Wed Mar 19 03:01:59 UTC 2025 I: starting to build stacks/trixie/armhf on jenkins on '2025-03-19 03:01'
Wed Mar 19 03:01:59 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_9/13344/console.log
Wed Mar 19 03:01:59 UTC 2025 I: Downloading source for trixie/stacks=2.68+dfsg-2
--2025-03-19 03:01:59-- http://deb.debian.org/debian/pool/main/s/stacks/stacks_2.68%2bdfsg-2.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2050 (2.0K) [text/prs.lines.tag]
Saving to: ‘stacks_2.68+dfsg-2.dsc’
0K .. 100% 221M=0s
2025-03-19 03:01:59 (221 MB/s) - ‘stacks_2.68+dfsg-2.dsc’ saved [2050/2050]
Wed Mar 19 03:01:59 UTC 2025 I: stacks_2.68+dfsg-2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: stacks
Binary: stacks
Architecture: any
Version: 2.68+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://creskolab.uoregon.edu/stacks/
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/stacks
Vcs-Git: https://salsa.debian.org/med-team/stacks.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), automake, zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev
Package-List:
stacks deb science optional arch=any
Checksums-Sha1:
84d9fefcc2da0bdeedd86d7dc994ef5b84012806 371032 stacks_2.68+dfsg.orig.tar.xz
a4b257a1997837310253bbae16d2e7b4b9eaee6b 12488 stacks_2.68+dfsg-2.debian.tar.xz
Checksums-Sha256:
d5277660330547502069d0976869038e9f47946ef7a8e91bf1213dbc0185072c 371032 stacks_2.68+dfsg.orig.tar.xz
e07482fc23eb570d9c43a560055b051f88430b001a86a9b40223e3d5dc4e283c 12488 stacks_2.68+dfsg-2.debian.tar.xz
Files:
13bbb30a0414696ac59e3d98d1723d00 371032 stacks_2.68+dfsg.orig.tar.xz
c534f4ad4dbee58b2bcbb1a06a37472b 12488 stacks_2.68+dfsg-2.debian.tar.xz
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Wed Mar 19 03:01:59 UTC 2025 I: Checking whether the package is not for us
Wed Mar 19 03:01:59 UTC 2025 I: Starting 1st build on remote node virt32a-armhf-rb.debian.net.
Wed Mar 19 03:01:59 UTC 2025 I: Preparing to do remote build '1' on virt32a-armhf-rb.debian.net.
Wed Mar 19 03:16:38 UTC 2025 I: Deleting $TMPDIR on virt32a-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Mar 18 15:02:06 -12 2025
I: pbuilder-time-stamp: 1742353326
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [stacks_2.68+dfsg-2.dsc]
I: copying [./stacks_2.68+dfsg.orig.tar.xz]
I: copying [./stacks_2.68+dfsg-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-2.dsc: unsupported subcommand
dpkg-source: info: extracting stacks in stacks-2.68+dfsg
dpkg-source: info: unpacking stacks_2.68+dfsg.orig.tar.xz
dpkg-source: info: unpacking stacks_2.68+dfsg-2.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 fix_spelling_errors.patch
dpkg-source: info: applying change_program_exit_to_success.patch
dpkg-source: info: applying offer_help_option_for_stacks_gdb.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/16047/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='b7883fc6fcbc41d0bcbdc6c6c4d1cf74'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='16047'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.cLoRbq8u/pbuilderrc_AM1S --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cLoRbq8u/b1 --logfile b1/build.log stacks_2.68+dfsg-2.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux virt32a 6.1.0-32-armmp-lpae #1 SMP Debian 6.1.129-1 (2025-03-06) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/16047/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), automake, zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19510 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on automake; however:
Package automake is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbam-dev; however:
Package libbam-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however:
Package libsparsehash-dev is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbam-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsparsehash-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} samtools{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget
0 packages upgraded, 98 newly installed, 0 to remove and 0 not upgraded.
