support_3.60 mount_2.30.2-0.3 multiarch-support_2.26-4+rpi1 nano_2.9.2-1 ncurses-base_6.0+20171125-1 ncurses-bin_6.0+20171125-1 openssl_1.1.0g-2 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-4 perl-base_5.26.1-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-4 pinentry-curses_1.0.0-3 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.14-4 python-minimal_2.7.14-4 python2.7_2.7.14-6 python2.7-minimal_2.7.14-6 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 samtools_1.7-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-stacks-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.11 systemd_236-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018c-1 udev_236-2 util-linux_2.30.2-0.3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Feb 18 16:21:11 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./stacks_2.0Beta8c+dfsg-1.dsc
dpkg-source: info: extracting stacks in /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg
dpkg-source: info: unpacking stacks_2.0Beta8c+dfsg.orig.tar.xz
dpkg-source: info: unpacking stacks_2.0Beta8c+dfsg-1.debian.tar.xz
dpkg-source: info: applying constants.php.patch
dpkg-source: info: applying email-settings.patch
dpkg-source: info: applying script-exe-paths
dpkg-source: info: applying use_debian_packaged_htslib.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-364bf9e6-9023-46ee-9153-28ac31bbfe87
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package stacks
dpkg-buildpackage: info: source version 2.0Beta8c+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build stacks-2.0Beta8c+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python2
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
dh_clean
rm -f ./constants.php
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
debian/rules build-arch
dh build-arch --with python2
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:35: installing 'config/ar-lib'
parallel-tests: installing 'config/test-driver'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
dh_auto_configure -- --enable-sparsehash --enable-bam \
--with-bam-include-path=/usr/include/samtools \
--with-bam-lib-path=/usr/lib
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib
configure: WARNING: unrecognized options: --disable-maintainer-mode, --enable-sparsehash, --with-bam-include-path, --with-bam-lib-path
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking whether g++ supports C++11 features by default... yes
checking for ranlib... ranlib
checking for ar... ar
checking the archiver (ar) interface... ar
checking for omp_set_num_threads in -lgomp... yes
checking for gzread in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for gcc option to support OpenMP... -fopenmp
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for clock_gettime... yes
checking for functional regular expressions... yes
checking for gawk... (cached) mawk
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode, --enable-sparsehash, --with-bam-include-path, --with-bam-lib-path
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
Making all in .
make[3]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-BamI.o `test -f 'src/BamI.cc' || echo './'`src/BamI.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-cmb.o `test -f 'src/cmb.cc' || echo './'`src/cmb.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-constants.o `test -f 'src/constants.cc' || echo './'`src/constants.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-DNASeq4.o `test -f 'src/DNASeq4.cc' || echo './'`src/DNASeq4.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-gzFasta.o `test -f 'src/gzFasta.cc' || echo './'`src/gzFasta.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/models.h:24,
from src/models.cc:30:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MarukiLowModel::LikData}; _Tp = MarukiLowModel::LikData; _Alloc = std::allocator<MarukiLowModel::LikData>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<MarukiLowModel::LikData>::iterator {aka __gnu_cxx::__normal_iterator<MarukiLowModel::LikData*, std::vector<MarukiLowModel::LikData> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {MarukiLowModel::LikData}; _Tp = MarukiLowModel::LikData; _Alloc = std::allocator<MarukiLowModel::LikData>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MarukiLowModel::LikData*, std::vector<MarukiLowModel::LikData> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-mst.o `test -f 'src/mst.cc' || echo './'`src/mst.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-nucleotides.o `test -f 'src/nucleotides.cc' || echo './'`src/nucleotides.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-Seq.o `test -f 'src/Seq.cc' || echo './'`src/Seq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libcore_a-Vcf.o `test -f 'src/Vcf.cc' || echo './'`src/Vcf.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/Vcf.h:24,
from src/Vcf.cc:3:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/bits/vector.tcc: In static member function 'static std::__cxx11::string VcfRecord::util::fmt_gt_gl(const std::vector<Nt2>&, const GtLiks&)':
/usr/include/c++/7/bits/vector.tcc:105:21: 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++/7/vector:64:0,
from src/constants.h:38,
from src/Vcf.h:24,
from src/Vcf.cc:3:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static GtLiks VcfRecord::util::parse_gt_gl(const std::vector<Nt2>&, const string&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++/7/bits/stl_vector.h:948:21: 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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/write.o src/write.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libpop_a-export_formats.o `test -f 'src/export_formats.cc' || echo './'`src/export_formats.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libpop_a-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo './'`src/genotype_dictionaries.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libpop_a-PopSum.o `test -f 'src/PopSum.cc' || echo './'`src/PopSum.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/libpop_a-Hwp.o `test -f 'src/Hwp.cc' || echo './'`src/Hwp.cc
src/Hwp.cc: In member function 'void HWMatrix::dump_matrix()':
src/Hwp.cc:383:72: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'std::size_t {aka unsigned int}' [-Wformat=]
snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]);
~~~~~~~~~~~~~~^
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-ustacks.o `test -f 'src/ustacks.cc' || echo './'`src/ustacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-cstacks.o `test -f 'src/cstacks.cc' || echo './'`src/cstacks.cc
In file included from /usr/include/c++/7/vector:69:0,
from src/PopSum.h:26,
from src/PopSum.cc:21:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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++/7/map:60:0,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/7/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++/7/bits/stl_tree.h:2130:5: 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++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const 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++/7/bits/stl_tree.h:2395:7: 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++/7/map:61:0,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/7/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++/7/bits/stl_map.h:493:4: 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++/7/map:60:0,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<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++/7/bits/stl_tree.h:2395:7: 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++/7/map:61:0,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/7/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::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++/7/bits/stl_map.h:512:4: 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++/7/bits/stl_map.h: In function 'double count_haplotypes_at_locus(int, int, const Datum**, std::map<std::__cxx11::basic_string<char>, double>&)':
/usr/include/c++/7/bits/stl_map.h:512:4: 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++/7/bits/stl_map.h: In member function 'LocStat* LocPopSum::haplotype_diversity(int, int, const Datum**)':
/usr/include/c++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: 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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-sstacks.o `test -f 'src/sstacks.cc' || echo './'`src/sstacks.cc
/usr/include/c++/7/bits/stl_map.h: In member function 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)':
/usr/include/c++/7/bits/stl_map.h:512:4: 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++/7/bits/stl_map.h:512:4: 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++/7/bits/stl_map.h:512:4: 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++/7/bits/stl_map.h:512:4: 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++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: 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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-process_radtags.o `test -f 'src/process_radtags.cc' || echo './'`src/process_radtags.cc
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator<AlignRes>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator {aka __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator<AlignRes>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Aln}; _Tp = Aln; _Alloc = std::allocator<Aln>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<Aln>::iterator {aka __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from src/MetaPopInfo.h:5,
from src/cstacks.cc:25:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator<AlignRes>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator {aka __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator<AlignRes>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/set:60:0,
from src/constants.h:41,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: 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++/7/algorithm:62:0,
from src/constants.h:51,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algobase.h:71:0,
from /usr/include/c++/7/vector:60,
from src/constants.h:38,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/predefined_ops.h: In member function 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Iterator2 = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Compare = bool (*)(Aln, Aln)]':
/usr/include/c++/7/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/7/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from src/constants.h:51,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from src/constants.h:51,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/vector.tcc: In function '_Z15search_for_gapsRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEE._omp_fn.0':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from src/constants.h:51,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Distance = int; _Tp = Aln; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(Aln, Aln)>]':
/usr/include/c++/7/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Distance = int; _Tp = Aln; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'int merge_gapped_alns(std::map<int, Stack*>&, std::map<int, Rem*>&, std::map<int, MergedStack*>&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from src/constants.h:42,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/7/bits/stl_map.h: In function 'int dump_stack_graph(std::__cxx11::string, std::map<int, Stack*>&, std::map<int, MergedStack*>&, std::vector<int>&, std::map<int, std::map<int, double> >&, std::map<int, std::set<int> >&)':
/usr/include/c++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: 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++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/c++/7/regex:51,
from src/sstacks.cc:25:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator<AlignRes>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator {aka __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator<AlignRes>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-process_shortreads.o `test -f 'src/process_shortreads.cc' || echo './'`src/process_shortreads.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter-kmer_filter.o `test -f 'src/kmer_filter.cc' || echo './'`src/kmer_filter.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-clone_filter.o `test -f 'src/clone_filter.cc' || echo './'`src/clone_filter.cc
In file included from /usr/include/c++/7/algorithm:62:0,
