stacks →
2.52+dfsg-1 →
armhf → 2020-03-31 11:57:26
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| stacks 2.52+dfsg-1 (armhf) Tue, 31 Mar 2020 11:28:10 +0000 |
+==============================================================================+
Package: stacks
Version: 2.52+dfsg-1
Source Version: 2.52+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-8ee7e875-7bc6-4bab-8f38-5e80da9e2418' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.4 MB in 25s (961 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://salsa.debian.org/med-team/stacks.git
Please use:
git clone https://salsa.debian.org/med-team/stacks.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 331 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main stacks 2.52+dfsg-1 (dsc) [2044 B]
Get:2 http://172.17.0.1/private bullseye-staging/main stacks 2.52+dfsg-1 (tar) [321 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main stacks 2.52+dfsg-1 (diff) [7368 B]
Fetched 331 kB in 0s (3000 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/stacks-vmXy3M/stacks-2.52+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/stacks-vmXy3M' 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-7tNVzY/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-7tNVzY/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-7tNVzY/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-7tNVzY/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2752 B/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:
libpam-cap netbase
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 33 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12270 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)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev
Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev
dpkg-deb: building package 'sbuild-build-depends-stacks-dummy' in '/<<BUILDDIR>>/resolver-7tNVzY/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-7tNVzY/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ Sources [522 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ Packages [601 B]
Fetched 2456 B in 1s (3148 B/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:
libpam-cap netbase
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 dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbam-dev libbrotli1 libbsd0
libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts3 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1
libpsl5 librtmp1 libsigsegv2 libsparsehash-dev libssh2-1 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf samtools sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl python3 cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbam-dev libbrotli1 libbsd0
libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts3 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1
libpsl5 librtmp1 libsigsegv2 libsparsehash-dev libssh2-1 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
po-debconf samtools sbuild-build-depends-stacks-dummy sensible-utils
zlib1g-dev
0 upgraded, 57 newly installed, 0 to remove and 33 not upgraded.
Need to get 27.8 MB of archives.
After this operation, 84.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7tNVzY/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.10 [184 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.1-1 [1157 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-4 [592 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.10 [1003 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libbam-dev armhf 0.1.19-4 [111 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7 [61.4 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7 [112 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7 [320 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7 [135 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1 [53.9 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.68.0-1 [284 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.5-3 [49.0 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-3 [319 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-3 [4796 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libsparsehash-dev all 2.0.3-1 [76.9 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.10-3 [477 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libk5crypto3:armhf.
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Unpacking libk5crypto3:armhf (1.17-7) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../39-libkeyutils1_1.6.1-2_armhf.deb ...
Unpacking libkeyutils1:armhf (1.6.1-2) ...
Selecting previously unselected package libssl1.1:armhf.
Preparing to unpack .../40-libssl1.1_1.1.1d-2_armhf.deb ...
Unpacking libssl1.1:armhf (1.1.1d-2) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../41-libkrb5-3_1.17-7_armhf.deb ...
Unpacking libkrb5-3:armhf (1.17-7) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../42-libgssapi-krb5-2_1.17-7_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.17-7) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../43-libnghttp2-14_1.40.0-1+b2_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.40.0-1+b2) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../44-libpsl5_0.21.0-1_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../45-librtmp1_2.4+20151223.gitfa8646d.1-2+b1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../46-libssh2-1_1.8.0-2.1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-2.1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../47-libcurl3-gnutls_7.68.0-1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.68.0-1) ...
Selecting previously unselected package libdeflate0.
Preparing to unpack .../48-libdeflate0_1.5-3_armhf.deb ...
Unpacking libdeflate0 (1.5-3) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../49-libhts3_1.10.2-3_armhf.deb ...
Unpacking libhts3:armhf (1.10.2-3) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../50-liblzma-dev_5.2.4-1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.4-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../51-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../52-libhts-dev_1.10.2-3_armhf.deb ...
Unpacking libhts-dev:armhf (1.10.2-3) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../53-libncurses6_6.2-1_armhf.deb ...
Unpacking libncurses6:armhf (6.2-1) ...
