stacks →
2.60+dfsg-1 →
armhf → 2021-11-07 05:42:28
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| stacks 2.60+dfsg-1 (armhf) Sun, 07 Nov 2021 05:34:03 +0000 |
+==============================================================================+
Package: stacks
Version: 2.60+dfsg-1
Source Version: 2.60+dfsg-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-78f7576f-b384-4105-b1e4-0ad90c41a590' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 9s (2810 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 342 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main stacks 2.60+dfsg-1 (dsc) [2040 B]
Get:2 http://172.17.0.1/private bookworm-staging/main stacks 2.60+dfsg-1 (tar) [332 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main stacks 2.60+dfsg-1 (diff) [7584 B]
Fetched 342 kB in 0s (2625 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/stacks-nFgTSe/stacks-2.60+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/stacks-nFgTSe' 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-EQ91M5/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-EQ91M5/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-EQ91M5/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (10.2 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (67.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12500 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 (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev
dpkg-deb: building package 'sbuild-build-depends-stacks-dummy' in '/<<BUILDDIR>>/resolver-EQ91M5/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-EQ91M5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ Sources [524 B]
Get:5 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ Packages [602 B]
Fetched 2459 B in 0s (11.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install stacks build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbam-dev libbrotli1
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3
libhtscodecs2 libicu67 liblzma-dev libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2 libsparsehash-dev
libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
po-debconf samtools sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config
liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl cwltool
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libgpm2 publicsuffix
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbam-dev libbrotli1
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3
libhtscodecs2 libicu67 liblzma-dev libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2 libsparsehash-dev
libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
po-debconf samtools sbuild-build-depends-stacks-dummy sensible-utils
zlib1g-dev
0 upgraded, 50 newly installed, 0 to remove and 4 not upgraded.
Need to get 24.5 MB of archives.
After this operation, 77.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-EQ91M5/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1 [823 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libbam-dev armhf 0.1.19+dfsg-4 [106 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.8-1 [40.4 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2 [4049 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf samtools armhf 1.13-4 [525 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../44-liblzma-dev_5.2.5-2_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.5-2) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../45-libhts-dev_1.13+ds-2_armhf.deb ...
Unpacking libhts-dev:armhf (1.13+ds-2) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../46-libncurses6_6.2+20201114-4_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-4) ...
Selecting previously unselected package libsparsehash-dev.
Preparing to unpack .../47-libsparsehash-dev_2.0.3-2_all.deb ...
Unpacking libsparsehash-dev (2.0.3-2) ...
Selecting previously unselected package samtools.
Preparing to unpack .../48-samtools_1.13-4_armhf.deb ...
Unpacking samtools (1.13-4) ...
Selecting previously unselected package sbuild-build-depends-stacks-dummy.
Preparing to unpack .../49-sbuild-build-depends-stacks-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.1.1-3) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.8-1) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libsparsehash-dev (2.0.3-2) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up liblzma-dev:armhf (5.2.5-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up libdeflate-dev:armhf (1.8-1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-2) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libbam-dev (0.1.19+dfsg-4) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-2) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.5-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.13+ds-2) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.13-4) ...