from /usr/include/c++/7/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /usr/include/c++/7/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from /usr/include/c++/7/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-populations.o `test -f 'src/populations.cc' || echo './'`src/populations.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-phasedstacks.o `test -f 'src/phasedstacks.cc' || echo './'`src/phasedstacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam-tsv2bam.o `test -f 'src/tsv2bam.cc' || echo './'`src/tsv2bam.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks-gstacks.o `test -f 'src/gstacks.cc' || echo './'`src/gstacks.cc
src/gstacks.cc: In member function 'bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const':
src/gstacks.cc:1069:51: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::__cxx11::basic_string<char>::size_type {aka unsigned int}' [-Wformat=]
snprintf(c, id_len, "%luM", query.length());
~~~~~~~~~~~~~~^
src/gstacks.cc: In member function 'std::size_t LocusProcessor::find_locus_overlap(SuffixTree*, GappedAln*, const DNASeq4&, std::__cxx11::string&) const':
src/gstacks.cc:1252:63: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::size_t {aka unsigned int}' [-Wformat=]
snprintf(buf, id_len, "%luM", alns.front().aln_len);
~~~~~~~~~~~~~~~~~~~~^
In file included from /usr/include/c++/7/vector:69:0,
from src/phasedstacks.h:39,
from src/phasedstacks.cc:25:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks-debruijn.o `test -f 'src/debruijn.cc' || echo './'`src/debruijn.cc
In file included from /usr/include/c++/7/vector:69:0,
from src/locus.h:26,
from src/export_formats.h:29,
from src/populations.cc:28:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/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++/7/bits/vector.tcc:105:21: 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++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Datum::SNPData}; _Tp = Datum::SNPData; _Alloc = std::allocator<Datum::SNPData>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<Datum::SNPData>::iterator {aka __gnu_cxx::__normal_iterator<Datum::SNPData*, std::vector<Datum::SNPData> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Datum::SNPData}; _Tp = Datum::SNPData; _Alloc = std::allocator<Datum::SNPData>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Datum::SNPData*, std::vector<Datum::SNPData> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/unordered_set:47:0,
from src/constants.h:43,
from src/debruijn.cc:5:
/usr/include/c++/7/bits/hashtable.h: In member function 'std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::iterator std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::erase(std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::const_iterator) [with _Key = Kmer; _Value = std::pair<const Kmer, KmMapValue>; _Alloc = std::allocator<std::pair<const Kmer, KmMapValue> >; _ExtractKey = std::__detail::_Select1st; _Equal = std::equal_to<Kmer>; _H1 = std::hash<Kmer>; _H2 = std::__detail::_Mod_range_hashing; _Hash = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits<true, false, true>]':
/usr/include/c++/7/bits/hashtable.h:1850:5: note: parameter passing for argument of type 'std::_Hashtable<Kmer, std::pair<const Kmer, KmMapValue>, std::allocator<std::pair<const Kmer, KmMapValue> >, std::__detail::_Select1st, std::equal_to<Kmer>, std::hash<Kmer>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >::const_iterator {aka std::__detail::_Node_const_iterator<std::pair<const Kmer, KmMapValue>, false, true>}' changed in GCC 7.1
_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_H1, _H2, _Hash, _RehashPolicy, _Traits>::
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/hashtable.h:1850:5: note: parameter passing for argument of type 'std::_Hashtable<Kmer, std::pair<const Kmer, KmMapValue>, std::allocator<std::pair<const Kmer, KmMapValue> >, std::__detail::_Select1st, std::equal_to<Kmer>, std::hash<Kmer>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >::const_iterator {aka std::__detail::_Node_const_iterator<std::pair<const Kmer, KmMapValue>, false, true>}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/debruijn.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Node}; _Tp = Node; _Alloc = std::allocator<Node>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<Node>::iterator {aka __gnu_cxx::__normal_iterator<Node*, std::vector<Node> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/unordered_set:47:0,
from src/constants.h:43,
from src/debruijn.cc:5:
/usr/include/c++/7/bits/hashtable.h: In member function 'void Graph::rebuild(const std::vector<const DNASeq4*>&, std::size_t)':
/usr/include/c++/7/bits/hashtable.h:755:42: note: parameter passing for argument of type 'std::_Hashtable<Kmer, std::pair<const Kmer, KmMapValue>, std::allocator<std::pair<const Kmer, KmMapValue> >, std::__detail::_Select1st, std::equal_to<Kmer>, std::hash<Kmer>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >::const_iterator {aka std::__detail::_Node_const_iterator<std::pair<const Kmer, KmMapValue>, false, true>}' changed in GCC 7.1
{ return erase(const_iterator(__it)); }
^
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/debruijn.cc:5:
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Node*, std::vector<Node> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks-SuffixTree.o `test -f 'src/SuffixTree.cc' || echo './'`src/SuffixTree.cc
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)> >]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:71:0,
from /usr/include/c++/7/vector:60,
from src/constants.h:38,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/predefined_ops.h: In function 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >; _Iterator2 = __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)>]':
/usr/include/c++/7/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/7/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)> >]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1847:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
if (__comp(__i, __first))
~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from src/constants.h:51,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >; _Distance = int; _Tp = STAln; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)> >]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:222:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