Selecting previously unselected package libsparsehash-dev.
Preparing to unpack .../54-libsparsehash-dev_2.0.3-1_all.deb ...
Unpacking libsparsehash-dev (2.0.3-1) ...
Selecting previously unselected package samtools.
Preparing to unpack .../55-samtools_1.10-3_armhf.deb ...
Unpacking samtools (1.10-3) ...
Selecting previously unselected package sbuild-build-depends-stacks-dummy.
Preparing to unpack .../56-sbuild-build-depends-stacks-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.1-1) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1d-2) ...
Setting up libdebhelper-perl (12.10) ...
Setting up libbrotli1:armhf (1.0.7-6) ...
Setting up libnghttp2-14:armhf (1.40.0-1+b2) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up libdeflate0 (1.5-3) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-4) ...
Setting up libsparsehash-dev (2.0.3-1) ...
Setting up libicu63:armhf (63.2-3) ...
Setting up libkrb5support0:armhf (1.17-7) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.2-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libbam-dev (0.1.19-4) ...
Setting up libk5crypto3:armhf (1.17-7) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-7) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-4) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
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 libgssapi-krb5-2:armhf (1.17-7) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up libcurl3-gnutls:armhf (7.68.0-1) ...
Setting up man-db (2.9.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhts3:armhf (1.10.2-3) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.10.2-3) ...
Setting up samtools (1.10-3) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.10) ...
Setting up sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-3+rpi1 gcc-9_9.3.0-3+rpi1 libc6-dev_2.30-2+rpi1 libstdc++-9-dev_9.3.0-3+rpi1 libstdc++6_10-20200312-2+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.0.0+b1 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-3+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.19-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-3+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200312-2+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-5 gcc-8-base_8.3.0-29+rpi1 gcc-9_9.3.0-3+rpi1 gcc-9-base_9.3.0-3+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-3 gnupg-l10n_2.2.19-3 gnupg-utils_2.2.19-3 gpg_2.2.19-3 gpg-agent_2.2.19-3 gpg-wks-client_2.2.19-3 gpg-wks-server_2.2.19-3 gpgconf_2.2.19-3 gpgsm_2.2.19-3 gpgv_2.2.19-3 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-6 libapt-pkg6.0_2.0.0+b1 libarchive-zip-perl_1.68-1 libasan5_9.3.0-3+rpi1 libassuan0_2.5.3-7 libatomic1_10-20200312-2+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbam-dev_0.1.19-4 libbinutils_2.34-5+rpi1 libblkid1_2.34-0.1 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-2+rpi1 libc-dev-bin_2.30-2+rpi1 libc6_2.30-2+rpi1 libc6-dev_2.30-2+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.32-1 libcap2-bin_1:2.32-1 libcc1-0_10-20200312-2+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.15-1 libcrypt1_1:4.4.15-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.10 libdeflate0_1.5-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.3.0-3+rpi1 libgcc-s1_10-20200312-2+rpi1 libgcc1_1:10-20200312-2+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_10-20200312-2+rpi1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-7 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7 libkrb5support0_1.17-7 libksba8_1.3.5-2 libldap-2.4-2_2.4.49+dfsg-2 libldap-common_2.4.49+dfsg-2 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.32-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpsl5_0.21.0-1 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsparsehash-dev_2.0.3-1 libsqlite3-0_3.31.1-4 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.3.0-3+rpi1 libstdc++6_10-20200312-2+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.3-1+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10-20200312-2+rpi1 libuchardet0_0.0.6-3 libudev1_244.3-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-4 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 samtools_1.10-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-stacks-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Mar 26 01:34:24 2020 UTC
gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1
gpgv: issuer "moeller@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./stacks_2.52+dfsg-1.dsc
dpkg-source: info: extracting stacks in /<<BUILDDIR>>/stacks-2.52+dfsg
dpkg-source: info: unpacking stacks_2.52+dfsg.orig.tar.xz
dpkg-source: info: unpacking stacks_2.52+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying script-exe-paths
dpkg-source: info: applying use_debian_packaged_htslib.patch
dpkg-source: info: applying 2to3.patch
Check disc 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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-8ee7e875-7bc6-4bab-8f38-5e80da9e2418
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package stacks
dpkg-buildpackage: info: source version 2.52+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
dh_clean
rm -f ./constants.php
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:33: installing 'config/ar-lib'
configure.ac:28: installing 'config/compile'
configure.ac:7: installing 'config/install-sh'
configure.ac:7: installing 'config/missing'
Makefile.am: installing 'config/depcomp'