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 gcc-10_10.3.0-11+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.9-2+rpi1
Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-11+rpi1 dash_0.5.11+git20210903+057cd650a4ed-1 debconf_1.5.78 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-11+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbam-dev_0.1.19+dfsg-4 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-4 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdeflate-dev_1.8-1 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-11+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.2-2+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.5-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.5-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.9-2+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 samtools_1.13-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-stacks-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 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 '/tmp/dpkg-verify-sig.bk5D60aP/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 1 18:45:08 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./stacks_2.60+dfsg-1.dsc
dpkg-source: info: extracting stacks in /<<BUILDDIR>>/stacks-2.60+dfsg
dpkg-source: info: unpacking stacks_2.60+dfsg.orig.tar.xz
dpkg-source: info: unpacking stacks_2.60+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying RisR.patch
dpkg-source: info: applying script-exe-paths
dpkg-source: info: applying use_debian_packaged_htslib.patch
dpkg-source: info: applying 2to3.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-78f7576f-b384-4105-b1e4-0ad90c41a590
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package stacks
dpkg-buildpackage: info: source version 2.60+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-2.60+dfsg'
dh_clean
rm -f ./constants.php
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:28: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:28: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:28: the top level
configure.ac:20: installing 'config/ar-lib'
configure.ac:15: installing 'config/compile'
configure.ac:42: installing 'config/config.guess'
configure.ac:42: installing 'config/config.sub'
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-2.60+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-option-checking --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
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free 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 the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... 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 for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for float.h... 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 _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether closedir returns void... no
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for GNU libc compatible malloc... 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
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc
In file included from /usr/include/c++/10/bits/stl_algobase.h:71,
from /usr/include/c++/10/vector:60,
from src/constants.h:40,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/predefined_ops.h: In function 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Iterator2 = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Compare = bool (*)(Aln, Aln)]':
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
155 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator' changed in GCC 7.1
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Aln>::iterator' changed in GCC 7.1
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc
In file included from /usr/include/c++/10/set:60,
from src/constants.h:43,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/10/bits/stl_tree.h:2460:7: 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' changed in GCC 7.1
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from src/constants.h:44,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1851:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1851 | if (__comp(__i, __first))
| ~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1886 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1929 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1930 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/vector.tcc: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/vector.tcc: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:82:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
82 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:84:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
84 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:86:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:91:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
91 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/input.o src/input.cc
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/vector.tcc: In function '_Z15search_for_gapsRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEE._omp_fn.0':
/usr/include/c++/10/bits/vector.tcc:121:21: 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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cc
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_heap.h:134:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
134 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:231:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
231 | if (__comp(__first + __secondChild,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
232 | __first + (__secondChild - 1)))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1673:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1673 | if (__comp(__i, __first))
| ~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1929 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1930 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1909:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1909 | while (__comp(__first, __pivot))
| ~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/bits/vector.tcc:121:21: 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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/locus.o src/locus.cc
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/models.h:24,
from src/models.cc:30:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MarukiLowModel::LikData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/set:60,
from src/constants.h:43,
from src/models.h:24,
from src/models.cc:30:
/usr/include/c++/10/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 = Nt2; _Val = std::pair<const Nt2, double>; _KeyOfValue = std::_Select1st<std::pair<const Nt2, double> >; _Compare = std::less<Nt2>; _Alloc = std::allocator<std::pair<const Nt2, double> >]':
/usr/include/c++/10/bits/stl_tree.h:2195:5: note: parameter passing for argument of type 'std::_Rb_tree<Nt2, std::pair<const Nt2, double>, std::_Select1st<std::pair<const Nt2, double> >, std::less<Nt2>, std::allocator<std::pair<const Nt2, double> > >::const_iterator' changed in GCC 7.1
2195 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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 = double; _Val = std::pair<const double, double>; _KeyOfValue = std::_Select1st<std::pair<const double, double> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, double> >]':
/usr/include/c++/10/bits/stl_tree.h:2195:5: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' changed in GCC 7.1
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/Vcf.h:24,
from src/Vcf.cc:23:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static std::string VcfRecord::util::fmt_gt_gl(const std::vector<Nt2>&, const GtLiks&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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++/10/algorithm:62,
from /usr/include/c++/10/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1824:5: 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
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/MetaPopInfo.h:5,
from src/cstacks.cc:25:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: 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
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/c++/10/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: 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
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/regex:51,
from src/sstacks.cc:25:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<std::__cxx11::basic_string<char>, AlignRes> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1929 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1930 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/MetaPopInfo.h:5,
from src/cstacks.cc:25:
/usr/include/c++/10/bits/vector.tcc: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/MetaPopInfo.h:5,
from src/cstacks.cc:25:
/usr/include/c++/10/bits/vector.tcc: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/c++/10/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/c++/10/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/c++/10/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1929 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1930 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/regex:51,
from src/sstacks.cc:25:
/usr/include/c++/10/bits/vector.tcc: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from /usr/include/c++/10/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/regex:51,
from src/sstacks.cc:25:
/usr/include/c++/10/bits/vector.tcc: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from /usr/include/c++/10/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc
/usr/include/c++/10/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++/10/bits/stl_algo.h:1950:5: 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
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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++/10/bits/stl_algo.h:1950:5: 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++/10/bits/stl_algo.h:1964:25: 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
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/regex:51,
from src/sstacks.cc:25:
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from /usr/include/c++/10/regex:38,
from src/sstacks.cc:25:
/usr/include/c++/10/bits/stl_algo.h:1979:25: 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
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: 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
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/bootstrap.o src/bootstrap.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc
src/export_formats.cc: In member function 'virtual int PhylipVarAllExport::post_processing()':
src/export_formats.cc:2331:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=]
2331 | sprintf(s, "%11lu", this->_seq_len);
| ~~~~^ ~~~~~~~~~~~~~~
| | |
| | std::size_t {aka unsigned int}
| long unsigned int
| %11u
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/populations.h:45,
from src/populations.cc:29:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/populations.h:45,
from src/populations.cc:29:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function '_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:2053:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2053 | __upper_bound(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2053:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/bootstrap.h:24,
from src/bootstrap.cc:21:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::array<double, 2>}; _Tp = std::array<double, 2>; _Alloc = std::allocator<std::array<double, 2> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::array<double, 2> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::array<double, 3>}; _Tp = std::array<double, 3>; _Alloc = std::allocator<std::array<double, 3> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::array<double, 3> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::array<double, 1>}; _Tp = std::array<double, 1>; _Alloc = std::allocator<std::array<double, 1> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::array<double, 1> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::array<double, 4>}; _Tp = std::array<double, 4>; _Alloc = std::allocator<std::array<double, 4> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::array<double, 4> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'int BSArchive::parse_archive()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::array<double, 2>*, std::vector<std::array<double, 2> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::array<double, 3>*, std::vector<std::array<double, 3> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::array<double, 1>*, std::vector<std::array<double, 1> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::array<double, 4>*, std::vector<std::array<double, 4> > >' 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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc
In file included from /usr/include/c++/10/map:60,
from src/mapping_utils.h:23,
from src/mapping_utils.cc:25:
/usr/include/c++/10/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++/10/bits/stl_tree.h:2195:5: 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' changed in GCC 7.1
2195 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc
In file included from /usr/include/c++/10/map:60,
from src/genotype_dictionaries.h:25,
from src/genotype_dictionaries.cc:1:
/usr/include/c++/10/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++/10/bits/stl_tree.h:2195:5: 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' changed in GCC 7.1
2195 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc
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++/10/vector:72,
from src/populations.h:41,
from src/populations.cc:29:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/populations.h:45,
from src/populations.cc:29:
/usr/include/c++/10/bits/stl_algo.h: In function '_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2101:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2101 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2102 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/populations.h:41,
from src/populations.cc:29:
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/populations.h:45,
from src/populations.cc:29:
/usr/include/c++/10/bits/stl_algo.h: In function '_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2101:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2101 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2102 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/populations.h:41,
from src/populations.cc:29:
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/populations.h:45,
from src/populations.cc:29:
/usr/include/c++/10/bits/stl_algo.h:2101:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2101 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2102 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2101:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2101 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2102 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/populations.h:41,
from src/populations.cc:29:
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/populations.h:45,
from src/populations.cc:29:
/usr/include/c++/10/bits/stl_algo.h: In function '_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1982:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1982 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:2101:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2101 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2102 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/populations.h:41,
from src/populations.cc:29:
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/vector:72,
from src/PopSum.h:26,
from src/PopSum.cc:21:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'LocusDivergence::LocusDivergence(const MetaPopInfo*)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: 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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc
In file included from /usr/include/c++/10/map:60,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/10/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++/10/bits/stl_tree.h:2195:5: 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' changed in GCC 7.1
2195 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_tree.h:2460:7: 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' changed in GCC 7.1
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/10/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/10/bits/stl_map.h:520:37: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_map.h:520:37: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/10/bits/stl_tree.h:2460:7: 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' changed in GCC 7.1
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2460:7: 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' changed in GCC 7.1
In file included from /usr/include/c++/10/map:61,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/10/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In member function 'LocStat* LocPopSum::haplotype_diversity(int, int, const Datum* const*)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc
/usr/include/c++/10/bits/stl_map.h: In member function 'double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector<int>&)':
/usr/include/c++/10/bits/stl_map.h:520:37: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:520:37: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In member function 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)':
/usr/include/c++/10/bits/stl_map.h:520:37: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:520:37: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/phasedstacks.h:39,