Need to get 38.8 MB of archives. After unpacking 126 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.23.1-1 [238 kB]
Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB]
Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.4-5 [84.9 kB]
Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-7 [272 kB]
Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB]
Get: 17 http://deb.debian.org/debian trixie/main armhf comerr-dev armhf 2.1-1.47.2-1 [55.1 kB]
Get: 18 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 19 http://deb.debian.org/debian trixie/main armhf libtool all 2.5.4-4 [539 kB]
Get: 20 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 21 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 22 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 23 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 24 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 25 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 26 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB]
Get: 27 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-6 [9086 kB]
Get: 28 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b2 [605 kB]
Get: 29 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.23.1-1 [1560 kB]
Get: 30 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 31 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 32 http://deb.debian.org/debian trixie/main armhf debhelper all 13.24.1 [920 kB]
Get: 33 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-5 [30.4 kB]
Get: 34 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-5 [76.0 kB]
Get: 35 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B]
Get: 36 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-5 [284 kB]
Get: 37 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-5 [116 kB]
Get: 38 http://deb.debian.org/debian trixie/main armhf libgssrpc4t64 armhf 1.21.3-5 [52.9 kB]
Get: 39 http://deb.debian.org/debian trixie/main armhf libkadm5clnt-mit12 armhf 1.21.3-5 [37.7 kB]
Get: 40 http://deb.debian.org/debian trixie/main armhf libkdb5-10t64 armhf 1.21.3-5 [37.6 kB]
Get: 41 http://deb.debian.org/debian trixie/main armhf libkadm5srv-mit12 armhf 1.21.3-5 [47.6 kB]
Get: 42 http://deb.debian.org/debian trixie/main armhf krb5-multidev armhf 1.21.3-5 [126 kB]
Get: 43 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB]
Get: 44 http://deb.debian.org/debian trixie/main armhf libbam-dev armhf 0.1.19+dfsg-6 [105 kB]
Get: 45 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b7 [284 kB]
Get: 46 http://deb.debian.org/debian trixie/main armhf libbrotli-dev armhf 1.1.0-2+b7 [294 kB]
Get: 47 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB]
Get: 48 http://deb.debian.org/debian trixie/main armhf libidn2-0 armhf 2.3.8-1 [105 kB]
Get: 49 http://deb.debian.org/debian trixie/main armhf libffi8 armhf 3.4.7-1 [20.3 kB]
Get: 50 http://deb.debian.org/debian trixie/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB]
Get: 51 http://deb.debian.org/debian trixie/main armhf libtasn1-6 armhf 4.20.0-2 [44.4 kB]
Get: 52 http://deb.debian.org/debian trixie/main armhf libgnutls30t64 armhf 3.8.9-2 [1382 kB]
Get: 53 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-9 [18.5 kB]
Get: 54 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-9 [50.4 kB]
Get: 55 http://deb.debian.org/debian trixie/main armhf libldap2 armhf 2.6.9+dfsg-2 [168 kB]
Get: 56 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB]
Get: 57 http://deb.debian.org/debian trixie/main armhf libnghttp3-9 armhf 1.8.0-1 [59.9 kB]
Get: 58 http://deb.debian.org/debian trixie/main armhf libngtcp2-16 armhf 1.11.0-1 [127 kB]
Get: 59 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls8 armhf 1.11.0-1 [26.7 kB]
Get: 60 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB]
Get: 61 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB]