parallel-tests: installing 'config/test-driver'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.52+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 --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, --enable-bam, --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 whether make supports the include directive... yes (GNU style)
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, --enable-bam, --with-bam-include-path, --with-bam-lib-path
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks.o src/ustacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/aln_utils.o src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/BamI.o src/BamI.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/catalog_utils.o src/catalog_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc
In file included from /usr/include/c++/9/vector:72,
from src/constants.h:40,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: 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++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Aln}; _Tp = Aln; _Alloc = std::allocator<Aln>]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc
In file included from /usr/include/c++/9/set:60,
from src/constants.h:43,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: 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
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__final_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++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1879 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/input.o src/input.cc
/usr/include/c++/9/bits/stl_algo.h: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/locus.o src/locus.cc
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/9/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++/9/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
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc
/usr/include/c++/9/bits/stl_algo.h: In function '_Z28search_for_gapped_remaindersRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEERS_IiP5StackS3_SaIS4_IS5_SB_EEERS_IiP3RemS3_SaIS4_IS5_SH_EEE._omp_fn.0':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/constants.h:44,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/9/bits/stl_map.h: In function 'int dump_stack_graph(std::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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/models.o src/models.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc
In file included from /usr/include/c++/9/vector:72,
from src/constants.h:40,
from src/models.h:24,
from src/models.cc:30:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MarukiLowModel::LikData*, std::vector<MarukiLowModel::LikData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/nucleotides.o src/nucleotides.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/renz.o src/renz.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Seq.o src/Seq.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sql_utilities.o src/sql_utilities.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/stacks.o src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/utils.o src/utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Vcf.o src/Vcf.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks.o src/cstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/c++/9/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(std::pair<std::__cxx11::basic_string<char>, AlignRes>&, std::pair<std::__cxx11::basic_string<char>, AlignRes>&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(std::pair<std::__cxx11::basic_string<char>, AlignRes>&, std::pair<std::__cxx11::basic_string<char>, AlignRes>&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /usr/include/c++/9/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >; _Distance = int; _Tp = std::pair<std::__cxx11::basic_string<char>, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(std::pair<std::__cxx11::basic_string<char>, AlignRes>&, std::pair<std::__cxx11::basic_string<char>, AlignRes>&)> >]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/MetaPopInfo.h:5,
from src/cstacks.cc:25:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/regex:51,
from src/sstacks.cc:25:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, AlignRes>}; _Tp = std::pair<std::__cxx11::basic_string<char>, AlignRes>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, AlignRes> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from /usr/include/c++/9/regex:52,
from src/sstacks.cc:25:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, AlignRes>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc
In file included from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/c++/9/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/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
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/algorithm:62,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /usr/include/c++/9/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/algorithm:62,
from /usr/include/c++/9/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::<lambda(std::pair<std::__cxx11::basic_string<char>, AlignRes>&, std::pair<std::__cxx11::basic_string<char>, AlignRes>&)> >]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/regex:51,
from src/sstacks.cc:25:
/usr/include/c++/9/bits/vector.tcc: In function 'bool verify_gapped_match(std::map<int, Locus*>&, QLocus*, std::set<int>&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/c++/9/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, AlignRes>*, std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+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++/9/map:61,
