Sun May 21 00:15:10 UTC 2023 I: starting to build sga/bookworm/amd64 on jenkins on '2023-05-21 00:14'
Sun May 21 00:15:10 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_32/17846/console.log
Sun May 21 00:15:10 UTC 2023 I: Downloading source for bookworm/sga=0.10.15-7
--2023-05-21 00:15:10-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/sga/sga_0.10.15-7.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2084 (2.0K) [text/prs.lines.tag]
Saving to: ‘sga_0.10.15-7.dsc’
0K .. 100% 95.0M=0s
2023-05-21 00:15:10 (95.0 MB/s) - ‘sga_0.10.15-7.dsc’ saved [2084/2084]
Sun May 21 00:15:10 UTC 2023 I: sga_0.10.15-7.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: sga
Binary: sga
Architecture: any
Version: 0.10.15-7
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe@debian.org>, Andreas Tille <tille@debian.org>
Homepage: https://github.com/jts/sga
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/sga
Vcs-Git: https://salsa.debian.org/med-team/sga.git
Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools <!nocheck>, python3 <!nocheck>, python3-ruffus <!nocheck>, python3-pysam <!nocheck>
Package-List:
sga deb science optional arch=any
Checksums-Sha1:
55b540d2f1cae3a44de8da6db8f413826bdb5f14 6569986 sga_0.10.15.orig.tar.gz
4598b0bf58446b932f202a8bfa7e9d9d3bc018de 214356 sga_0.10.15-7.debian.tar.xz
Checksums-Sha256:
1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b 6569986 sga_0.10.15.orig.tar.gz
708c923249099329004802eb6fe1b549b6421e5d3cf10d81c624db65e381117f 214356 sga_0.10.15-7.debian.tar.xz
Files:
990aed1593f8072650c6366e5cf32519 6569986 sga_0.10.15.orig.tar.gz
420c1f46b48f89950ac7e500402215e8 214356 sga_0.10.15-7.debian.tar.xz
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Sun May 21 00:15:10 UTC 2023 I: Checking whether the package is not for us
Sun May 21 00:15:10 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Sun May 21 00:15:10 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Sun May 21 00:26:23 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Jun 21 18:38:22 -12 2024
I: pbuilder-time-stamp: 1719038302
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [sga_0.10.15-7.dsc]
I: copying [./sga_0.10.15.orig.tar.gz]
I: copying [./sga_0.10.15-7.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Sep 17 02:05:16 2021 -12
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./sga_0.10.15-7.dsc: no acceptable signature found
dpkg-source: info: extracting sga in sga-0.10.15
dpkg-source: info: unpacking sga_0.10.15.orig.tar.gz
dpkg-source: info: unpacking sga_0.10.15-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0002-no-rpath.patch
dpkg-source: info: applying 0003-do-not-dist-unsup-script.patch
dpkg-source: info: applying 0004-Add-help-to-sga-bam2de.pl.patch
dpkg-source: info: applying 0005-Remove-extensions-on-scripts-we-ship.patch
dpkg-source: info: applying 0006-remove-google-addsense.patch
dpkg-source: info: applying gcc-7.patch
dpkg-source: info: applying no_privacy_breach_url.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying no_enforcing_c++98.patch
dpkg-source: info: applying gcc9.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/986957/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='d53ea91cd8fc419ea71c138abf4bd101'
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='986957'
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.EV9fxeni/pbuilderrc_1baV --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EV9fxeni/b1 --logfile b1/build.log sga_0.10.15-7.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos15-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 2023 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 2023 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 2023 more
-rwsr-xr-x 1 root root 59704 Mar 22 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 2023 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 2023 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/986957/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: amd64
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), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools, python3, python3-ruffus, python3-pysam
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19596 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 dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however:
Package libsparsehash-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev | libz-dev; however:
Package zlib1g-dev is not installed.
Package libz-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbamtools-dev; however:
Package libbamtools-dev is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on python3-ruffus; however:
Package python3-ruffus is not installed.
pbuilder-satisfydepends-dummy depends on python3-pysam; however:
Package python3-pysam 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} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} help2man{a} intltool-debian{a} libabsl20220623{a} libann0{a} libaom3{a} libarchive-zip-perl{a} libavif15{a} libbamtools-dev{a} libbamtools2.5.2{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcurl3-gnutls{a} libdatrie1{a} libdav1d6{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif1{a} libhts3{a} libhtscodecs2{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} liblab-gamut1{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libnuma1{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librav1e0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsm6{a} libsparsehash-dev{a} libssh2-1{a} libsub-override-perl{a} libsvtav1enc1{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libx265-199{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libyuv0{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pysam{a} python3-ruffus{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} x11-common{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl fonts-liberation2 libarchive-cpio-perl libglib2.0-data libgpm2 libgts-bin libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs
0 packages upgraded, 129 newly installed, 0 to remove and 0 not upgraded.
Need to get 52.5 MB of archives. After unpacking 189 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 libcdt5 amd64 2.42.2-7+b3 [39.8 kB]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 libcgraph6 amd64 2.42.2-7+b3 [63.2 kB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 libaom3 amd64 3.6.0-1 [1851 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 libdav1d6 amd64 1.0.0-2 [495 kB]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libabsl20220623 amd64 20220623.1-1 [391 kB]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libgav1-1 amd64 0.18.0-1+b1 [332 kB]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 librav1e0 amd64 0.5.1-6 [763 kB]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 libsvtav1enc1 amd64 1.4.1+dfsg-1 [2121 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 libyuv0 amd64 0.0~git20230123.b2528b0-1 [168 kB]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 libavif15 amd64 0.11.1-1 [93.8 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 libde265-0 amd64 1.0.11-1 [185 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 libx265-199 amd64 3.5-2+b1 [1150 kB]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 libheif1 amd64 1.15.1-1 [215 kB]
Get: 69 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get: 70 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB]
Get: 71 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB]
Get: 72 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB]
Get: 73 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB]
Get: 74 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get: 75 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB]
Get: 76 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get: 77 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get: 78 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB]
Get: 79 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB]
Get: 80 http://deb.debian.org/debian bookworm/main amd64 libxpm4 amd64 1:3.5.12-1.1 [48.4 kB]
Get: 81 http://deb.debian.org/debian bookworm/main amd64 libgd3 amd64 2.3.3-9 [124 kB]
Get: 82 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB]
Get: 83 http://deb.debian.org/debian bookworm/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-5+b1 [160 kB]
Get: 84 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB]
Get: 85 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB]
Get: 86 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB]
Get: 87 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get: 88 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB]
Get: 89 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB]
Get: 90 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB]
Get: 91 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB]
Get: 92 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB]
Get: 93 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB]
Get: 94 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB]
Get: 95 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB]
Get: 96 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB]
Get: 97 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB]
Get: 98 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB]
Get: 99 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB]
Get: 100 http://deb.debian.org/debian bookworm/main amd64 libpathplan4 amd64 2.42.2-7+b3 [42.2 kB]
Get: 101 http://deb.debian.org/debian bookworm/main amd64 libgvc6 amd64 2.42.2-7+b3 [678 kB]
Get: 102 http://deb.debian.org/debian bookworm/main amd64 libgvpr2 amd64 2.42.2-7+b3 [189 kB]
Get: 103 http://deb.debian.org/debian bookworm/main amd64 liblab-gamut1 amd64 2.42.2-7+b3 [198 kB]
Get: 104 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB]
Get: 105 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB]
Get: 106 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB]
Get: 107 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB]
Get: 108 http://deb.debian.org/debian bookworm/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB]
Get: 109 http://deb.debian.org/debian bookworm/main amd64 libxaw7 amd64 2:1.0.14-1 [201 kB]
Get: 110 http://deb.debian.org/debian bookworm/main amd64 graphviz amd64 2.42.2-7+b3 [611 kB]
Get: 111 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB]
Get: 112 http://deb.debian.org/debian bookworm/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-4 [149 kB]
Get: 113 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get: 114 http://deb.debian.org/debian bookworm/main amd64 libbamtools-dev amd64 2.5.2+dfsg-4 [214 kB]
Get: 115 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get: 116 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get: 117 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get: 118 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB]
Get: 119 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get: 120 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 121 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get: 122 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB]
Get: 123 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get: 124 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB]
Get: 125 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB]
Get: 126 http://deb.debian.org/debian bookworm/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get: 127 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB]
Get: 128 http://deb.debian.org/debian bookworm/main amd64 python3-ruffus all 2.8.4-5 [151 kB]
Get: 129 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB]
Fetched 52.5 MB in 1s (36.3 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package liblocale-gettext-perl.