if (__comp(__first + __secondChild,
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
__first + (__secondChild - 1)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from src/locus.h:28,
from src/export_formats.h:29,
from src/populations.cc:28:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__final_insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from src/locus.h:28,
from src/export_formats.h:29,
from src/populations.cc:28:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from src/locus.h:28,
from src/export_formats.h:29,
from src/populations.cc:28:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'int bootstrap_fst_approximate_dist(std::vector<double>&, std::vector<int>&, double*, int*, std::map<int, std::vector<double> >&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const STAln&}; _Tp = STAln; _Alloc = std::allocator<STAln>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<STAln>::iterator {aka __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'int bootstrap_popstats_approximate_dist(std::vector<double>&, std::vector<double>&, std::vector<int>&, double*, int*, int, std::map<int, std::vector<double> >&, std::map<int, std::vector<double> >&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__final_insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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
rm -f libcore.a
ar cru libcore.a src/libcore_a-aln_utils.o src/libcore_a-BamI.o src/libcore_a-catalog_utils.o src/libcore_a-cmb.o src/libcore_a-constants.o src/libcore_a-DNANSeq.o src/libcore_a-DNASeq4.o src/libcore_a-DNASeq.o src/libcore_a-gzFasta.o src/libcore_a-input.o src/libcore_a-kmers.o src/libcore_a-locus.o src/libcore_a-log_utils.o src/libcore_a-MetaPopInfo.o src/libcore_a-models.o src/libcore_a-mstack.o src/libcore_a-mst.o src/libcore_a-nucleotides.o src/libcore_a-renz.o src/libcore_a-Seq.o src/libcore_a-sql_utilities.o src/libcore_a-stacks.o src/libcore_a-utils.o src/libcore_a-Vcf.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcore.a
rm -f libclean.a
ar cru libclean.a src/clean.o src/file_io.o src/write.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libclean.a
rm -f libpop.a
ar cru libpop.a src/libpop_a-export_formats.o src/libpop_a-genotype_dictionaries.o src/libpop_a-PopSum.o src/libpop_a-Hwp.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpop.a
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks-ustacks.o libcore.a -lhts -lz -lgomp
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator<AlignRes>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator {aka __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator<AlignRes>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks-cstacks.o libcore.a -lhts -lz -lgomp
g++ -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks-sstacks.o libcore.a -lhts -lz -lgomp
g++ -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags-process_radtags.o libcore.a libclean.a -lhts -lz -lgomp
g++ -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads-process_shortreads.o libcore.a libclean.a -lhts -lz -lgomp
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {STAln}; _Tp = STAln; _Alloc = std::allocator<STAln>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<STAln>::iterator {aka __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {STAln}; _Tp = STAln; _Alloc = std::allocator<STAln>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {STLink}; _Tp = STLink; _Alloc = std::allocator<STLink>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<STLink>::iterator {aka __gnu_cxx::__normal_iterator<STLink*, std::vector<STLink> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter-kmer_filter.o libcore.a libclean.a -lhts -lz -lgomp
g++ -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter-clone_filter.o libcore.a libclean.a -lhts -lz -lgomp
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks-phasedstacks.o libcore.a -lhts -lz -lgomp
/usr/include/c++/7/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, Nt2>}; _Tp = std::pair<double, Nt2>; _Alloc = std::allocator<std::pair<double, Nt2> >]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<std::pair<double, Nt2> >::iterator {aka __gnu_cxx::__normal_iterator<std::pair<double, Nt2>*, std::vector<std::pair<double, Nt2> > >}' changed in GCC 7.1
g++ -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam-tsv2bam.o libcore.a -lhts -lz -lgomp
g++ -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations-populations.o libcore.a libpop.a -lhts -lz -lgomp
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from src/constants.h:51,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from src/constants.h:51,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)> >]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STLink*, std::vector<STLink> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from src/constants.h:38,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from src/constants.h:38,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/vector.tcc: In member function 'void LocusProcessor::write_one_locus(const CLocAlnSet&, const std::vector<SiteCounts>&, const std::vector<SiteCall>&, const std::vector<std::map<unsigned int, PhasedHet> >&)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, Nt2>*, std::vector<std::pair<double, Nt2> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from src/constants.h:38,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/7/bits/stl_vector.h:948:21: 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++ -fopenmp -I/usr/include/htslib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o gstacks src/gstacks-gstacks.o src/gstacks-debruijn.o src/gstacks-SuffixTree.o libcore.a -lhts -lz -lgomp
make[3]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
#ln -s /usr/share/automake-1.14/tap-driver.sh tests/tap-driver.sh
#dh_auto_test
# Does not work even after this trick. See
# https://groups.google.com/forum/#!msg/stacks-users/TA2tMEqb4Mg/pQy4fUCYi9kJ
true
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with python2
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<BUILDDIR>>/stacks-2.0Beta8c\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
Making install in .