Get: 62 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB]
Get: 63 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.12.1-3 [316 kB]
Get: 64 http://deb.debian.org/debian trixie/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB]
Get: 65 http://deb.debian.org/debian trixie/main armhf libunbound8 armhf 1.22.0-1+b1 [539 kB]
Get: 66 http://deb.debian.org/debian trixie/main armhf libgnutls-dane0t64 armhf 3.8.9-2 [446 kB]
Get: 67 http://deb.debian.org/debian trixie/main armhf libgnutls-openssl27t64 armhf 3.8.9-2 [446 kB]
Get: 68 http://deb.debian.org/debian trixie/main armhf libidn2-dev armhf 2.3.8-1 [97.7 kB]
Get: 69 http://deb.debian.org/debian trixie/main armhf libp11-kit-dev armhf 0.25.5-3 [208 kB]
Get: 70 http://deb.debian.org/debian trixie/main armhf libtasn1-6-dev armhf 4.20.0-2 [93.4 kB]
Get: 71 http://deb.debian.org/debian trixie/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-3 [328 kB]
Get: 72 http://deb.debian.org/debian trixie/main armhf libgmp-dev armhf 2:6.3.0+dfsg-3 [592 kB]
Get: 73 http://deb.debian.org/debian trixie/main armhf nettle-dev armhf 3.10.1-1 [1314 kB]
Get: 74 http://deb.debian.org/debian trixie/main armhf libgnutls28-dev armhf 3.8.9-2 [1337 kB]
Get: 75 http://deb.debian.org/debian trixie/main armhf libkrb5-dev armhf 1.21.3-5 [16.1 kB]
Get: 76 http://deb.debian.org/debian trixie/main armhf libldap-dev armhf 2.6.9+dfsg-2 [286 kB]
Get: 77 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB]
Get: 78 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB]
Get: 79 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-4 [26.1 kB]
Get: 80 http://deb.debian.org/debian trixie/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB]
Get: 81 http://deb.debian.org/debian trixie/main armhf libnghttp3-dev armhf 1.8.0-1 [84.8 kB]
Get: 82 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls-dev armhf 1.11.0-1 [32.2 kB]
Get: 83 http://deb.debian.org/debian trixie/main armhf libngtcp2-dev armhf 1.11.0-1 [178 kB]
Get: 84 http://deb.debian.org/debian trixie/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB]
Get: 85 http://deb.debian.org/debian trixie/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB]
Get: 86 http://deb.debian.org/debian trixie/main armhf libssl-dev armhf 3.4.1-1 [2429 kB]
Get: 87 http://deb.debian.org/debian trixie/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB]
Get: 88 http://deb.debian.org/debian trixie/main armhf libzstd-dev armhf 1.5.6+dfsg-2 [326 kB]
Get: 89 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.12.1-3 [441 kB]
Get: 90 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.23-1+b1 [36.7 kB]
Get: 91 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.23-1+b1 [44.8 kB]
Get: 92 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.1-2 [63.2 kB]
Get: 93 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.21+ds-1 [408 kB]
Get: 94 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.4-1 [311 kB]
Get: 95 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.21+ds-1 [1657 kB]
Get: 96 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.5+20250216-2 [82.8 kB]
Get: 97 http://deb.debian.org/debian trixie/main armhf libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get: 98 http://deb.debian.org/debian trixie/main armhf samtools armhf 1.21-1 [633 kB]
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/stacks-2.68+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../stacks_2.68+dfsg-2_source.changes
dpkg-buildpackage: info: source package stacks
dpkg-buildpackage: info: source version 2.68+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
dh_clean
rm -f ./constants.php
make[1]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
configure.ac:28: warning: The macro 'AC_HEADER_STDC' is obsolete.
configure.ac:28: You should run autoupdate.