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Preparing to unpack .../liblocale-gettext-perl_1.07-5_amd64.deb ...
Unpacking liblocale-gettext-perl (1.07-5) ...
Selecting previously unselected package libpython3.11-minimal:amd64.
Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:amd64 (3.11.2-6) ...
Setting up libexpat1:amd64 (2.5.0-1) ...
Setting up python3.11-minimal (3.11.2-6) ...
Selecting previously unselected package python3-minimal.
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Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ...
Unpacking python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.0.0_all.deb ...
Unpacking media-types (10.0.0) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ...
Unpacking readline-common (8.2-1.3) ...
Selecting previously unselected package libreadline8:amd64.
Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ...
Unpacking libreadline8:amd64 (8.2-1.3) ...
Selecting previously unselected package libpython3.11-stdlib:amd64.
Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ...
Unpacking python3.11 (3.11.2-6) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package python3.
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Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ...
Unpacking python3 (3.11.2-1+b1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../002-libmagic-mgc_1%3a5.44-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../003-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../004-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../005-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../006-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../007-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../008-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../009-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../010-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../011-m4_1.4.19-3_amd64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../012-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../013-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../014-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../015-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../016-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../017-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../018-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../019-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../020-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../021-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
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Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:amd64.
Preparing to unpack .../023-libelf1_0.188-2.1_amd64.deb ...
Unpacking libelf1:amd64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../024-dwz_0.15-1_amd64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../025-libicu72_72.1-3_amd64.deb ...
Unpacking libicu72:amd64 (72.1-3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../026-libxml2_2.9.14+dfsg-1.2_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../027-gettext_0.21-12_amd64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../028-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
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Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
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Unpacking debhelper (13.11.4) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../031-python3-lib2to3_3.11.2-3_all.deb ...
Unpacking python3-lib2to3 (3.11.2-3) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../032-python3-distutils_3.11.2-3_all.deb ...
Unpacking python3-distutils (3.11.2-3) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../033-dh-python_5.20230130_all.deb ...
Unpacking dh-python (5.20230130) ...
Selecting previously unselected package libbrotli1:amd64.
Preparing to unpack .../034-libbrotli1_1.0.9-2+b6_amd64.deb ...
Unpacking libbrotli1:amd64 (1.0.9-2+b6) ...
Selecting previously unselected package libpng16-16:amd64.
Preparing to unpack .../035-libpng16-16_1.6.39-2_amd64.deb ...
Unpacking libpng16-16:amd64 (1.6.39-2) ...
Selecting previously unselected package libfreetype6:amd64.
Preparing to unpack .../036-libfreetype6_2.12.1+dfsg-5_amd64.deb ...
Unpacking libfreetype6:amd64 (2.12.1+dfsg-5) ...
Selecting previously unselected package fonts-dejavu-core.
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Unpacking fonts-dejavu-core (2.37-6) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../038-fontconfig-config_2.14.1-4_amd64.deb ...
Unpacking fontconfig-config (2.14.1-4) ...
Selecting previously unselected package libfontconfig1:amd64.
Preparing to unpack .../039-libfontconfig1_2.14.1-4_amd64.deb ...
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Processing triggers for libc-bin (2.36-9) ...
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/sga-0.10.15/ && 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 > ../sga_0.10.15-7_source.changes
dpkg-buildpackage: info: source package sga
dpkg-buildpackage: info: source version 0.10.15-7
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --with python3 --sourcedirectory=src
dh_auto_clean -O--sourcedirectory=src
dh_autoreconf_clean -O--sourcedirectory=src
dh_clean -O--sourcedirectory=src
debian/rules binary
dh binary --with python3 --sourcedirectory=src
dh_update_autotools_config -O--sourcedirectory=src
dh_autoreconf -O--sourcedirectory=src
configure.ac:7: warning: The macro `AC_CONFIG_HEADER' is obsolete.
configure.ac:7: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:7: the top level
configure.ac:24: warning: The macro `AC_TRY_LINK' is obsolete.
configure.ac:24: You should run autoupdate.
./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
m4/m4_ax_openmp.m4:70: AX_OPENMP is expanded from...
configure.ac:24: the top level
configure.ac:12: installing './compile'
configure.ac:5: installing './install-sh'
configure.ac:5: installing './missing'
Algorithm/Makefile.am: installing './depcomp'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/sga-0.10.15'
dh_auto_configure -- --with-bamtools=/usr/
cd src && ./configure --build=x86_64-linux-gnu --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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-bamtools=/usr/
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for ranlib... ranlib
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 zlib.h... yes
checking for library containing gzopen... -lz
checking for library containing clock_gettime... none required
checking for OpenMP flag of C++ compiler... -fopenmp
checking for host type... you are not using osx so multi-threading should work.
checking for google/sparse_hash_set... yes
checking for google/sparse_hash_set... (cached) yes
checking for google/sparse_hash_map... yes
checking for unordered_map... yes
checking for tr1/unordered_map... yes
checking for ext/hash_map... yes
checking for unordered_set... yes
checking for tr1/unordered_set... yes
checking for ext/hash_set... yes
checking for api/BamReader.h... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating Thirdparty/Makefile
config.status: creating Util/Makefile
config.status: creating SQG/Makefile
config.status: creating Bigraph/Makefile
config.status: creating Algorithm/Makefile
config.status: creating StringGraph/Makefile
config.status: creating Concurrency/Makefile
config.status: creating SuffixTools/Makefile
config.status: creating GraphDiff/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SGA/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/build/sga-0.10.15'
dh_auto_build -O--sourcedirectory=src
cd src && make -j16
make[1]: Entering directory '/build/sga-0.10.15/src'
make all-recursive
make[2]: Entering directory '/build/sga-0.10.15/src'
Making all in bin
make[3]: Entering directory '/build/sga-0.10.15/src/bin'
cp -n sga-bam2de.pl sga-bam2de
cp -n sga-mergeDriver.pl sga-mergeDriver
make[3]: Leaving directory '/build/sga-0.10.15/src/bin'
Making all in Thirdparty
make[3]: Entering directory '/build/sga-0.10.15/src/Thirdparty'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gzstream.o gzstream.C
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o stdaln.o stdaln.c
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o overlapper.o overlapper.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o multiple_alignment.o multiple_alignment.cpp
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o bcr.o bcr.c
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MurmurHash3.o MurmurHash3.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o count_min_sketch.o count_min_sketch.cpp
MurmurHash3.cpp: In function 'void MurmurHash3_x86_32(const void*, int, uint32_t, void*)':
MurmurHash3.cpp:132:14: warning: this statement may fall through [-Wimplicit-fallthrough=]
132 | case 3: k1 ^= tail[2] << 16;
| ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:133:3: note: here
133 | case 2: k1 ^= tail[1] << 8;
| ^~~~