from src/phasedstacks.cc:25:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'int bucket_dprime(std::vector<double>&, std::vector<double>&, PhasedSummary*)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: 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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc
src/gstacks.cc: In member function 'bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const':
src/gstacks.cc:1347:32: 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=]
1347 | 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:1533:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=]
1533 | 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++/10/vector:72,
from src/constants.h:40,
from src/debruijn.cc:5:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Node>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void Graph::rebuild(const std::vector<const DNASeq4*>&, std::size_t)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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/bootstrap.o 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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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++/10/bits/stl_algobase.h:71,
from /usr/include/c++/10/vector:60,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/predefined_ops.h: In function 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >; _Iterator2 = __gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)>]':
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
155 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:231:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
231 | if (__comp(__first + __secondChild,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
232 | __first + (__secondChild - 1)))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1851:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1851 | if (__comp(__i, __first))
| ~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:82:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
82 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:84:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
84 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:86:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:91:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
91 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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++/10/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<STAln>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AlignRes>::iterator' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<STAln>::iterator' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<STLink>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/vector:67,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<double, Nt2> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1929 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1930 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1929:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/vector.tcc: In member function 'int GappedAln::trace_local_alignment(const string&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/vector.tcc: In member function 'bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/bits/vector.tcc: In member function 'std::size_t LocusProcessor::find_locus_overlap(SuffixTree*, GappedAln*, const DNASeq4&, std::string&) const':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/bits/vector.tcc: In member function 'int GappedAln::trace_global_alignment(const string&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, Nt2>*, std::vector<std::pair<double, Nt2> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from src/constants.h:40,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/stacks-2.60+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-2.60+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.60+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-2.60+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
dh_auto_install --no-parallel
make -j1 install DESTDIR=/<<BUILDDIR>>/stacks-2.60\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make[4]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.60+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-2.60+dfsg/debian/stacks/usr/bin'
/bin/mkdir -p '/<<BUILDDIR>>/stacks-2.60+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-2.60+dfsg/debian/stacks/usr/bin'
make install-data-hook
make[5]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
sed -e 's,_VERSION_,2.60,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl > /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst
mv /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl
chmod +x /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/denovo_map.pl
sed -e 's,_VERSION_,2.60,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl > /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl.subst
mv /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl
chmod +x /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/ref_map.pl
sed -i.bkp -e 's,_VERSION_,2.60,' /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments
sed -i.bkp -e 's,_VERSION_,2.60,' /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-samtools-tview
rm -f /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp
rm -f /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp
chmod +x /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments
chmod +x /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-dist-extract
chmod +x /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/bin/stacks-gdb
make[5]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make[4]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.60+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?' $f ; \
done
dh_install
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_perl -a
debian/rules override_dh_link
make[1]: Entering directory '/<<BUILDDIR>>/stacks-2.60+dfsg'
dh_link
mkdir -p debian/stacks/usr/lib/debian-med/bin
cd debian/stacks/usr/lib/debian-med/bin && \
for f in `ls /<<BUILDDIR>>/stacks-2.60+dfsg/debian/stacks/usr/lib/stacks/bin` ; do \
ln -s ../../stacks/bin/$f ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/stacks-2.60+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/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/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/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/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/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/cstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/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/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/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_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: package could avoid a useless dependency if debian/stacks/usr/lib/stacks/bin/sstacks debian/stacks/usr/lib/stacks/bin/clone_filter debian/stacks/usr/lib/stacks/bin/kmer_filter debian/stacks/usr/lib/stacks/bin/gstacks debian/stacks/usr/lib/stacks/bin/phasedstacks debian/stacks/usr/lib/stacks/bin/cstacks debian/stacks/usr/lib/stacks/bin/process_radtags debian/stacks/usr/lib/stacks/bin/tsv2bam debian/stacks/usr/lib/stacks/bin/populations debian/stacks/usr/lib/stacks/bin/process_shortreads debian/stacks/usr/lib/stacks/bin/ustacks 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_2.60+dfsg-1_armhf.deb'.
dpkg-deb: building package 'stacks' in '../stacks_2.60+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../stacks_2.60+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 2021-11-07T05:42:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
stacks_2.60+dfsg-1_armhf.changes:
---------------------------------
Format: 1.8
Date: Tue, 02 Nov 2021 00:08:37 +0530
Source: stacks
Binary: stacks stacks-dbgsym
Architecture: armhf
Version: 2.60+dfsg-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
stacks - pipeline for building loci from short-read DNA sequences
Changes:
stacks (2.60+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version 2.60+dfsg
* Run cme
Checksums-Sha1:
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6a7ae3c38187ef9c3374cf79c696ade76d128079 5726 stacks_2.60+dfsg-1_armhf.buildinfo
685350c8b305b89d84670c8fc559dcf9574888a0 834904 stacks_2.60+dfsg-1_armhf.deb
Checksums-Sha256:
491eff40dff4800ee5dd7548bc390ed5a1631b9b02a1f091d1da5e7de6e15105 26542496 stacks-dbgsym_2.60+dfsg-1_armhf.deb
43e5da9d16aa6948af65cf3dc61e0ffb679a933c781f17a82d84407eb5c3a88f 5726 stacks_2.60+dfsg-1_armhf.buildinfo
985d196fd73bb7b133105e9c93dd3e05ff5711dc8a7d11132caf1278492814f4 834904 stacks_2.60+dfsg-1_armhf.deb
Files:
ffe29aa2e2bd3469f156e1709d0a274c 26542496 debug optional stacks-dbgsym_2.60+dfsg-1_armhf.deb
b0c19f6722e56ca7c7add63b50919d95 5726 science optional stacks_2.60+dfsg-1_armhf.buildinfo
682791049f0eb51ec0d322e1b7d07056 834904 science optional stacks_2.60+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
stacks-dbgsym_2.60+dfsg-1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 26542496 bytes: control archive=1100 bytes.