make[2]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks'
/usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin'
/usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/export_sql.pl scripts/sort_read_pairs.pl scripts/exec_velvet.pl scripts/load_sequences.pl scripts/index_radtags.pl scripts/load_radtags.pl scripts/stacks_export_notify.pl scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/sql'
/usr/bin/install -c -m 644 sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/sql'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php'
/usr/bin/install -c -m 644 php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php php/stacks_functions.php php/view_sequence.php php/sequence_blast.php php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php/images'
/usr/bin/install -c -m 644 php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png php/images/stacks_logo_rev_small.png '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php/images'
make install-data-hook
make[4]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
sed -e 's,_VERSION_,2.0Beta8c,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/denovo_map.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/denovo_map.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/denovo_map.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/denovo_map.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/denovo_map.pl
sed -e 's,_VERSION_,2.0Beta8c,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/ref_map.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/ref_map.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/ref_map.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/ref_map.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/ref_map.pl
sed -e 's,_VERSION_,2.0Beta8c,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/export_sql.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/export_sql.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/export_sql.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/export_sql.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/export_sql.pl
sed -e 's,_VERSION_,2.0Beta8c,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/index_radtags.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/index_radtags.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/index_radtags.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/index_radtags.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/index_radtags.pl
sed -e 's,_VERSION_,2.0Beta8c,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_radtags.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_radtags.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_radtags.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_radtags.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_radtags.pl
sed -e 's,_VERSION_,2.0Beta8c,' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/sort_read_pairs.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/sort_read_pairs.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/sort_read_pairs.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/sort_read_pairs.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/sort_read_pairs.pl
sed -e 's,_VERSION_,2.0Beta8c,' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/exec_velvet.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/exec_velvet.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/exec_velvet.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/exec_velvet.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/exec_velvet.pl
sed -e 's,_VERSION_,2.0Beta8c,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_sequences.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_sequences.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_sequences.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_sequences.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/load_sequences.pl
sed -e 's,_VERSION_,2.0Beta8c,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' \
/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks_export_notify.pl > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks_export_notify.pl.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks_export_notify.pl.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks_export_notify.pl
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks_export_notify.pl
sed -e 's,_PKGDATADIR_,/usr/share/stacks/,g' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' \
/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php/constants.php.dist > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php/constants.php.dist.subst
mv /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php/constants.php.dist.subst /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php/constants.php.dist
echo 2.0Beta8c > /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php/version.php
/bin/bash /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/config/install-sh -d -m 755 /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/share/stacks/php/export
sed -i.bkp -e 's,_VERSION_,2.0Beta8c,' /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks-integrate-alignments
rm -f /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks-integrate-alignments.bkp
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks-integrate-alignments
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks-dist-extract
chmod +x /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/tmp/usr/bin/stacks-gdb
make[4]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
cp php/constants.php.dist ./constants.php
dh_install
# Skip this bit if not building stacks
! cd debian/stacks/usr/lib/stacks/bin || \
for f in *.pl ; do \
ln -s "$f" "`basename $f .pl`" ; \
done
# Skip this bit if not building stacks-web
# Note - directory perms will be set in postinst
dh_installdirs -pstacks-web /var/lib/stacks/export
dh_installdirs: No packages to build. Architecture mismatch: armhf, want: all any
if [ -e debian/stacks-web/usr/share/stacks/php ] ; then \
rmdir debian/stacks-web/usr/share/stacks/php/export ; \
ln -s /var/lib/stacks/export \
debian/stacks-web/usr/share/stacks/php/export ; \
fi
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_python2 -a
W: dh_python2:479: Please add dh-python package to Build-Depends
dh_perl -a
debian/rules override_dh_link
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
dh_link
mkdir -p debian/stacks/usr/lib/debian-med/bin
cd debian/stacks/usr/lib/debian-med/bin && \
for f in `ls /<<BUILDDIR>>/stacks-2.0Beta8c+dfsg/debian/stacks/usr/lib/stacks/bin` ; do \
ln -s ../../stacks/bin/$f ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.0Beta8c+dfsg'
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/kmer_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/populations contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/cstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/phasedstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_radtags contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/clone_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/gstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_shortreads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/tsv2bam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/sstacks 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/stacks/usr/lib/stacks/bin/kmer_filter debian/stacks/usr/lib/stacks/bin/populations debian/stacks/usr/lib/stacks/bin/cstacks debian/stacks/usr/lib/stacks/bin/phasedstacks debian/stacks/usr/lib/stacks/bin/process_radtags debian/stacks/usr/lib/stacks/bin/clone_filter debian/stacks/usr/lib/stacks/bin/gstacks debian/stacks/usr/lib/stacks/bin/process_shortreads debian/stacks/usr/lib/stacks/bin/tsv2bam debian/stacks/usr/lib/stacks/bin/ustacks debian/stacks/usr/lib/stacks/bin/sstacks were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package stacks: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package stacks: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'stacks' in '../stacks_2.0Beta8c+dfsg-1_armhf.deb'.
dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.0Beta8c+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../stacks_2.0Beta8c+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build stacks-2.0Beta8c+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-02-24T05:14:01Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
stacks_2.0Beta8c+dfsg-1_armhf.changes:
--------------------------------------
Format: 1.8
Date: Sun, 18 Feb 2018 17:15:06 +0100
Source: stacks
Binary: stacks stacks-web
Architecture: armhf
Version: 2.0Beta8c+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
stacks - pipeline for building loci from short-read DNA sequences
stacks-web - web interface for displaying loci from short-read sequences
Changes:
stacks (2.0Beta8c+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Remove code copy of htslib and use Debian packaged version of htslib
instead
* Standards-Version: 4.1.3
* debhelper 11
Checksums-Sha1:
5877b3874f4401c16b32a24e2f6a18e6ca4e990d 24309264 stacks-dbgsym_2.0Beta8c+dfsg-1_armhf.deb
6359ebcf05d4675bf873f18a69670f482f72ee8d 5679 stacks_2.0Beta8c+dfsg-1_armhf.buildinfo
647a0e1001262612da9a7453668d941c901f03b1 733760 stacks_2.0Beta8c+dfsg-1_armhf.deb
Checksums-Sha256:
146104070d42b0bd9a0d19f105f8abf7cc7304f44f1206c6aa76bbe286659a24 24309264 stacks-dbgsym_2.0Beta8c+dfsg-1_armhf.deb
534ccbbe0636904a10ce6c949fb8c03c3cf4e2895282652a60ed707531075518 5679 stacks_2.0Beta8c+dfsg-1_armhf.buildinfo
a2da59efe0d11d3e80f8c7900b2cad126230177609f14064989b059b307a2353 733760 stacks_2.0Beta8c+dfsg-1_armhf.deb
Files:
f213a64d58086a65b435b5cdf5989d9d 24309264 debug optional stacks-dbgsym_2.0Beta8c+dfsg-1_armhf.deb
ece0b6ad93e117c0333eb9b34329cd36 5679 science optional stacks_2.0Beta8c+dfsg-1_armhf.buildinfo
a231f7d14d67c22c8faa090e39b4acca 733760 science optional stacks_2.0Beta8c+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
stacks-dbgsym_2.0Beta8c+dfsg-1_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 24309264 bytes: control archive=1048 bytes.
796 bytes, 12 lines control
1166 bytes, 11 lines md5sums
Package: stacks-dbgsym
Source: stacks
Version: 2.0Beta8c+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 24991
Depends: stacks (= 2.0Beta8c+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for stacks
Build-Ids: 04617f5279bea21ae300c81079387fd07113f747 48ddc0c16dd2202389816968e031e5c6971f1372 6da089834fac59a6351a12d5a572ce8a8854c024 6f4487f0d7231523ebfa9622e77a852ef8194ecb 8029ac26d5cfe22d8e378ef58e21d29b835dc1d4 8145c6794e7a5e36fdee3dca2e2447092f2e77bc 899c993a2b59efacc20f98b1581b472cfebab71f a1215aad349a98f45b895926d6a12a762a61cb88 ac3be0155f677744765cbcff37df5c950a726c43 c183070cab3d3b4cc08cf35963068bcb23926b79 d84f46391fac290a89ede2bb587469c48b2f91a8
drwxr-xr-x root/root 0 2018-02-18 16:15 ./
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/04/
-rw-r--r-- root/root 2320852 2018-02-18 16:15 ./usr/lib/debug/.build-id/04/617f5279bea21ae300c81079387fd07113f747.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/48/
-rw-r--r-- root/root 934248 2018-02-18 16:15 ./usr/lib/debug/.build-id/48/ddc0c16dd2202389816968e031e5c6971f1372.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/6d/
-rw-r--r-- root/root 3754940 2018-02-18 16:15 ./usr/lib/debug/.build-id/6d/a089834fac59a6351a12d5a572ce8a8854c024.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/6f/
-rw-r--r-- root/root 4038860 2018-02-18 16:15 ./usr/lib/debug/.build-id/6f/4487f0d7231523ebfa9622e77a852ef8194ecb.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/80/
-rw-r--r-- root/root 1901524 2018-02-18 16:15 ./usr/lib/debug/.build-id/80/29ac26d5cfe22d8e378ef58e21d29b835dc1d4.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/81/
-rw-r--r-- root/root 2651628 2018-02-18 16:15 ./usr/lib/debug/.build-id/81/45c6794e7a5e36fdee3dca2e2447092f2e77bc.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/89/
-rw-r--r-- root/root 1269772 2018-02-18 16:15 ./usr/lib/debug/.build-id/89/9c993a2b59efacc20f98b1581b472cfebab71f.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/a1/
-rw-r--r-- root/root 3106376 2018-02-18 16:15 ./usr/lib/debug/.build-id/a1/215aad349a98f45b895926d6a12a762a61cb88.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/ac/