MurmurHash3.cpp:133:14: warning: this statement may fall through [-Wimplicit-fallthrough=]
133 | case 2: k1 ^= tail[1] << 8;
| ~~~^~~~~~~~~~~~~~~
MurmurHash3.cpp:134:3: note: here
134 | case 1: k1 ^= tail[0];
| ^~~~
MurmurHash3.cpp: In function 'void MurmurHash3_x86_128(const void*, int, uint32_t, void*)':
MurmurHash3.cpp:207:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
207 | case 15: k4 ^= tail[14] << 16;
| ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:208:3: note: here
208 | case 14: k4 ^= tail[13] << 8;
| ^~~~
MurmurHash3.cpp:208:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
208 | case 14: k4 ^= tail[13] << 8;
| ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:209:3: note: here
209 | case 13: k4 ^= tail[12] << 0;
| ^~~~
MurmurHash3.cpp:210:56: warning: this statement may fall through [-Wimplicit-fallthrough=]
210 | k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4;
| ~~~^~~~~
MurmurHash3.cpp:212:3: note: here
212 | case 12: k3 ^= tail[11] << 24;
| ^~~~
MurmurHash3.cpp:212:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
212 | case 12: k3 ^= tail[11] << 24;
| ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:213:3: note: here
213 | case 11: k3 ^= tail[10] << 16;
| ^~~~
MurmurHash3.cpp:213:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
213 | case 11: k3 ^= tail[10] << 16;
| ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:214:3: note: here
214 | case 10: k3 ^= tail[ 9] << 8;
| ^~~~
MurmurHash3.cpp:214:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
214 | case 10: k3 ^= tail[ 9] << 8;
| ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:215:3: note: here
215 | case 9: k3 ^= tail[ 8] << 0;
| ^~~~
MurmurHash3.cpp:216:56: warning: this statement may fall through [-Wimplicit-fallthrough=]
216 | k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3;
| ~~~^~~~~
MurmurHash3.cpp:218:3: note: here
218 | case 8: k2 ^= tail[ 7] << 24;
| ^~~~
MurmurHash3.cpp:218:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
218 | case 8: k2 ^= tail[ 7] << 24;
| ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:219:3: note: here
219 | case 7: k2 ^= tail[ 6] << 16;
| ^~~~
MurmurHash3.cpp:219:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
219 | case 7: k2 ^= tail[ 6] << 16;
| ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:220:3: note: here
220 | case 6: k2 ^= tail[ 5] << 8;
| ^~~~
MurmurHash3.cpp:220:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
220 | case 6: k2 ^= tail[ 5] << 8;
| ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:221:3: note: here
221 | case 5: k2 ^= tail[ 4] << 0;
| ^~~~
MurmurHash3.cpp:222:56: warning: this statement may fall through [-Wimplicit-fallthrough=]
222 | k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2;
| ~~~^~~~~
MurmurHash3.cpp:224:3: note: here
224 | case 4: k1 ^= tail[ 3] << 24;
| ^~~~
MurmurHash3.cpp:224:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
224 | case 4: k1 ^= tail[ 3] << 24;
| ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:225:3: note: here
225 | case 3: k1 ^= tail[ 2] << 16;
| ^~~~
MurmurHash3.cpp:225:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
225 | case 3: k1 ^= tail[ 2] << 16;
| ~~~^~~~~~~~~~~~~~~~~
MurmurHash3.cpp:226:3: note: here
226 | case 2: k1 ^= tail[ 1] << 8;
| ^~~~
MurmurHash3.cpp:226:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
226 | case 2: k1 ^= tail[ 1] << 8;
| ~~~^~~~~~~~~~~~~~~~
MurmurHash3.cpp:227:3: note: here
227 | case 1: k1 ^= tail[ 0] << 0;
| ^~~~
MurmurHash3.cpp: In function 'void MurmurHash3_x64_128(const void*, int, uint32_t, void*)':
MurmurHash3.cpp:296:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
296 | case 15: k2 ^= uint64_t(tail[14]) << 48;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:297:3: note: here
297 | case 14: k2 ^= uint64_t(tail[13]) << 40;
| ^~~~
MurmurHash3.cpp:297:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
297 | case 14: k2 ^= uint64_t(tail[13]) << 40;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:298:3: note: here
298 | case 13: k2 ^= uint64_t(tail[12]) << 32;
| ^~~~
MurmurHash3.cpp:298:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
298 | case 13: k2 ^= uint64_t(tail[12]) << 32;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:299:3: note: here
299 | case 12: k2 ^= uint64_t(tail[11]) << 24;
| ^~~~
MurmurHash3.cpp:299:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
299 | case 12: k2 ^= uint64_t(tail[11]) << 24;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:300:3: note: here
300 | case 11: k2 ^= uint64_t(tail[10]) << 16;
| ^~~~
MurmurHash3.cpp:300:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
300 | case 11: k2 ^= uint64_t(tail[10]) << 16;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:301:3: note: here
301 | case 10: k2 ^= uint64_t(tail[ 9]) << 8;
| ^~~~
MurmurHash3.cpp:301:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
301 | case 10: k2 ^= uint64_t(tail[ 9]) << 8;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:302:3: note: here
302 | case 9: k2 ^= uint64_t(tail[ 8]) << 0;
| ^~~~
MurmurHash3.cpp:303:56: warning: this statement may fall through [-Wimplicit-fallthrough=]
303 | k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2;
| ~~~^~~~~
MurmurHash3.cpp:305:3: note: here
305 | case 8: k1 ^= uint64_t(tail[ 7]) << 56;
| ^~~~
MurmurHash3.cpp:305:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
305 | case 8: k1 ^= uint64_t(tail[ 7]) << 56;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:306:3: note: here
306 | case 7: k1 ^= uint64_t(tail[ 6]) << 48;
| ^~~~
MurmurHash3.cpp:306:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
306 | case 7: k1 ^= uint64_t(tail[ 6]) << 48;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:307:3: note: here
307 | case 6: k1 ^= uint64_t(tail[ 5]) << 40;
| ^~~~
MurmurHash3.cpp:307:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
307 | case 6: k1 ^= uint64_t(tail[ 5]) << 40;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:308:3: note: here
308 | case 5: k1 ^= uint64_t(tail[ 4]) << 32;
| ^~~~
MurmurHash3.cpp:308:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
308 | case 5: k1 ^= uint64_t(tail[ 4]) << 32;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:309:3: note: here
309 | case 4: k1 ^= uint64_t(tail[ 3]) << 24;
| ^~~~
MurmurHash3.cpp:309:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
309 | case 4: k1 ^= uint64_t(tail[ 3]) << 24;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:310:3: note: here
310 | case 3: k1 ^= uint64_t(tail[ 2]) << 16;
| ^~~~
MurmurHash3.cpp:310:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
310 | case 3: k1 ^= uint64_t(tail[ 2]) << 16;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:311:3: note: here
311 | case 2: k1 ^= uint64_t(tail[ 1]) << 8;
| ^~~~
MurmurHash3.cpp:311:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
311 | case 2: k1 ^= uint64_t(tail[ 1]) << 8;
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
MurmurHash3.cpp:312:3: note: here
312 | case 1: k1 ^= uint64_t(tail[ 0]) << 0;
| ^~~~
bcr.c: In function 'ld_restore':
bcr.c:183:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
183 | fread(&ld->max, sizeof(int), 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bcr.c:186:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
186 | fread(&x, sizeof(int), 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bcr.c:189:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
189 | fread(ld->a[i], 8, x, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s1_start' [-Wmissing-field-initializers]
37 | OverlapperParams default_params = { 2, -6, -3, -2, ALT_OVERLAP };
| ^
overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s1_end' [-Wmissing-field-initializers]
overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s2_start' [-Wmissing-field-initializers]
overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s2_end' [-Wmissing-field-initializers]
overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::use_m_ops' [-Wmissing-field-initializers]
overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::gap_s1_start' [-Wmissing-field-initializers]
38 | OverlapperParams ungapped_params = { 2, -10000, -3, -2, ALT_OVERLAP };
| ^
overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::gap_s1_end' [-Wmissing-field-initializers]
overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::gap_s2_start' [-Wmissing-field-initializers]
overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::gap_s2_end' [-Wmissing-field-initializers]
overlapper.cpp:38:69: warning: missing initializer for member 'OverlapperParams::use_m_ops' [-Wmissing-field-initializers]
stdaln.c: In function 'aln_local_core':
stdaln.c:756:17: warning: 'free' called on pointer '*(int **)((char *)(void *) ivtmp.564_1204)' with nonzero offset 4 [-Wfree-nonheap-object]
756 | free(s_array[i]);
| ^~~~~~~~~~~~~~~~
rm -f libthirdparty.a
ar cru libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libthirdparty.a
make[3]: Leaving directory '/build/sga-0.10.15/src/Thirdparty'
Making all in Util