./lib/autoconf/headers.m4:663: 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: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 '/build/reproducible-path/stacks-2.68+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 sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/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 xargs -n works... 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... /usr/bin/grep
checking for egrep... /usr/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 or later... 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 '/build/reproducible-path/stacks-2.68+dfsg'
dh_auto_build
make -j3
make[1]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
make all-recursive
make[2]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
make[3]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/ustacks.o src/ustacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/aln_utils.o src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/BamI.o src/BamI.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/catalog_utils.o src/catalog_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc
In file included from /usr/include/c++/14/set:62,
from src/constants.h:43,
from src/ustacks.h:24,
from src/ustacks.cc:25:
/usr/include/c++/14/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(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++/14/bits/stl_tree.h:2454:7: 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
2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_algobase.h:71,
from /usr/include/c++/14/bits/specfun.h:43,
from /usr/include/c++/14/cmath:3906,
from src/constants.h:38:
/usr/include/c++/14/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++/14/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/14/bits/predefined_ops.h:157:9: 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc
In file included from /usr/include/c++/14/map:63,
from src/constants.h:44:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from '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> >&)' at src/ustacks.cc:2599:46:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from '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> >&)' at src/ustacks.cc:2599:83:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from '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> >&)' at src/ustacks.cc:2604:42:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/algorithm:61,
from src/constants.h:53:
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1750 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1770 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1750 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1770 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1777:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1777 | if (__comp(__i, __first))
| ~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/14/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1812 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_algo.h:61:
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_local_alignment(const std::string&, const std::string&)' at src/GappedAln.h:928:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_local_alignment(const std::string&, const std::string&)' at src/GappedAln.h:928:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Distance = int; _Tp = Aln; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h:232:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
232 | if (__comp(__first + __secondChild,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
233 | __first + (__secondChild - 1)))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/14/bits/stl_algo.h:1589:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1589 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1589:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1589:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1595:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1595 | if (__comp(__i, __first))
| ~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]',
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]' at /usr/include/c++/14/bits/stl_algo.h:1884:27:
/usr/include/c++/14/bits/stl_algo.h:1868:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1868 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]',
inlined from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]' at /usr/include/c++/14/bits/stl_algo.h:1855:34,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]' at /usr/include/c++/14/bits/stl_algo.h:1889:38:
/usr/include/c++/14/bits/stl_algo.h:88:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
88 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:90:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
90 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:92:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
92 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:97:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
97 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:99:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
99 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]':
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = bool (*)(Aln, Aln)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from '_Z28search_for_gapped_remaindersRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEERS_IiP5StackS3_SaIS4_IS5_SB_EEERS_IiP3RemS3_SaIS4_IS5_SH_EEE._omp_fn.0' at src/ustacks.cc:967:17:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1908 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = bool (*)(Aln, Aln)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int merge_gapped_alns(std::map<int, Stack*>&, std::map<int, Rem*>&, std::map<int, MergedStack*>&)' at src/ustacks.cc:300:13:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1908 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Aln, Aln)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Aln*, vector<Aln> >; _Compare = bool (*)(Aln, Aln)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int merge_gapped_alns(std::map<int, Stack*>&, std::map<int, Rem*>&, std::map<int, MergedStack*>&)' at src/ustacks.cc:316:13:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Aln*, std::vector<Aln> >' changed in GCC 7.1
1908 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/input.o src/input.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/locus.o src/locus.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/models.o src/models.cc
src/MetaPopInfo.cc: In member function 'void MetaPopInfo::fill_pop_indexes(std::map<int, std::pair<int, int> >&) const':
src/MetaPopInfo.cc:427:30: warning: narrowing conversion of 'i' from 'std::size_t' {aka 'unsigned int'} to 'int' [-Wnarrowing]
427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} );
| ^
In file included from /usr/include/c++/14/bits/stl_algo.h:61,
from /usr/include/c++/14/algorithm:61,
from src/constants.h:53,
from src/models.h:24,
from src/models.cc:30:
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = pair<double, double>*; _Distance = int; _Tp = pair<double, double>; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/14/set:62,
from src/constants.h:43:
/usr/include/c++/14/bits/stl_tree.h: In 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(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++/14/bits/stl_tree.h:2206:5: 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
2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/nucleotides.o src/nucleotides.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/renz.o src/renz.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/Seq.o src/Seq.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/sql_utilities.o src/sql_utilities.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/stacks.o src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/utils.o src/utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/Vcf.o src/Vcf.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/cstacks.o src/cstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc
In file included from /usr/include/c++/14/algorithm:61,
from src/constants.h:53,