-rw-r--r-- root/root 2249664 2018-02-18 16:15 ./usr/lib/debug/.build-id/ac/3be0155f677744765cbcff37df5c950a726c43.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/c1/
-rw-r--r-- root/root 1578772 2018-02-18 16:15 ./usr/lib/debug/.build-id/c1/83070cab3d3b4cc08cf35963068bcb23926b79.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debug/.build-id/d8/
-rw-r--r-- root/root 1758528 2018-02-18 16:15 ./usr/lib/debug/.build-id/d8/4f46391fac290a89ede2bb587469c48b2f91a8.debug
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/share/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/share/doc/stacks-dbgsym -> stacks
stacks_2.0Beta8c+dfsg-1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 733760 bytes: control archive=1976 bytes.
953 bytes, 18 lines control
2112 bytes, 31 lines md5sums
171 bytes, 9 lines * postinst #!/bin/sh
251 bytes, 14 lines * prerm #!/bin/sh
Package: stacks
Version: 2.0Beta8c+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3924
Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libhts2 (>= 1.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.6), python:any (>= 2.6.6-7~), samtools, libdbi-perl
Recommends: libspreadsheet-writeexcel-perl
Section: science
Priority: optional
Homepage: http://creskolab.uoregon.edu/stacks/
Description: pipeline for building loci from short-read DNA sequences
Stacks is a software pipeline for building loci from short-read sequences,
such as those generated on the Illumina platform. Stacks was developed to work
with restriction enzyme-based data, such as RAD-seq, for the purpose of
building genetic maps and conducting population genomics and phylogeography.
.
Note that this package installs Stacks such that all commands must be run as:
$ stacks <cmdname> <args>
drwxr-xr-x root/root 0 2018-02-18 16:15 ./
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/bin/
-rwxr-xr-x root/root 771 2018-02-18 16:15 ./usr/bin/stacks
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/count_fixed_catalog_snps.py -> ../../stacks/bin/count_fixed_catalog_snps.py
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/cstacks -> ../../stacks/bin/cstacks
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/exec_velvet -> ../../stacks/bin/exec_velvet
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/exec_velvet.pl -> ../../stacks/bin/exec_velvet.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/export_sql -> ../../stacks/bin/export_sql
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/export_sql.pl -> ../../stacks/bin/export_sql.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/gstacks -> ../../stacks/bin/gstacks
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/index_radtags -> ../../stacks/bin/index_radtags
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/index_radtags.pl -> ../../stacks/bin/index_radtags.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/integrate_alignments.py -> ../../stacks/bin/integrate_alignments.py
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/load_radtags -> ../../stacks/bin/load_radtags
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/load_radtags.pl -> ../../stacks/bin/load_radtags.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/load_sequences -> ../../stacks/bin/load_sequences
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/load_sequences.pl -> ../../stacks/bin/load_sequences.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/populations -> ../../stacks/bin/populations
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/ref_map -> ../../stacks/bin/ref_map
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/sort_read_pairs -> ../../stacks/bin/sort_read_pairs
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/sort_read_pairs.pl -> ../../stacks/bin/sort_read_pairs.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/sstacks -> ../../stacks/bin/sstacks
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/stacks_export_notify -> ../../stacks/bin/stacks_export_notify