make[3]: Entering directory '/build/sga-0.10.15/src/Util'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Util.o `test -f 'Util.cpp' || echo './'`Util.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Alphabet.o `test -f 'Alphabet.cpp' || echo './'`Alphabet.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Contig.o `test -f 'Contig.cpp' || echo './'`Contig.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ReadTable.o `test -f 'ReadTable.cpp' || echo './'`ReadTable.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ReadInfoTable.o `test -f 'ReadInfoTable.cpp' || echo './'`ReadInfoTable.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SeqReader.o `test -f 'SeqReader.cpp' || echo './'`SeqReader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-DNAString.o `test -f 'DNAString.cpp' || echo './'`DNAString.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Match.o `test -f 'Match.cpp' || echo './'`Match.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Pileup.o `test -f 'Pileup.cpp' || echo './'`Pileup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BitChar.o `test -f 'BitChar.cpp' || echo './'`BitChar.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Interval.o `test -f 'Interval.cpp' || echo './'`Interval.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SeqCoord.o `test -f 'SeqCoord.cpp' || echo './'`SeqCoord.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-MultiOverlap.o `test -f 'MultiOverlap.cpp' || echo './'`MultiOverlap.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-QualityVector.o `test -f 'QualityVector.cpp' || echo './'`QualityVector.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SGAStats.o `test -f 'SGAStats.cpp' || echo './'`SGAStats.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Quality.o `test -f 'Quality.cpp' || echo './'`Quality.cpp
In file included from Pileup.h:12,
from Pileup.cpp:10:
Pileup.cpp: In member function 'DNADouble Pileup::calculateSimpleAlphaProb() const':
Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \
| ^~
Pileup.cpp:46:5: note: in expansion of macro 'WARN_ONCE'
46 | WARN_ONCE("Fix Pileup::calculateSimpleDNADouble numerical stability");
| ^~~~~~~~~
Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
33 | printf("WARNING: [%s]\n", (x)); _warn_once = false;
| ^~~~~~~~~~
Pileup.cpp:46:5: note: in expansion of macro 'WARN_ONCE'
46 | WARN_ONCE("Fix Pileup::calculateSimpleDNADouble numerical stability");
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-PrimerScreen.o `test -f 'PrimerScreen.cpp' || echo './'`PrimerScreen.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BitVector.o `test -f 'BitVector.cpp' || echo './'`BitVector.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-CorrectionThresholds.o `test -f 'CorrectionThresholds.cpp' || echo './'`CorrectionThresholds.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-KmerDistribution.o `test -f 'KmerDistribution.cpp' || echo './'`KmerDistribution.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ClusterReader.o `test -f 'ClusterReader.cpp' || echo './'`ClusterReader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-MultiAlignment.o `test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-StdAlnTools.o `test -f 'StdAlnTools.cpp' || echo './'`StdAlnTools.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-VCFUtil.o `test -f 'VCFUtil.cpp' || echo './'`VCFUtil.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-QualityTable.o `test -f 'QualityTable.cpp' || echo './'`QualityTable.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BloomFilter.o `test -f 'BloomFilter.cpp' || echo './'`BloomFilter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp
rm -f libutil.a
ar cru libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-SGAStats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o libutil_a-VariantIndex.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libutil.a
make[3]: Leaving directory '/build/sga-0.10.15/src/Util'
Making all in SQG
make[3]: Entering directory '/build/sga-0.10.15/src/SQG'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsqg_a-SQG.o `test -f 'SQG.cpp' || echo './'`SQG.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsqg_a-ASQG.o `test -f 'ASQG.cpp' || echo './'`ASQG.cpp
rm -f libsqg.a
ar cru libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libsqg.a
make[3]: Leaving directory '/build/sga-0.10.15/src/SQG'
Making all in Bigraph
make[3]: Entering directory '/build/sga-0.10.15/src/Bigraph'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Bigraph.o `test -f 'Bigraph.cpp' || echo './'`Bigraph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Vertex.o `test -f 'Vertex.cpp' || echo './'`Vertex.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Edge.o `test -f 'Edge.cpp' || echo './'`Edge.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-EdgeDesc.o `test -f 'EdgeDesc.cpp' || echo './'`EdgeDesc.cpp
In file included from ../Util/EncodedString.h:22,
from Vertex.h:23,
from Vertex.cpp:9:
../Util/EncodedString.h: In instantiation of 'void EncodedString<Codec>::_copy(const EncodedString<Codec>&) [with Codec = DNACodec]':
../Util/EncodedString.h:43:18: required from 'EncodedString<Codec>::EncodedString(const EncodedString<Codec>&) [with Codec = DNACodec]'
/usr/include/c++/12/bits/move.h:204:11: required from 'std::_Require<std::__not_<std::__is_tuple_like<_Tp> >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = EncodedString<DNACodec>; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]'
Vertex.cpp:46:18: required from here
../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
236 | assert(m_capacity = other.m_capacity);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
rm -f libbigraph.a
ar cru libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libbigraph.a
make[3]: Leaving directory '/build/sga-0.10.15/src/Bigraph'
Making all in Algorithm
make[3]: Entering directory '/build/sga-0.10.15/src/Algorithm'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapAlgorithm.o `test -f 'OverlapAlgorithm.cpp' || echo './'`OverlapAlgorithm.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-SearchSeed.o `test -f 'SearchSeed.cpp' || echo './'`SearchSeed.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapBlock.o `test -f 'OverlapBlock.cpp' || echo './'`OverlapBlock.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-SearchHistory.o `test -f 'SearchHistory.cpp' || echo './'`SearchHistory.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ErrorCorrectProcess.o `test -f 'ErrorCorrectProcess.cpp' || echo './'`ErrorCorrectProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-QCProcess.o `test -f 'QCProcess.cpp' || echo './'`QCProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapTools.o `test -f 'OverlapTools.cpp' || echo './'`OverlapTools.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-DPAlignment.o `test -f 'DPAlignment.cpp' || echo './'`DPAlignment.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ConnectProcess.o `test -f 'ConnectProcess.cpp' || echo './'`ConnectProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StringGraphGenerator.o `test -f 'StringGraphGenerator.cpp' || echo './'`StringGraphGenerator.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-FMMergeProcess.o `test -f 'FMMergeProcess.cpp' || echo './'`FMMergeProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StatsProcess.o `test -f 'StatsProcess.cpp' || echo './'`StatsProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ClusterProcess.o `test -f 'ClusterProcess.cpp' || echo './'`ClusterProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ReadCluster.o `test -f 'ReadCluster.cpp' || echo './'`ReadCluster.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-LRAlignment.o `test -f 'LRAlignment.cpp' || echo './'`LRAlignment.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StringThreader.o `test -f 'StringThreader.cpp' || echo './'`StringThreader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ExtensionDP.o `test -f 'ExtensionDP.cpp' || echo './'`ExtensionDP.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-HaplotypeBuilder.o `test -f 'HaplotypeBuilder.cpp' || echo './'`HaplotypeBuilder.cpp
In file included from SearchHistory.h:12,
from OverlapBlock.h:15,
from OverlapBlock.cpp:11:
OverlapBlock.cpp: In member function 'std::string OverlapBlock::getFullString(const std::string&) const':
../Util/Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \
| ^~
OverlapBlock.cpp:88:9: note: in expansion of macro 'WARN_ONCE'
88 | WARN_ONCE("getFullString() called on block with no history")
| ^~~~~~~~~
../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
33 | printf("WARNING: [%s]\n", (x)); _warn_once = false;
| ^~~~~~~~~~
OverlapBlock.cpp:88:9: note: in expansion of macro 'WARN_ONCE'
88 | WARN_ONCE("getFullString() called on block with no history")
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-GapFillProcess.o `test -f 'GapFillProcess.cpp' || echo './'`GapFillProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-VariationBuilderCommon.o `test -f 'VariationBuilderCommon.cpp' || echo './'`VariationBuilderCommon.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-KmerOverlaps.o `test -f 'KmerOverlaps.cpp' || echo './'`KmerOverlaps.cpp