from src/MetaPopInfo.h:8,
from src/cstacks.cc:25:
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1750 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1770 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: 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++/14/bits/stl_algo.h:61:
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_local_alignment(const std::string&, const std::string&)' at src/GappedAln.h:928:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_local_alignment(const std::string&, const std::string&)' at src/GappedAln.h:928:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/regex:52,
from src/sstacks.cc:25:
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
/usr/include/c++/14/bits/stl_algo.h:1750:5: 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
1750 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/regex:55:
/usr/include/c++/14/bits/stl_tree.h: In 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(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, AlignRes>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]':
/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> > >::const_iterator' changed in GCC 7.1
2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: 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
1770 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: 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++/14/bits/stl_algo.h:61:
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Distance = int; _Tp = pair<__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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
/usr/include/c++/14/bits/stl_heap.h:224:5: 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
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, AlignRes>&}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, AlignRes>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]':
/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> > >::const_iterator' changed in GCC 7.1
2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1750 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1770 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_local_alignment(const std::string&, const std::string&)' at src/GappedAln.h:928:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_local_alignment(const std::string&, const std::string&)' at src/GappedAln.h:928:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: 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
1876 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: 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++/14/bits/stl_algo.h:1890:32: 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
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Compare = 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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)>]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from '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&)' at src/sstacks.cc:1033:13:
/usr/include/c++/14/bits/stl_algo.h:1905:32: 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
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)> >]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<__cxx11::basic_string<char>, AlignRes>*, vector<pair<__cxx11::basic_string<char>, AlignRes> > >; _Compare = 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(pair<__cxx11::basic_string<char>, AlignRes>&, pair<__cxx11::basic_string<char>, AlignRes>&)>]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from '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&)' at src/sstacks.cc:1033:13:
/usr/include/c++/14/bits/stl_algo.h:1817:32: 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
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: 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
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/regex:56:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, AlignRes>&}; _Key = std::__cxx11::basic_string<char>; _Tp = AlignRes; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]',
inlined from 'std::__enable_if_t<((bool)std::is_constructible<std::pair<const _Key, _Tp>, _Pair>::value), std::pair<typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind<std::pair<const _Key, _Tp> >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair<std::__cxx11::basic_string<char>, AlignRes>&; _Key = std::__cxx11::basic_string<char>; _Tp = AlignRes; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >]' at /usr/include/c++/14/bits/stl_map.h:859:27,
inlined from '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&)' at src/sstacks.cc:1042:40:
/usr/include/c++/14/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map<std::__cxx11::basic_string<char>, AlignRes>::const_iterator' {aka 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, AlignRes>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, AlignRes> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, AlignRes> > >::const_iterator'} changed in GCC 7.1
640 | return _M_t._M_emplace_hint_unique(__pos,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
641 | std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/write.o src/write.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/process_shortreads.o src/process_shortreads.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/kmer_filter.o src/kmer_filter.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/clone_filter.o src/clone_filter.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/populations.o src/populations.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/bootstrap.o src/bootstrap.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/export_formats.o src/export_formats.cc
src/export_formats.cc: In member function 'virtual int PhylipVarAllExport::post_processing()':
src/export_formats.cc:2458:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=]
2458 | sprintf(s, "%11lu", this->_seq_len);
| ~~~~^ ~~~~~~~~~~~~~~
| | |
| | std::size_t {aka unsigned int}
| long unsigned int
| %11u
In file included from /usr/include/c++/14/bits/stl_algo.h:61,
from /usr/include/c++/14/algorithm:61,
from src/constants.h:53,
from src/populations.h:45,
from src/populations.cc:29:
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1770 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h: In function '_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Tp = double; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1980:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1980 | __upper_bound(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1980:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1812 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc
In file included from /usr/include/c++/14/map:62,
from src/PopSum.h:27,
from src/PopSum.cc:21:
/usr/include/c++/14/bits/stl_tree.h: In 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(const_iterator, const key_type&) [with _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/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(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<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++/14/bits/stl_tree.h:2454:7: 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
2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/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(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++/14/bits/stl_tree.h:2454:7: 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
/usr/include/c++/14/bits/stl_tree.h: In 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(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++/14/bits/stl_tree.h:2206:5: 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
2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/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(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++/14/bits/stl_tree.h:2454:7: 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
2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/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(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++/14/bits/stl_tree.h:2454:7: 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