786 bytes, 12 lines control
1252 bytes, 12 lines md5sums
Package: stacks-dbgsym
Source: stacks
Version: 2.60+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 27343
Depends: stacks (= 2.60+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for stacks
Build-Ids: 35dda80497635a6ab19b73b7f6001c32224be733 41038697e1f2f7df34deae4d662cb5867034f394 5718e987caa59483b2a16cf3d522c903e8e9fbd1 5812c01c300faa440a5ff26ae5af0c0f6446e9b6 6da4e4776caa84fb4ed3bd8ed31d2d045d151c92 83284f7cb9253bcc96c5b6ab10786ed9b863ca57 8818c5fdae6980062f58d08f051acf3eb7a07f06 939c05ae4010a5e8f5fc8b910feb9fd60197cf55 c0e2df9e873be8bf9c3d825558a9d80d099b6a44 c5208e1149c6d048bee5bc6082133dd645e2ccd3 f6b8340001eb2af6a8cdd995e8937b80127541b6
drwxr-xr-x root/root 0 2021-11-01 18:38 ./
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/35/
-rw-r--r-- root/root 4411492 2021-11-01 18:38 ./usr/lib/debug/.build-id/35/dda80497635a6ab19b73b7f6001c32224be733.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/41/
-rw-r--r-- root/root 963388 2021-11-01 18:38 ./usr/lib/debug/.build-id/41/038697e1f2f7df34deae4d662cb5867034f394.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/57/
-rw-r--r-- root/root 2297752 2021-11-01 18:38 ./usr/lib/debug/.build-id/57/18e987caa59483b2a16cf3d522c903e8e9fbd1.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/58/
-rw-r--r-- root/root 2736732 2021-11-01 18:38 ./usr/lib/debug/.build-id/58/12c01c300faa440a5ff26ae5af0c0f6446e9b6.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/6d/
-rw-r--r-- root/root 1701272 2021-11-01 18:38 ./usr/lib/debug/.build-id/6d/a4e4776caa84fb4ed3bd8ed31d2d045d151c92.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/83/
-rw-r--r-- root/root 1382380 2021-11-01 18:38 ./usr/lib/debug/.build-id/83/284f7cb9253bcc96c5b6ab10786ed9b863ca57.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/88/
-rw-r--r-- root/root 1968444 2021-11-01 18:38 ./usr/lib/debug/.build-id/88/18c5fdae6980062f58d08f051acf3eb7a07f06.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/93/
-rw-r--r-- root/root 5301052 2021-11-01 18:38 ./usr/lib/debug/.build-id/93/9c05ae4010a5e8f5fc8b910feb9fd60197cf55.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/c0/
-rw-r--r-- root/root 1925884 2021-11-01 18:38 ./usr/lib/debug/.build-id/c0/e2df9e873be8bf9c3d825558a9d80d099b6a44.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/c5/
-rw-r--r-- root/root 2023488 2021-11-01 18:38 ./usr/lib/debug/.build-id/c5/208e1149c6d048bee5bc6082133dd645e2ccd3.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.build-id/f6/
-rw-r--r-- root/root 2002512 2021-11-01 18:38 ./usr/lib/debug/.build-id/f6/b8340001eb2af6a8cdd995e8937b80127541b6.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1257064 2021-11-01 18:38 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/stacks.debug
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/share/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/share/doc/stacks-dbgsym -> stacks
stacks_2.60+dfsg-1_armhf.deb
----------------------------
new Debian package, version 2.0.
size 834904 bytes: control archive=1656 bytes.