In file included from ReadCluster.cpp:10:
In constructor 'ClusterNode::ClusterNode(ClusterNode&&)',
inlined from 'ClusterNode ReadCluster::addSeed(const std::string&, bool)' at ReadCluster.cpp:60:20:
ReadCluster.h:17:8: warning: 'emptyNode.ClusterNode::fwdCanonicalID' may be used uninitialized [-Wmaybe-uninitialized]
17 | struct ClusterNode
| ^~~~~~~~~~~
ReadCluster.cpp: In member function 'ClusterNode ReadCluster::addSeed(const std::string&, bool)':
ReadCluster.cpp:55:25: note: 'emptyNode.ClusterNode::fwdCanonicalID' was declared here
55 | ClusterNode emptyNode;
| ^~~~~~~~~
In constructor 'ClusterNode::ClusterNode(ClusterNode&&)',
inlined from 'ClusterNode ReadCluster::addSeed(const std::string&, bool)' at ReadCluster.cpp:60:20:
ReadCluster.h:17:8: warning: '*(unsigned char*)((char*)&emptyNode + offsetof(ClusterNode, ClusterNode::isReverseInterval))' may be used uninitialized [-Wmaybe-uninitialized]
17 | struct ClusterNode
| ^~~~~~~~~~~
ReadCluster.cpp: In member function 'ClusterNode ReadCluster::addSeed(const std::string&, bool)':
ReadCluster.cpp:55:25: note: '*(unsigned char*)((char*)&emptyNode + offsetof(ClusterNode, ClusterNode::isReverseInterval))' was declared here
55 | ClusterNode emptyNode;
| ^~~~~~~~~
rm -f libalgorithm.a
ar cru libalgorithm.a libalgorithm_a-OverlapAlgorithm.o libalgorithm_a-SearchSeed.o libalgorithm_a-OverlapBlock.o libalgorithm_a-SearchHistory.o libalgorithm_a-ErrorCorrectProcess.o libalgorithm_a-QCProcess.o libalgorithm_a-OverlapTools.o libalgorithm_a-DPAlignment.o libalgorithm_a-ConnectProcess.o libalgorithm_a-StringGraphGenerator.o libalgorithm_a-FMMergeProcess.o libalgorithm_a-StatsProcess.o libalgorithm_a-ClusterProcess.o libalgorithm_a-ReadCluster.o libalgorithm_a-LRAlignment.o libalgorithm_a-StringThreader.o libalgorithm_a-ExtensionDP.o libalgorithm_a-HaplotypeBuilder.o libalgorithm_a-GapFillProcess.o libalgorithm_a-VariationBuilderCommon.o libalgorithm_a-KmerOverlaps.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libalgorithm.a
make[3]: Leaving directory '/build/sga-0.10.15/src/Algorithm'
Making all in StringGraph
make[3]: Entering directory '/build/sga-0.10.15/src/StringGraph'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGUtil.o `test -f 'SGUtil.cpp' || echo './'`SGUtil.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGAlgorithms.o `test -f 'SGAlgorithms.cpp' || echo './'`SGAlgorithms.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGVisitors.o `test -f 'SGVisitors.cpp' || echo './'`SGVisitors.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-CompleteOverlapSet.o `test -f 'CompleteOverlapSet.cpp' || echo './'`CompleteOverlapSet.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-RemovalAlgorithm.o `test -f 'RemovalAlgorithm.cpp' || echo './'`RemovalAlgorithm.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGSearch.o `test -f 'SGSearch.cpp' || echo './'`SGSearch.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGWalk.o `test -f 'SGWalk.cpp' || echo './'`SGWalk.cpp
In file included from ../Bigraph/GraphCommon.h:14,
from ../Bigraph/Bigraph.h:16,
from SGAlgorithms.h:13,
from SGAlgorithms.cpp:9:
SGAlgorithms.cpp: In function 'Edge* SGAlgorithms::createEdgesFromOverlap(StringGraph*, const Overlap&, bool, size_t)':
../Util/Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \
| ^~
SGAlgorithms.cpp:60:9: note: in expansion of macro 'WARN_ONCE'
60 | WARN_ONCE("Edge limit reached for vertex when loading graph");
| ^~~~~~~~~
../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
33 | printf("WARNING: [%s]\n", (x)); _warn_once = false;
| ^~~~~~~~~~
SGAlgorithms.cpp:60:9: note: in expansion of macro 'WARN_ONCE'
60 | WARN_ONCE("Edge limit reached for vertex when loading graph");
| ^~~~~~~~~
rm -f libstringgraph.a
ar cru libstringgraph.a libstringgraph_a-SGUtil.o libstringgraph_a-SGAlgorithms.o libstringgraph_a-SGVisitors.o libstringgraph_a-CompleteOverlapSet.o libstringgraph_a-RemovalAlgorithm.o libstringgraph_a-SGSearch.o libstringgraph_a-SGWalk.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libstringgraph.a
make[3]: Leaving directory '/build/sga-0.10.15/src/StringGraph'
Making all in Concurrency
make[3]: Entering directory '/build/sga-0.10.15/src/Concurrency'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libconcurrency_a-OverlapProcess.o `test -f 'OverlapProcess.cpp' || echo './'`OverlapProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libconcurrency_a-RmdupProcess.o `test -f 'RmdupProcess.cpp' || echo './'`RmdupProcess.cpp
rm -f libconcurrency.a
ar cru libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libconcurrency.a
make[3]: Leaving directory '/build/sga-0.10.15/src/Concurrency'
Making all in SuffixTools
make[3]: Entering directory '/build/sga-0.10.15/src/SuffixTools'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-STCommon.o `test -f 'STCommon.cpp' || echo './'`STCommon.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-Occurrence.o `test -f 'Occurrence.cpp' || echo './'`Occurrence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SuffixArray.o `test -f 'SuffixArray.cpp' || echo './'`SuffixArray.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SuffixCompare.o `test -f 'SuffixCompare.cpp' || echo './'`SuffixCompare.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-InverseSuffixArray.o `test -f 'InverseSuffixArray.cpp' || echo './'`InverseSuffixArray.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SACAInducedCopying.o `test -f 'SACAInducedCopying.cpp' || echo './'`SACAInducedCopying.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTAlgorithms.o `test -f 'BWTAlgorithms.cpp' || echo './'`BWTAlgorithms.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTDiskConstruction.o `test -f 'BWTDiskConstruction.cpp' || echo './'`BWTDiskConstruction.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReader.o `test -f 'BWTReader.cpp' || echo './'`BWTReader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriter.o `test -f 'BWTWriter.cpp' || echo './'`BWTWriter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SAReader.o `test -f 'SAReader.cpp' || echo './'`SAReader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SAWriter.o `test -f 'SAWriter.cpp' || echo './'`SAWriter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-GapArray.o `test -f 'GapArray.cpp' || echo './'`GapArray.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-RankProcess.o `test -f 'RankProcess.cpp' || echo './'`RankProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SBWT.o `test -f 'SBWT.cpp' || echo './'`SBWT.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-RLBWT.o `test -f 'RLBWT.cpp' || echo './'`RLBWT.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriterBinary.o `test -f 'BWTWriterBinary.cpp' || echo './'`BWTWriterBinary.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReaderBinary.o `test -f 'BWTReaderBinary.cpp' || echo './'`BWTReaderBinary.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriterAscii.o `test -f 'BWTWriterAscii.cpp' || echo './'`BWTWriterAscii.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReaderAscii.o `test -f 'BWTReaderAscii.cpp' || echo './'`BWTReaderAscii.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTIntervalCache.o `test -f 'BWTIntervalCache.cpp' || echo './'`BWTIntervalCache.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-QuickBWT.o `test -f 'QuickBWT.cpp' || echo './'`QuickBWT.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SampledSuffixArray.o `test -f 'SampledSuffixArray.cpp' || echo './'`SampledSuffixArray.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTCABauerCoxRosone.o `test -f 'BWTCABauerCoxRosone.cpp' || echo './'`BWTCABauerCoxRosone.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTCARopebwt.o `test -f 'BWTCARopebwt.cpp' || echo './'`BWTCARopebwt.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-PopulationIndex.o `test -f 'PopulationIndex.cpp' || echo './'`PopulationIndex.cpp
In file included from ../Util/EncodedString.h:22,
from Occurrence.h:13,
from RLBWT.h:13,
from BWT.h:18,
from BWTDiskConstruction.h:19,
from BWTDiskConstruction.cpp:12:
../Util/EncodedString.h: In instantiation of 'void EncodedString<Codec>::_copy(const EncodedString<Codec>&) [with Codec = DNACodec]':
../Util/EncodedString.h:43:18: required from 'EncodedString<Codec>::EncodedString(const EncodedString<Codec>&) [with Codec = DNACodec]'
/usr/include/c++/12/bits/new_allocator.h:175:4: required from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString<DNACodec>; _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>]'
/usr/include/c++/12/bits/alloc_traits.h:516:17: required from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString<DNACodec>; _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>; allocator_type = std::allocator<EncodedString<DNACodec> >]'
/usr/include/c++/12/bits/vector.tcc:117:30: required from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>; _Alloc = std::allocator<EncodedString<DNACodec> >; reference = EncodedString<DNACodec>&]'