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
inlined from '_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Tp = double]',
inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [with StatT = SumStat]' at src/bootstrap.h:268:39,
inlined from '_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22:
/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2028 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2029 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Tp = double]',
inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [with StatT = PopPair]' at src/bootstrap.h:268:39,
inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22:
/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2028 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2029 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
inlined from '_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
inlined from '_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Tp = double]',
inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [with StatT = LocStat]' at src/bootstrap.h:268:39,
inlined from '_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22:
/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2028 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2029 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18,
inlined from '_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:250:21:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Tp = double]',
inlined from 'double Bootstrap<StatT>::pval(double, std::vector<double>&) [with StatT = HapStat]' at src/bootstrap.h:268:39,
inlined from '_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0' at src/bootstrap.h:251:22:
/usr/include/c++/14/bits/stl_algo.h:2028:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
2028 | return std::__upper_bound(__first, __last, __val,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2029 | __gnu_cxx::__ops::__val_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/map:63:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](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> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2089:47:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](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> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2090:55:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](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> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2094:51:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](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> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2095:59:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2101:30:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
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> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2111:61:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2111:82:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
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> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2112:65:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2112:86:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
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> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2123:51:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
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> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2123:88:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2124:35:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector<int>&)' at src/PopSum.cc:2124:57:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/14/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++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](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++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](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> >]',
inlined from 'double count_haplotypes_at_locus(int, int, const Datum* const*, std::map<std::__cxx11::basic_string<char>, double>&)' at src/PopSum.cc:1049:45:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
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 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> >]',
inlined from 'LocStat* LocPopSum::haplotype_diversity(int, int, const Datum* const*)' at src/PopSum.cc:937:39:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
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> >]',
inlined from 'LocStat* LocPopSum::haplotype_diversity(int, int, const Datum* const*)' at src/PopSum.cc:938:39:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](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> >]',
inlined from 'double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector<int>&)' at src/PopSum.cc:2167:47:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](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> >]',
inlined from 'double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector<int>&)' at src/PopSum.cc:2168:55:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector<int>&)' at src/PopSum.cc:2173:30:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector<int>&)' at src/PopSum.cc:2187:68:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
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> >]',
inlined from 'double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector<int>&)' at src/PopSum.cc:2190:53:
/usr/include/c++/14/bits/stl_map.h:513:44: 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
513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
514 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
515 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector<int>&)' at src/PopSum.cc:2190:72:
/usr/include/c++/14/bits/stl_map.h:532:44: 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
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc
src/gstacks.cc: In member function 'bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const':
src/gstacks.cc:1369:32: 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=]
1369 | 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:1555:38: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=]
1555 | snprintf(buf, id_len, "%luM", alns.front().aln_len);
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int std::size_t {aka unsigned int}
| %u
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc
g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o src/SuffixTree.o src/SuffixTree.cc
rm -f libcore.a
ar cr 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
In file included from /usr/include/c++/14/algorithm:61,
from src/constants.h:53,
from src/gstacks.h:23,
from src/gstacks.cc:23:
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1750 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_algobase.h:71,
from /usr/include/c++/14/bits/specfun.h:43,
from /usr/include/c++/14/cmath:3906,
from src/constants.h:38:
/usr/include/c++/14/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++/14/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/14/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1770 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1777:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1777 | if (__comp(__i, __first))
| ~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_algo.h:61:
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h:232:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
232 | if (__comp(__first + __secondChild,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
233 | __first + (__secondChild - 1)))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<STAln*, 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)> >]',
inlined from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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)> >]' at /usr/include/c++/14/bits/stl_algo.h:1855:34,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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)> >]' at /usr/include/c++/14/bits/stl_algo.h:1889:38:
/usr/include/c++/14/bits/stl_algo.h:88:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
88 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:90:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
90 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:92:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
92 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:97:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
97 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:99:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
99 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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)> >]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<STAln*, vector<STAln> >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)>]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const' at src/gstacks.cc:1397:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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)> >]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<STAln*, 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)> >]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<STAln*, vector<STAln> >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const::<lambda(STAln, STAln)>]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector<STAln>&, std::vector<STAln>&) const' at src/gstacks.cc:1397:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<STAln*, std::vector<STAln> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
rm -f libclean.a
ar cr libclean.a src/clean.o src/kmers.o src/file_io.o src/write.o
ranlib libclean.a
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1750 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1770 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
rm -f libpop.a
ar cr libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o
ranlib libcore.a
ranlib libpop.a
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1876 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_local_alignment(const std::string&, const std::string&)' at src/GappedAln.h:928:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_local_alignment(const std::string&, const std::string&)' at src/GappedAln.h:928:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1905 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1906 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1907 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const AlignRes&, const AlignRes&)>]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<AlignRes*, vector<AlignRes> >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]' at /usr/include/c++/14/bits/stl_algo.h:4805:18,
inlined from 'int GappedAln::trace_global_alignment(const std::string&, const std::string&)' at src/GappedAln.h:782:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignRes*, std::vector<AlignRes> >' changed in GCC 7.1
1822 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/stacks-2.68+dfsg=. -fstack-protector-strong -fstack-clash-protection -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 '/build/reproducible-path/stacks-2.68+dfsg'
make[2]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
make[1]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
set -e \
; TAP_DRIVER=$( ls -d1 /usr/share/automake-*/tap-driver.sh | tail -n-1 ) \
; if [ -e "$TAP_DRIVER" ] \
; then ln -s "$TAP_DRIVER" 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 '/build/reproducible-path/stacks-2.68+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
dh_auto_install --no-parallel
make -j1 install DESTDIR=/build/reproducible-path/stacks-2.68\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
make[3]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
make[4]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
/usr/bin/mkdir -p '/build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin'
/usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin'
/usr/bin/mkdir -p '/build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin'
/usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-private-alleles scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin'
make install-data-hook
make[5]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
sed -e 's,_VERSION_,2.68,' -e 's,_BINDIR_,/usr/libexec/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl > /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst
mv /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl.subst /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl
chmod +x /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/denovo_map.pl
sed -e 's,_VERSION_,2.68,' -e 's,_BINDIR_,/usr/libexec/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl > /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl.subst
mv /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl.subst /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl
chmod +x /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/ref_map.pl
sed -i.bkp -e 's,_VERSION_,2.68,' /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments
sed -i.bkp -e 's,_VERSION_,2.68,' /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-samtools-tview
rm -f /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments.bkp
rm -f /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-samtools-tview.bkp
chmod +x /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-integrate-alignments
chmod +x /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-dist-extract
chmod +x /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/bin/stacks-gdb
make[5]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
make[4]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
make[3]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
make[2]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
make[1]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
mkdir -p debian/stacks/usr/libexec/stacks
mv debian/stacks/usr/bin debian/stacks/usr/libexec/stacks
cd debian/stacks/usr/libexec/stacks/bin && \
for f in *.pl ; do \
ln -s "$f" "`basename $f .pl`" ; \
sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $f ; \
done
dh_install
make[1]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
dh_installdocs
dh_installchangelogs
dh_perl
debian/rules override_dh_link
make[1]: Entering directory '/build/reproducible-path/stacks-2.68+dfsg'
dh_link
mkdir -p debian/stacks/usr/libexec/debian-med/bin
cd debian/stacks/usr/libexec/debian-med/bin && \
for f in `ls /build/reproducible-path/stacks-2.68+dfsg/debian/stacks/usr/libexec/stacks/bin` ; do \
ln -s ../../stacks/bin/$f ; \
done
make[1]: Leaving directory '/build/reproducible-path/stacks-2.68+dfsg'
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dpkg-shlibdeps: warning: debian/stacks/usr/libexec/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/libexec/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/libexec/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/libexec/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/libexec/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/libexec/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/libexec/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/libexec/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/libexec/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/libexec/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/libexec/stacks/bin/cstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb
dh_gencontrol
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
dh_builddeb
dpkg-deb: building package 'stacks' in '../stacks_2.68+dfsg-2_armhf.deb'.
dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.68+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../stacks_2.68+dfsg-2_armhf.buildinfo
dpkg-genchanges --build=binary -O../stacks_2.68+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/16047 and its subdirectories
I: Current time: Tue Mar 18 15:15:17 -12 2025
I: pbuilder-time-stamp: 1742354117
Wed Mar 19 03:16:42 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt64z-armhf-rb.debian.net.