from /usr/include/c++/9/regex:52,
from src/sstacks.cc:25:
/usr/include/c++/9/bits/stl_map.h: In function '_Z15search_for_gapsRSt3mapIiP5LocusSt4lessIiESaISt4pairIKiS1_EEERS_IiP6QLocusS3_SaIS4_IS5_SB_EEERSt13unordered_mapIPKcSt6vectorIiSaIiEE12hash_charptr5eqstrSaIS4_IKSI_SL_EEERS_IiS4_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiES3_SaIS4_IS5_SZ_EEEd._omp_fn.0':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/write.o src/write.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads.o src/process_shortreads.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter.o src/kmer_filter.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter.o src/clone_filter.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations.o src/populations.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/export_formats.o src/export_formats.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc
src/export_formats.cc: In member function 'virtual int PhylipVarAllExport::post_processing()':
src/export_formats.cc:2319:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=]
2319 | sprintf(s, "%11lu", this->_seq_len);
| ~~~~^ ~~~~~~~~~~~~~~
| | |
| | std::size_t {aka unsigned int}
| long unsigned int
| %11u
In file included from /usr/include/c++/9/vector:72,
from src/populations.h:40,
from src/populations.cc:29:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc
In file included from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/populations.h:44,
from src/populations.cc:29:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1879 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/populations.h:44,
from src/populations.cc:29:
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/populations.h:44,
from src/populations.cc:29:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
src/Hwp.cc: In member function 'void HWMatrix::dump_matrix()':
src/Hwp.cc:383:43: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=]
383 | snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]);
| ~~~^ ~~~~~~~~~~~~~~
| | |
| long unsigned int std::size_t {aka unsigned int}
| %*u
In file included from /usr/include/c++/9/vector:72,
from src/PopSum.h:26,
from src/PopSum.cc:21:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/9/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++/9/bits/stl_tree.h:2187:5: 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
2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: 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
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h:2452:7: 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
/usr/include/c++/9/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++/9/bits/stl_tree.h:2452:7: 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
In file included from /usr/include/c++/9/map:61,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/9/bits/stl_map.h: In function 'double count_haplotypes_at_locus(int, int, const Datum* const*, std::map<std::__cxx11::basic_string<char>, double>&)':
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'LocStat* LocPopSum::haplotype_diversity(int, int, const Datum* const*)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc
/usr/include/c++/9/bits/stl_map.h: In member function 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)':
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector<int>&)':
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
src/gstacks.cc: In member function 'bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const':
src/gstacks.cc:1319:32: 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=]
1319 | snprintf(c, id_len, "%luM", query.length());
| ~~^ ~~~~~~~~~~~~~~
| | |
| | std::__cxx11::basic_string<char>::size_type {aka unsigned int}
| long unsigned int
| %u
src/gstacks.cc: In member function 'std::size_t LocusProcessor::find_locus_overlap(SuffixTree*, GappedAln*, const DNASeq4&, std::string&) const':
src/gstacks.cc:1505:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=]
1505 | snprintf(buf, id_len, "%luM", alns.front().aln_len);
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int std::size_t {aka unsigned int}
| %u
In file included from /usr/include/c++/9/vector:72,
from src/phasedstacks.h:39,
from src/phasedstacks.cc:25:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc
In file included from /usr/include/c++/9/vector:72,
from src/constants.h:40,
from src/debruijn.cc:5:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void Graph::rebuild(const std::vector<const DNASeq4*>&, std::size_t)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Node*, std::vector<Node> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/SuffixTree.o src/SuffixTree.cc
rm -f libcore.a
ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/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/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpop.a
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp
In file included from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STLink*, std::vector<STLink> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp
In file included from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/stacks-2.52+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o -lhts libcore.a -lz -lgomp
make[3]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
if [ -e /usr/share/automake-1.16/tap-driver.sh ] ; then \
ln -s /usr/share/automake-1.16/tap-driver.sh tests/tap-driver.sh ; \
else \