/usr/include/c++/12/bits/stl_vector.h:1294:21: required from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = EncodedString<DNACodec>; _Alloc = std::allocator<EncodedString<DNACodec> >; value_type = EncodedString<DNACodec>]'
BWTDiskConstruction.cpp:252:36: required from here
../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
236 | assert(m_capacity = other.m_capacity);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
rm -f libsuffixtools.a
ar cru libsuffixtools.a libsuffixtools_a-STCommon.o libsuffixtools_a-Occurrence.o libsuffixtools_a-SuffixArray.o libsuffixtools_a-SuffixCompare.o libsuffixtools_a-InverseSuffixArray.o libsuffixtools_a-SACAInducedCopying.o libsuffixtools_a-BWTAlgorithms.o libsuffixtools_a-BWTDiskConstruction.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-SAReader.o libsuffixtools_a-SAWriter.o libsuffixtools_a-GapArray.o libsuffixtools_a-RankProcess.o libsuffixtools_a-SBWT.o libsuffixtools_a-RLBWT.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-BWTWriterBinary.o libsuffixtools_a-BWTReaderBinary.o libsuffixtools_a-BWTWriterAscii.o libsuffixtools_a-BWTReaderAscii.o libsuffixtools_a-BWTIntervalCache.o libsuffixtools_a-QuickBWT.o libsuffixtools_a-SampledSuffixArray.o libsuffixtools_a-BWTCABauerCoxRosone.o libsuffixtools_a-BWTCARopebwt.o libsuffixtools_a-PopulationIndex.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libsuffixtools.a
make[3]: Leaving directory '/build/sga-0.10.15/src/SuffixTools'
Making all in Scaffold
make[3]: Entering directory '/build/sga-0.10.15/src/Scaffold'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldVertex.o `test -f 'ScaffoldVertex.cpp' || echo './'`ScaffoldVertex.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldEdge.o `test -f 'ScaffoldEdge.cpp' || echo './'`ScaffoldEdge.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldGraph.o `test -f 'ScaffoldGraph.cpp' || echo './'`ScaffoldGraph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldVisitors.o `test -f 'ScaffoldVisitors.cpp' || echo './'`ScaffoldVisitors.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldLink.o `test -f 'ScaffoldLink.cpp' || echo './'`ScaffoldLink.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldRecord.o `test -f 'ScaffoldRecord.cpp' || echo './'`ScaffoldRecord.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldGroup.o `test -f 'ScaffoldGroup.cpp' || echo './'`ScaffoldGroup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldSearch.o `test -f 'ScaffoldSearch.cpp' || echo './'`ScaffoldSearch.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldWalk.o `test -f 'ScaffoldWalk.cpp' || echo './'`ScaffoldWalk.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldAlgorithms.o `test -f 'ScaffoldAlgorithms.cpp' || echo './'`ScaffoldAlgorithms.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldSequenceCollection.o `test -f 'ScaffoldSequenceCollection.cpp' || echo './'`ScaffoldSequenceCollection.cpp
In file included from ../Bigraph/GraphCommon.h:14,
from ../Bigraph/Bigraph.h:16,
from ScaffoldVertex.h:12,
from ScaffoldGroup.h:13,
from ScaffoldGroup.cpp:10:
ScaffoldGroup.cpp: In member function 'void ScaffoldGroup::getSecondaryLinks()':
../Util/Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \
| ^~
ScaffoldGroup.cpp:279:13: note: in expansion of macro 'WARN_ONCE'
279 | WARN_ONCE("Recalculate xzDir");
| ^~~~~~~~~
../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
33 | printf("WARNING: [%s]\n", (x)); _warn_once = false;
| ^~~~~~~~~~
ScaffoldGroup.cpp:279:13: note: in expansion of macro 'WARN_ONCE'
279 | WARN_ONCE("Recalculate xzDir");
| ^~~~~~~~~
rm -f libscaffold.a
ar cru libscaffold.a libscaffold_a-ScaffoldVertex.o libscaffold_a-ScaffoldEdge.o libscaffold_a-ScaffoldGraph.o libscaffold_a-ScaffoldVisitors.o libscaffold_a-ScaffoldLink.o libscaffold_a-ScaffoldRecord.o libscaffold_a-ScaffoldGroup.o libscaffold_a-ScaffoldSearch.o libscaffold_a-ScaffoldWalk.o libscaffold_a-ScaffoldAlgorithms.o libscaffold_a-ScaffoldSequenceCollection.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libscaffold.a
make[3]: Leaving directory '/build/sga-0.10.15/src/Scaffold'
Making all in GraphDiff
make[3]: Entering directory '/build/sga-0.10.15/src/GraphDiff'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelUtil.o `test -f 'DindelUtil.cpp' || echo './'`DindelUtil.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelRealignWindow.o `test -f 'DindelRealignWindow.cpp' || echo './'`DindelRealignWindow.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelHMM.o `test -f 'DindelHMM.cpp' || echo './'`DindelHMM.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-OverlapHaplotypeBuilder.o `test -f 'OverlapHaplotypeBuilder.cpp' || echo './'`OverlapHaplotypeBuilder.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-StringHaplotypeBuilder.o `test -f 'StringHaplotypeBuilder.cpp' || echo './'`StringHaplotypeBuilder.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.o `test -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'`DeBruijnHaplotypeBuilder.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o `test -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'`PairedDeBruijnHaplotypeBuilder.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-HapgenUtil.o `test -f 'HapgenUtil.cpp' || echo './'`HapgenUtil.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-VCFTester.o `test -f 'VCFTester.cpp' || echo './'`VCFTester.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-GraphCompare.o `test -f 'GraphCompare.cpp' || echo './'`GraphCompare.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-OverlapExtractorWithCorrection.o `test -f 'OverlapExtractorWithCorrection.cpp' || echo './'`OverlapExtractorWithCorrection.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DBGPathGuide.o `test -f 'DBGPathGuide.cpp' || echo './'`DBGPathGuide.cpp
DeBruijnHaplotypeBuilder.cpp: In member function 'Vertex* DeBruijnHaplotypeBuilder::extendUnambiguously(Vertex*, StringGraph*, EdgeDir, size_t, size_t)':
DeBruijnHaplotypeBuilder.cpp:227:16: warning: variable 'ext_count' set but not used [-Wunused-but-set-variable]
227 | size_t ext_count = 0;
| ^~~~~~~~~
DindelUtil.cpp: In function 'DindelReturnCode DindelUtil::runDindelPairMatePair(const std::string&, const StringVector&, const StringVector&, const GraphCompareParameters&, std::ostream&, std::ostream&, std::ostream&, DindelReadReferenceAlignmentVector*)':
DindelUtil.cpp:65:10: warning: variable 'has_complex_variant' set but not used [-Wunused-but-set-variable]
65 | bool has_complex_variant = false;
| ^~~~~~~~~~~~~~~~~~~
DindelRealignWindow.cpp: In member function 'void DindelHaplotype::write(std::ostream&) const':
DindelRealignWindow.cpp:762:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
762 | for (size_t x=0; x<m_seq.size(); x++)
| ^~~
DindelRealignWindow.cpp:763:26: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
763 | out << m_seq[x]; out << std::endl;
| ^~~
DindelRealignWindow.cpp:764:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
764 | for (size_t x=0; x<m_refPos.size(); x++)
| ^~~
DindelRealignWindow.cpp:765:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
765 | out << " " << m_refPos[x]-m_refPos[0]; out << std::endl;
| ^~~
DindelRealignWindow.cpp: In member function 'void DindelSequenceHash::print() const':
DindelRealignWindow.cpp:1037:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
1037 | for (std::list<int>::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl;
| ^~~
DindelRealignWindow.cpp:1037:115: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
1037 | for (std::list<int>::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl;
| ^~~
DindelRealignWindow.cpp: In member function 'void DindelRealignWindow::computeHaplotypePairLikelihoods(std::vector<double>&, std::unordered_map<std::__cxx11::basic_string<char>, std::__cxx11::list<int> >&, const std::vector<std::vector<double> >&)':
DindelRealignWindow.cpp:2589:12: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
2589 | for (int h1=0;h1<numAH;h1++)
| ^~~
DindelRealignWindow.cpp:2600:16: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
2600 | if (DEBUG_CALLINDEL) {
| ^~
DindelRealignWindow.cpp: In member function 'void DindelRealignWindow::addCalledHaplotypeMatePairs(int, DindelRealignWindowResult&, const std::vector<DindelMultiHaplotype>&, const std::vector<std::unordered_map<int, double> >&, double, int)':
DindelRealignWindow.cpp:2743:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
2743 | for (size_t x=0;x<vars.size();x++) std::cout << " " << vars[x].getID(); std::cout << std::endl;
| ^~~
DindelRealignWindow.cpp:2743:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
2743 | for (size_t x=0;x<vars.size();x++) std::cout << " " << vars[x].getID(); std::cout << std::endl;
| ^~~
DindelRealignWindow.cpp: In member function 'void DindelRealignWindow::addCalledHaplotypeSingleRead(int, DindelRealignWindowResult&, const std::vector<DindelMultiHaplotype>&, const std::vector<std::unordered_map<int, double> >&, double, int)':
DindelRealignWindow.cpp:2906:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