Wed Mar 19 03:16:42 UTC 2025 I: Preparing to do remote build '2' on virt64z-armhf-rb.debian.net.
Wed Mar 19 03:23:14 UTC 2025 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net.
Wed Mar 19 03:23:16 UTC 2025 I: stacks_2.68+dfsg-2_armhf.changes:
Format: 1.8
Date: Sun, 16 Feb 2025 10:54:31 +0100
Source: stacks
Binary: stacks stacks-dbgsym
Architecture: armhf
Version: 2.68+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
stacks - pipeline for building loci from short-read DNA sequences
Closes: 1095396
Changes:
stacks (2.68+dfsg-2) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* Remove Tim Booth <tbooth@ceh.ac.uk> since address is bouncing
(Thank you for your work on this package, Tim)
.
[ Étienne Mollier ]
* d/control: explicitly build-depend on automake.
* d/rules: reinforce the fetch the TAP driver for any automake version.
Unfortunately this change is not sufficient to put upstream's super
secret test suite on tracks, so it is still disabled for the moment.
(Closes: #1095396)
* use_debian_packaged_htslib.patch: normalise Last-Update timestamp.
Checksums-Sha1:
a5873fe4e2bb7f1264fe17d681ae15c2794ec4ab 28082148 stacks-dbgsym_2.68+dfsg-2_armhf.deb
eb93aee2ca460bad689975061055dbbb18085262 6881 stacks_2.68+dfsg-2_armhf.buildinfo
f264a37b8af9019ed0499cc3bd4fab26c394c084 1070824 stacks_2.68+dfsg-2_armhf.deb
Checksums-Sha256:
774ecc4f0126c91b2cc3a52877087020dd8d930008951a0db250b1ab9136ff1d 28082148 stacks-dbgsym_2.68+dfsg-2_armhf.deb
01c81cfe9a15c42b3c18cce549aad4ce05dc02ae002d00a07038d5eeb1525a5b 6881 stacks_2.68+dfsg-2_armhf.buildinfo
78d26072d4d174eab45ac01a98f7f5dd307d237ca0f0d46f62a07ddaf7cb1ddf 1070824 stacks_2.68+dfsg-2_armhf.deb
Files:
d93737ead99c93399d92864942bed6d1 28082148 debug optional stacks-dbgsym_2.68+dfsg-2_armhf.deb
ced380c3502e08c4ccc69512b992da76 6881 science optional stacks_2.68+dfsg-2_armhf.buildinfo
becf60b15eccb39c7d58d30992f527b9 1070824 science optional stacks_2.68+dfsg-2_armhf.deb
Wed Mar 19 03:23:17 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-armhf_9-13344.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.cLoRbq8u/stacks_2.68+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.cLoRbq8u/stacks_2.68+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.cLoRbq8u/stacks_2.68+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.cLoRbq8u/b1/stacks_2.68+dfsg-2_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.cLoRbq8u/b2/stacks_2.68+dfsg-2_armhf.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 226ms
CPU time consumed: 227ms
Wed Mar 19 03:23:17 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Wed Mar 19 03:23:17 UTC 2025 I: stacks from trixie built successfully and reproducibly on armhf.
Wed Mar 19 03:23:19 UTC 2025 I: Submitting .buildinfo files to external archives:
Wed Mar 19 03:23:19 UTC 2025 I: Submitting 8.0K b1/stacks_2.68+dfsg-2_armhf.buildinfo.asc
Wed Mar 19 03:23:19 UTC 2025 I: Submitting 8.0K b2/stacks_2.68+dfsg-2_armhf.buildinfo.asc
Wed Mar 19 03:23:20 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Wed Mar 19 03:23:20 UTC 2025 I: Done submitting .buildinfo files.
Wed Mar 19 03:23:20 UTC 2025 I: Removing signed stacks_2.68+dfsg-2_armhf.buildinfo.asc files:
removed './b1/stacks_2.68+dfsg-2_armhf.buildinfo.asc'
removed './b2/stacks_2.68+dfsg-2_armhf.buildinfo.asc'