echo "Make sure /usr/share/automake-*/tap-driver.sh exists and is linked" ; \
false ; \
fi
# dh_auto_test
rm tests/tap-driver.sh
# FIXME: 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-2.52+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
dh_auto_install --no-parallel
make -j1 install DESTDIR=/<<BUILDDIR>>/stacks-2.52\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[4]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin'
/usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin'
/usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin'
make install-data-hook
make[5]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
sed -e 's,_VERSION_,2.52,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/denovo_map.pl > /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst
mv /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/denovo_map.pl
chmod +x /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/denovo_map.pl
sed -e 's,_VERSION_,2.52,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/ref_map.pl > /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/ref_map.pl.subst
mv /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/ref_map.pl
chmod +x /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/ref_map.pl
sed -i.bkp -e 's,_VERSION_,2.52,' /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments
sed -i.bkp -e 's,_VERSION_,2.52,' /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/stacks-samtools-tview
rm -f /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp
rm -f /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp
chmod +x /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments
chmod +x /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/stacks-dist-extract
chmod +x /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/bin/stacks-gdb
make[5]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[4]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
mkdir -p debian/stacks/usr/lib/stacks
mv debian/stacks/usr/bin debian/stacks/usr/lib/stacks
cd debian/stacks/usr/lib/stacks/bin && \
for f in *.pl ; do \
ln -s "$f" "`basename $f .pl`" ; \
sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $f ; \
done
dh_install
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_perl -a
debian/rules override_dh_link
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
dh_link
mkdir -p debian/stacks/usr/lib/debian-med/bin
cd debian/stacks/usr/lib/debian-med/bin && \
for f in `ls /<<BUILDDIR>>/stacks-2.52+dfsg/debian/stacks/usr/lib/stacks/bin` ; do \
ln -s ../../stacks/bin/$f ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.52+dfsg'
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/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/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/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/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/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/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/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/sstacks 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: package could avoid a useless dependency if debian/stacks/usr/lib/stacks/bin/phasedstacks debian/stacks/usr/lib/stacks/bin/clone_filter debian/stacks/usr/lib/stacks/bin/tsv2bam debian/stacks/usr/lib/stacks/bin/kmer_filter debian/stacks/usr/lib/stacks/bin/populations debian/stacks/usr/lib/stacks/bin/process_radtags debian/stacks/usr/lib/stacks/bin/process_shortreads debian/stacks/usr/lib/stacks/bin/ustacks debian/stacks/usr/lib/stacks/bin/gstacks debian/stacks/usr/lib/stacks/bin/sstacks debian/stacks/usr/lib/stacks/bin/cstacks 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: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.52+dfsg-1_armhf.deb'.
dpkg-deb: building package 'stacks' in '../stacks_2.52+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../stacks_2.52+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-03-31T11:57:11Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
stacks_2.52+dfsg-1_armhf.changes:
---------------------------------
Format: 1.8
Date: Thu, 26 Mar 2020 02:25:20 +0100
Source: stacks
Binary: stacks stacks-dbgsym
Architecture: armhf
Version: 2.52+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
stacks - pipeline for building loci from short-read DNA sequences
Changes:
stacks (2.52+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 12 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Use secure URI in Homepage field. (routine-update)
* Removed additional autogenerated files from upstream
Checksums-Sha1:
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4248ed344ee93d7321c95a577a58fc837345414e 5603 stacks_2.52+dfsg-1_armhf.buildinfo
9c85de428f104c3d52249e2d3e3c09966ebc8aa2 816588 stacks_2.52+dfsg-1_armhf.deb
Checksums-Sha256:
2b4911968ae6bbf59f7194f9a252fa8779721f187aa8c1d126b66119caaacd1a 26846908 stacks-dbgsym_2.52+dfsg-1_armhf.deb
fddf992d4b426ed31b602002d697df0ea686eb4e5c320b0e2e954bdc05a58e4b 5603 stacks_2.52+dfsg-1_armhf.buildinfo
ce2a7b5eca32aad9e3b65fc78f27f3dbe6b80b9ff9a963e8b0965f46d208b915 816588 stacks_2.52+dfsg-1_armhf.deb
Files:
2a441b8e2c19d65d7ee278bd8276298f 26846908 debug optional stacks-dbgsym_2.52+dfsg-1_armhf.deb
bc93763a889b2e811d2260c9e4bbd179 5603 science optional stacks_2.52+dfsg-1_armhf.buildinfo
5d2ce32aec9c7bf5ef6bdc790d9f371a 816588 science optional stacks_2.52+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
stacks-dbgsym_2.52+dfsg-1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 26846908 bytes: control archive=1096 bytes.