2906 | for (size_t x=0;x<vars.size();x++) std::cout << " " << vars[x].getID(); std::cout << std::endl;
| ^~~
DindelRealignWindow.cpp:2906:85: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
2906 | for (size_t x=0;x<vars.size();x++) std::cout << " " << vars[x].getID(); std::cout << std::endl;
| ^~~
rm -f libgraphdiff.a
ar cru libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o libgraphdiff_a-DBGPathGuide.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgraphdiff.a
make[3]: Leaving directory '/build/sga-0.10.15/src/GraphDiff'
Making all in SGA
make[3]: Entering directory '/build/sga-0.10.15/src/SGA'
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-sga.o `test -f 'sga.cpp' || echo './'`sga.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-index.o `test -f 'index.cpp' || echo './'`index.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-overlap.o `test -f 'overlap.cpp' || echo './'`overlap.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-assemble.o `test -f 'assemble.cpp' || echo './'`assemble.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-correct.o `test -f 'correct.cpp' || echo './'`correct.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-oview.o `test -f 'oview.cpp' || echo './'`oview.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-preprocess.o `test -f 'preprocess.cpp' || echo './'`preprocess.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-rmdup.o `test -f 'rmdup.cpp' || echo './'`rmdup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-merge.o `test -f 'merge.cpp' || echo './'`merge.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-subgraph.o `test -f 'subgraph.cpp' || echo './'`subgraph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-scaffold.o `test -f 'scaffold.cpp' || echo './'`scaffold.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-scaffold2fasta.o `test -f 'scaffold2fasta.cpp' || echo './'`scaffold2fasta.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-connect.o `test -f 'connect.cpp' || echo './'`connect.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-walk.o `test -f 'walk.cpp' || echo './'`walk.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-filter.o `test -f 'filter.cpp' || echo './'`filter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-kmer-count.o `test -f 'kmer-count.cpp' || echo './'`kmer-count.cpp
In file included from ../Util/EncodedString.h:22,
from ../SuffixTools/Occurrence.h:13,
from ../SuffixTools/RLBWT.h:13,
from ../SuffixTools/BWT.h:18,
from ../SuffixTools/BWTDiskConstruction.h:19,
from index.cpp:18:
../Util/EncodedString.h: In instantiation of 'void EncodedString<Codec>::_copy(const EncodedString<Codec>&) [with Codec = DNACodec]':
../Util/EncodedString.h:43:18: required from 'EncodedString<Codec>::EncodedString(const EncodedString<Codec>&) [with Codec = DNACodec]'
/usr/include/c++/12/bits/new_allocator.h:175:4: required from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString<DNACodec>; _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>]'
/usr/include/c++/12/bits/alloc_traits.h:516:17: required from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString<DNACodec>; _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>; allocator_type = std::allocator<EncodedString<DNACodec> >]'
/usr/include/c++/12/bits/vector.tcc:117:30: required from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString<DNACodec>}; _Tp = EncodedString<DNACodec>; _Alloc = std::allocator<EncodedString<DNACodec> >; reference = EncodedString<DNACodec>&]'
/usr/include/c++/12/bits/stl_vector.h:1294:21: required from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = EncodedString<DNACodec>; _Alloc = std::allocator<EncodedString<DNACodec> >; value_type = EncodedString<DNACodec>]'
index.cpp:130:27: required from here
../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
236 | assert(m_capacity = other.m_capacity);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-stats.o `test -f 'stats.cpp' || echo './'`stats.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-fm-merge.o `test -f 'fm-merge.cpp' || echo './'`fm-merge.cpp
In file included from connect.cpp:15:
connect.cpp: In function 'int connectMain(int, char**)':
../Util/Util.h:32:53: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \
| ^~
connect.cpp:297:17: note: in expansion of macro 'WARN_ONCE'
297 | WARN_ONCE("check orientation of result");
| ^~~~~~~~~
../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
33 | printf("WARNING: [%s]\n", (x)); _warn_once = false;
| ^~~~~~~~~~
connect.cpp:297:17: note: in expansion of macro 'WARN_ONCE'
297 | WARN_ONCE("check orientation of result");
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gmap.o `test -f 'gmap.cpp' || echo './'`gmap.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-filterBAM.o `test -f 'filterBAM.cpp' || echo './'`filterBAM.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-cluster.o `test -f 'cluster.cpp' || echo './'`cluster.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gen-ssa.o `test -f 'gen-ssa.cpp' || echo './'`gen-ssa.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-bwt2fa.o `test -f 'bwt2fa.cpp' || echo './'`bwt2fa.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-graph-diff.o `test -f 'graph-diff.cpp' || echo './'`graph-diff.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-graph-concordance.o `test -f 'graph-concordance.cpp' || echo './'`graph-concordance.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-preqc.o `test -f 'preqc.cpp' || echo './'`preqc.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-overlap-long.o `test -f 'overlap-long.cpp' || echo './'`overlap-long.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-variant-detectability.o `test -f 'variant-detectability.cpp' || echo './'`variant-detectability.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-rewrite-evidence-bam.o `test -f 'rewrite-evidence-bam.cpp' || echo './'`rewrite-evidence-bam.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-somatic-variant-filters.o `test -f 'somatic-variant-filters.cpp' || echo './'`somatic-variant-filters.cpp
graph-concordance.cpp: In function 'std::string reconstructHaplotype(const VCFRecord&, VariantRecordVector, const ReadTable&, const BWTIndexSet&, size_t)':
graph-concordance.cpp:214:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
214 | if(end > chr.seq.length())
| ~~~~^~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-haplotype-filter.o `test -f 'haplotype-filter.cpp' || echo './'`haplotype-filter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-OverlapCommon.o `test -f 'OverlapCommon.cpp' || echo './'`OverlapCommon.cpp
In file included from rewrite-evidence-bam.cpp:18:
/usr//include/bamtools/api/algorithms/Sort.h:64:18: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
64 | typedef std::binary_function<BamAlignment, BamAlignment, bool> AlignmentSortBase;
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from rewrite-evidence-bam.cpp:10:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from ../Thirdparty/rapidjson/reader.h:7,
from ../Thirdparty/rapidjson/document.h:4,
from preqc.cpp:27:
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF8<CharType>::TakeBOM(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef170' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:170:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
170 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static rapidjson::UTF8<CharType>::Ch rapidjson::UTF8<CharType>::Take(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef183' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:183:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
183 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF8<CharType>::PutBOM(OutputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef189' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:189:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
189 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF8<CharType>::Put(OutputByteStream&, Ch)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef195' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:195:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
195 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16<CharType>::Encode(OutputStream&, unsigned int)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef219' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:219:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
219 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static bool rapidjson::UTF16<CharType>::Decode(InputStream&, unsigned int*)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef234' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:234:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
234 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static bool rapidjson::UTF16<CharType>::Validate(InputStream&, OutputStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef252' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:252:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