1002 bytes, 21 lines control
1868 bytes, 27 lines md5sums
Package: stacks
Version: 2.60+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4335
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, littler
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 2021-11-01 18:38 ./
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/bin/
-rwxr-xr-x root/root 771 2021-11-01 18:35 ./usr/bin/stacks
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/count_fixed_catalog_snps.py -> ../../stacks/bin/count_fixed_catalog_snps.py
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/cstacks -> ../../stacks/bin/cstacks
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/gstacks -> ../../stacks/bin/gstacks
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/integrate_alignments.py -> ../../stacks/bin/integrate_alignments.py
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/populations -> ../../stacks/bin/populations
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/ref_map -> ../../stacks/bin/ref_map
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/sstacks -> ../../stacks/bin/sstacks
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./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 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/debian-med/bin/ustacks -> ../../stacks/bin/ustacks
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/stacks/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/lib/stacks/bin/
-rwxr-xr-x root/root 277228 2021-11-01 18:38 ./usr/lib/stacks/bin/clone_filter
-rwxr-xr-x root/root 8652 2021-11-01 18:38 ./usr/lib/stacks/bin/count_fixed_catalog_snps.py
-rwxr-xr-x root/root 350788 2021-11-01 18:38 ./usr/lib/stacks/bin/cstacks
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/stacks/bin/denovo_map -> denovo_map.pl
-rwxr-xr-x root/root 30920 2021-11-01 18:38 ./usr/lib/stacks/bin/denovo_map.pl
-rwxr-xr-x root/root 604428 2021-11-01 18:38 ./usr/lib/stacks/bin/gstacks
-rwxr-xr-x root/root 10879 2021-11-01 18:38 ./usr/lib/stacks/bin/integrate_alignments.py
-rwxr-xr-x root/root 211668 2021-11-01 18:38 ./usr/lib/stacks/bin/kmer_filter
-rwxr-xr-x root/root 281180 2021-11-01 18:38 ./usr/lib/stacks/bin/phasedstacks
-rwxr-xr-x root/root 864344 2021-11-01 18:38 ./usr/lib/stacks/bin/populations
-rwxr-xr-x root/root 331816 2021-11-01 18:38 ./usr/lib/stacks/bin/process_radtags
-rwxr-xr-x root/root 281768 2021-11-01 18:38 ./usr/lib/stacks/bin/process_shortreads
lrwxrwxrwx root/root 0 2021-11-01 18:38 ./usr/lib/stacks/bin/ref_map -> ref_map.pl
-rwxr-xr-x root/root 15360 2021-11-01 18:38 ./usr/lib/stacks/bin/ref_map.pl
-rwxr-xr-x root/root 342492 2021-11-01 18:38 ./usr/lib/stacks/bin/sstacks
-rwxr-xr-x root/root 1040 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-count-reads-per-sample-per-locus
-rwxr-xr-x root/root 773 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-dist-extract
-rwxr-xr-x root/root 1207 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-gdb
-rwxr-xr-x root/root 1773 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-hist2d-loci-samples-coverage
-rwxr-xr-x root/root 22248 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-integrate-alignments
-rwxr-xr-x root/root 3037 2021-11-01 18:38 ./usr/lib/stacks/bin/stacks-samtools-tview
-rwxr-xr-x root/root 346256 2021-11-01 18:38 ./usr/lib/stacks/bin/tsv2bam
-rwxr-xr-x root/root 363508 2021-11-01 18:38 ./usr/lib/stacks/bin/ustacks
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/share/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-11-01 18:38 ./usr/share/doc/stacks/
-rw-r--r-- root/root 229 2021-11-01 18:35 ./usr/share/doc/stacks/NEWS.Debian.gz
-rw-r--r-- root/root 1451 2021-11-01 18:35 ./usr/share/doc/stacks/README.Debian
-rw-r--r-- root/root 1914 2021-11-01 18:38 ./usr/share/doc/stacks/changelog.Debian.gz
-rw-r--r-- root/root 30175 2021-10-26 18:25 ./usr/share/doc/stacks/changelog.gz
-rw-r--r-- root/root 1684 2021-11-01 18:35 ./usr/share/doc/stacks/copyright
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 323568
Build-Time: 343
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 137
Job: stacks_2.60+dfsg-1
Machine Architecture: armhf
Package: stacks
Package-Time: 496
Source-Version: 2.60+dfsg-1
Space: 323568
Status: successful
Version: 2.60+dfsg-1
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Finished at 2021-11-07T05:42:19Z
Build needed 00:08:16, 323568k disk space