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/stacks_export_notify.pl -> ../../stacks/bin/stacks_export_notify.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/debian-med/bin/ustacks -> ../../stacks/bin/ustacks
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/stacks/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/
-rwxr-xr-x root/root 248184 2018-02-18 16:15 ./usr/lib/stacks/bin/clone_filter
-rwxr-xr-x root/root 8615 2018-02-18 16:15 ./usr/lib/stacks/bin/count_fixed_catalog_snps.py
-rwxr-xr-x root/root 309568 2018-02-18 16:15 ./usr/lib/stacks/bin/cstacks
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/denovo_map -> denovo_map.pl
-rwxr-xr-x root/root 35218 2018-02-18 16:15 ./usr/lib/stacks/bin/denovo_map.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/exec_velvet -> exec_velvet.pl
-rwxr-xr-x root/root 8924 2018-02-18 16:15 ./usr/lib/stacks/bin/exec_velvet.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/export_sql -> export_sql.pl
-rwxr-xr-x root/root 31823 2018-02-18 16:15 ./usr/lib/stacks/bin/export_sql.pl
-rwxr-xr-x root/root 518272 2018-02-18 16:15 ./usr/lib/stacks/bin/gstacks
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/index_radtags -> index_radtags.pl
-rwxr-xr-x root/root 20394 2018-02-18 16:15 ./usr/lib/stacks/bin/index_radtags.pl
-rwxr-xr-x root/root 10849 2018-02-18 16:15 ./usr/lib/stacks/bin/integrate_alignments.py
-rwxr-xr-x root/root 199056 2018-02-18 16:15 ./usr/lib/stacks/bin/kmer_filter
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/load_radtags -> load_radtags.pl
-rwxr-xr-x root/root 15096 2018-02-18 16:15 ./usr/lib/stacks/bin/load_radtags.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/load_sequences -> load_sequences.pl
-rwxr-xr-x root/root 6250 2018-02-18 16:15 ./usr/lib/stacks/bin/load_sequences.pl
-rwxr-xr-x root/root 289072 2018-02-18 16:15 ./usr/lib/stacks/bin/phasedstacks
-rwxr-xr-x root/root 597600 2018-02-18 16:15 ./usr/lib/stacks/bin/populations
-rwxr-xr-x root/root 298144 2018-02-18 16:15 ./usr/lib/stacks/bin/process_radtags
-rwxr-xr-x root/root 264884 2018-02-18 16:15 ./usr/lib/stacks/bin/process_shortreads
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/ref_map -> ref_map.pl
-rwxr-xr-x root/root 27278 2018-02-18 16:15 ./usr/lib/stacks/bin/ref_map.pl
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/sort_read_pairs -> sort_read_pairs.pl
-rwxr-xr-x root/root 14920 2018-02-18 16:15 ./usr/lib/stacks/bin/sort_read_pairs.pl
-rwxr-xr-x root/root 350504 2018-02-18 16:15 ./usr/lib/stacks/bin/sstacks
-rwxr-xr-x root/root 760 2018-02-18 16:15 ./usr/lib/stacks/bin/stacks-dist-extract
-rwxr-xr-x root/root 1202 2018-02-18 16:15 ./usr/lib/stacks/bin/stacks-gdb
-rwxr-xr-x root/root 5696 2018-02-18 16:15 ./usr/lib/stacks/bin/stacks-integrate-alignments
lrwxrwxrwx root/root 0 2018-02-18 16:15 ./usr/lib/stacks/bin/stacks_export_notify -> stacks_export_notify.pl
-rwxr-xr-x root/root 6459 2018-02-18 16:15 ./usr/lib/stacks/bin/stacks_export_notify.pl
-rwxr-xr-x root/root 329744 2018-02-18 16:15 ./usr/lib/stacks/bin/tsv2bam
-rwxr-xr-x root/root 309832 2018-02-18 16:15 ./usr/lib/stacks/bin/ustacks
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/share/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/share/doc/stacks/
-rw-r--r-- root/root 1451 2018-02-18 16:15 ./usr/share/doc/stacks/README.Debian
-rw-r--r-- root/root 1224 2018-02-18 16:15 ./usr/share/doc/stacks/changelog.Debian.gz
-rw-r--r-- root/root 25646 2018-02-03 19:17 ./usr/share/doc/stacks/changelog.gz
-rw-r--r-- root/root 1360 2018-02-18 16:15 ./usr/share/doc/stacks/copyright
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/share/python/
drwxr-xr-x root/root 0 2018-02-18 16:15 ./usr/share/python/runtime.d/
-rwxr-xr-x root/root 122 2018-02-18 16:15 ./usr/share/python/runtime.d/stacks.rtupdate
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 304604
Build-Time: 237
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 287
Job: stacks_2.0Beta8c+dfsg-1
Machine Architecture: armhf
Package: stacks
Package-Time: 541
Source-Version: 2.0Beta8c+dfsg-1
Space: 304604
Status: successful
Version: 2.0Beta8c+dfsg-1
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Finished at 2018-02-24T05:14:01Z
Build needed 00:09:01, 304604k disk space