786 bytes, 12 lines control
1252 bytes, 12 lines md5sums
Package: stacks-dbgsym
Source: stacks
Version: 2.52+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 27708
Depends: stacks (= 2.52+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for stacks
Build-Ids: 0dd5a62b4bd1ea839d6cd3b667c47b28f68a780a 34983c90206674f7f6f6ad471dc81071f35891cd 568edcffa9baa777d4bc5dc72d5a58441a13fafe 692dbd1ffff2c6b72757f966f63a267f4f06bc8a 700d26b7e15bbeb0a5305ab7d03400597d25d853 7eac79c818560a74dbaf965bb5db2df64a3ef122 a65ba30894ba317fe6329c1e145dca1d8e1d6ca3 b7dc831c95b219726d730d11437918cd93cba646 d781ea1e387c19bf49efc6d5fb8acf817727b0c2 dde20988d60bc2b08102c4f1b92fb4606821beff e579d092266e2538cc083e24375a80976ce0fe43
drwxr-xr-x root/root 0 2020-03-26 01:25 ./
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/0d/
-rw-r--r-- root/root 2035784 2020-03-26 01:25 ./usr/lib/debug/.build-id/0d/d5a62b4bd1ea839d6cd3b667c47b28f68a780a.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 2114160 2020-03-26 01:25 ./usr/lib/debug/.build-id/34/983c90206674f7f6f6ad471dc81071f35891cd.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/56/
-rw-r--r-- root/root 1087180 2020-03-26 01:25 ./usr/lib/debug/.build-id/56/8edcffa9baa777d4bc5dc72d5a58441a13fafe.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/69/
-rw-r--r-- root/root 1741884 2020-03-26 01:25 ./usr/lib/debug/.build-id/69/2dbd1ffff2c6b72757f966f63a267f4f06bc8a.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/70/
-rw-r--r-- root/root 2047468 2020-03-26 01:25 ./usr/lib/debug/.build-id/70/0d26b7e15bbeb0a5305ab7d03400597d25d853.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/7e/
-rw-r--r-- root/root 1450364 2020-03-26 01:25 ./usr/lib/debug/.build-id/7e/ac79c818560a74dbaf965bb5db2df64a3ef122.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/a6/
-rw-r--r-- root/root 2810944 2020-03-26 01:25 ./usr/lib/debug/.build-id/a6/5ba30894ba317fe6329c1e145dca1d8e1d6ca3.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/b7/
-rw-r--r-- root/root 5103984 2020-03-26 01:25 ./usr/lib/debug/.build-id/b7/dc831c95b219726d730d11437918cd93cba646.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/d7/
-rw-r--r-- root/root 1998344 2020-03-26 01:25 ./usr/lib/debug/.build-id/d7/81ea1e387c19bf49efc6d5fb8acf817727b0c2.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/dd/
-rw-r--r-- root/root 4452560 2020-03-26 01:25 ./usr/lib/debug/.build-id/dd/e20988d60bc2b08102c4f1b92fb4606821beff.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.build-id/e5/
-rw-r--r-- root/root 2292040 2020-03-26 01:25 ./usr/lib/debug/.build-id/e5/79d092266e2538cc083e24375a80976ce0fe43.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1207612 2020-03-26 01:25 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/stacks.debug
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/share/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/share/doc/stacks-dbgsym -> stacks
stacks_2.52+dfsg-1_armhf.deb
----------------------------
new Debian package, version 2.0.
size 816588 bytes: control archive=1628 bytes.
993 bytes, 21 lines control
1798 bytes, 26 lines md5sums
Package: stacks
Version: 2.52+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4197
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 9), zlib1g (>= 1:1.2.6), samtools, libdbi-perl
Recommends: libspreadsheet-writeexcel-perl, python3
Conflicts: stacks-web
Replaces: stacks-web
Provides: stacks-web
Section: science
Priority: optional
Homepage: https://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 2020-03-26 01:25 ./
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/bin/
-rwxr-xr-x root/root 771 2020-03-26 01:24 ./usr/bin/stacks
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/count_fixed_catalog_snps.py -> ../../stacks/bin/count_fixed_catalog_snps.py
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/cstacks -> ../../stacks/bin/cstacks
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/gstacks -> ../../stacks/bin/gstacks
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/integrate_alignments.py -> ../../stacks/bin/integrate_alignments.py
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/populations -> ../../stacks/bin/populations
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/ref_map -> ../../stacks/bin/ref_map
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/sstacks -> ../../stacks/bin/sstacks
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/stacks-count-reads-per-sample-per-locus -> ../../stacks/bin/stacks-count-reads-per-sample-per-locus
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/debian-med/bin/ustacks -> ../../stacks/bin/ustacks
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/stacks/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/lib/stacks/bin/
-rwxr-xr-x root/root 273132 2020-03-26 01:25 ./usr/lib/stacks/bin/clone_filter
-rwxr-xr-x root/root 8652 2020-03-26 01:25 ./usr/lib/stacks/bin/count_fixed_catalog_snps.py
-rwxr-xr-x root/root 350784 2020-03-26 01:25 ./usr/lib/stacks/bin/cstacks
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/stacks/bin/denovo_map -> denovo_map.pl
-rwxr-xr-x root/root 30261 2020-03-26 01:25 ./usr/lib/stacks/bin/denovo_map.pl
-rwxr-xr-x root/root 592140 2020-03-26 01:25 ./usr/lib/stacks/bin/gstacks
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-rwxr-xr-x root/root 223956 2020-03-26 01:25 ./usr/lib/stacks/bin/kmer_filter
-rwxr-xr-x root/root 285276 2020-03-26 01:25 ./usr/lib/stacks/bin/phasedstacks
-rwxr-xr-x root/root 770092 2020-03-26 01:25 ./usr/lib/stacks/bin/populations
-rwxr-xr-x root/root 323548 2020-03-26 01:25 ./usr/lib/stacks/bin/process_radtags
-rwxr-xr-x root/root 285864 2020-03-26 01:25 ./usr/lib/stacks/bin/process_shortreads
lrwxrwxrwx root/root 0 2020-03-26 01:25 ./usr/lib/stacks/bin/ref_map -> ref_map.pl
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-rwxr-xr-x root/root 342492 2020-03-26 01:25 ./usr/lib/stacks/bin/sstacks
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-rwxr-xr-x root/root 773 2020-03-26 01:25 ./usr/lib/stacks/bin/stacks-dist-extract
-rwxr-xr-x root/root 1207 2020-03-26 01:25 ./usr/lib/stacks/bin/stacks-gdb
-rwxr-xr-x root/root 1783 2020-03-26 01:25 ./usr/lib/stacks/bin/stacks-hist2d-loci-samples-coverage
-rwxr-xr-x root/root 5752 2020-03-26 01:25 ./usr/lib/stacks/bin/stacks-integrate-alignments
-rwxr-xr-x root/root 3037 2020-03-26 01:25 ./usr/lib/stacks/bin/stacks-samtools-tview
-rwxr-xr-x root/root 333968 2020-03-26 01:25 ./usr/lib/stacks/bin/tsv2bam
-rwxr-xr-x root/root 355316 2020-03-26 01:25 ./usr/lib/stacks/bin/ustacks
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/share/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-03-26 01:25 ./usr/share/doc/stacks/
-rw-r--r-- root/root 1451 2020-03-26 01:24 ./usr/share/doc/stacks/README.Debian
-rw-r--r-- root/root 1675 2020-03-26 01:25 ./usr/share/doc/stacks/changelog.Debian.gz
-rw-r--r-- root/root 28482 2020-03-05 20:58 ./usr/share/doc/stacks/changelog.gz
-rw-r--r-- root/root 1684 2020-03-26 01:25 ./usr/share/doc/stacks/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 333876
Build-Time: 1319
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 373
Job: stacks_2.52+dfsg-1
Machine Architecture: armhf
Package: stacks
Package-Time: 1741
Source-Version: 2.52+dfsg-1
Space: 333876
Status: successful
Version: 2.52+dfsg-1
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Finished at 2020-03-31T11:57:11Z
Build needed 00:29:01, 333876k disc space