252 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef253' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:253:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
253 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF16LE<CharType>::TakeBOM(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef271' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:271:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
271 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF16LE<CharType>::Take(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef278' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:278:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
278 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16LE<CharType>::PutBOM(OutputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef286' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:286:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
286 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16LE<CharType>::Put(OutputByteStream&, CharType)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef292' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:292:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
292 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF16BE<CharType>::TakeBOM(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef303' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:303:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
303 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF16BE<CharType>::Take(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef310' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:310:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
310 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16BE<CharType>::PutBOM(OutputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef318' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:318:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
318 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF16BE<CharType>::Put(OutputByteStream&, CharType)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef324' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:324:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
324 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32<CharType>::Encode(OutputStream&, unsigned int)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef348' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:348:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
348 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 4);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static bool rapidjson::UTF32<CharType>::Decode(InputStream&, unsigned int*)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef355' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:355:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
355 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static bool rapidjson::UTF32<CharType>::Validate(InputStream&, OutputStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef363' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:363:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
363 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF32LE<CharType>::TakeBOM(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef375' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:375:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
375 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF32LE<CharType>::Take(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef382' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:382:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
382 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32LE<CharType>::PutBOM(OutputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef392' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:392:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
392 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32LE<CharType>::Put(OutputByteStream&, CharType)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef398' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:398:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
398 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF32BE<CharType>::TakeBOM(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef411' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:411:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
411 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static CharType rapidjson::UTF32BE<CharType>::Take(InputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef418' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:418:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
418 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32BE<CharType>::PutBOM(OutputByteStream&)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef428' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:428:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
428 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h: In static member function 'static void rapidjson::UTF32BE<CharType>::Put(OutputByteStream&, CharType)':
../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef 'StaticAssertTypedef434' locally defined but not used [-Wunused-local-typedefs]
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2'
111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y
| ^
../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN'
109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y)
| ^~~~~~~~~~~~~~~~~
../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro 'RAPIDJSON_JOIN'
115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__)
| ^~~~~~~~~~~~~~
../Thirdparty/rapidjson/encodings.h:434:17: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT'
434 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1);
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -L/usr//lib -L/usr//lib/bamtools -Wl,-z,relro -Wl,-z,now -o sga sga-sga.o sga-index.o sga-overlap.o sga-assemble.o sga-correct.o sga-oview.o sga-preprocess.o sga-rmdup.o sga-merge.o sga-subgraph.o sga-scaffold.o sga-scaffold2fasta.o sga-connect.o sga-walk.o sga-filter.o sga-kmer-count.o sga-stats.o sga-fm-merge.o sga-gmap.o sga-filterBAM.o sga-cluster.o sga-gen-ssa.o sga-bwt2fa.o sga-graph-diff.o sga-graph-concordance.o sga-gapfill.o sga-preqc.o sga-overlap-long.o sga-variant-detectability.o sga-rewrite-evidence-bam.o sga-somatic-variant-filters.o sga-haplotype-filter.o sga-OverlapCommon.o ../Scaffold/libscaffold.a ../GraphDiff/libgraphdiff.a ../StringGraph/libstringgraph.a ../Concurrency/libconcurrency.a ../Algorithm/libalgorithm.a ../SuffixTools/libsuffixtools.a ../Bigraph/libbigraph.a ../Util/libutil.a ../SQG/libsqg.a ../Thirdparty/libthirdparty.a -lz -lbamtools
make[3]: Leaving directory '/build/sga-0.10.15/src/SGA'
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make[2]: Leaving directory '/build/sga-0.10.15/src'
make[1]: Leaving directory '/build/sga-0.10.15/src'
dh_auto_test -O--sourcedirectory=src
cd src && make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1
make[1]: Entering directory '/build/sga-0.10.15/src'
Making check in bin
make[2]: Entering directory '/build/sga-0.10.15/src/bin'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/bin'
Making check in Thirdparty
make[2]: Entering directory '/build/sga-0.10.15/src/Thirdparty'
make[2]: Nothing to be done for 'check'.
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Making check in Util
make[2]: Entering directory '/build/sga-0.10.15/src/Util'
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Making check in SQG
make[2]: Entering directory '/build/sga-0.10.15/src/SQG'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/SQG'
Making check in Bigraph
make[2]: Entering directory '/build/sga-0.10.15/src/Bigraph'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/Bigraph'
Making check in Algorithm
make[2]: Entering directory '/build/sga-0.10.15/src/Algorithm'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/Algorithm'
Making check in StringGraph
make[2]: Entering directory '/build/sga-0.10.15/src/StringGraph'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/StringGraph'
Making check in Concurrency
make[2]: Entering directory '/build/sga-0.10.15/src/Concurrency'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/Concurrency'
Making check in SuffixTools
make[2]: Entering directory '/build/sga-0.10.15/src/SuffixTools'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/SuffixTools'
Making check in Scaffold
make[2]: Entering directory '/build/sga-0.10.15/src/Scaffold'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/Scaffold'
Making check in GraphDiff
make[2]: Entering directory '/build/sga-0.10.15/src/GraphDiff'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/GraphDiff'
Making check in SGA
make[2]: Entering directory '/build/sga-0.10.15/src/SGA'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/sga-0.10.15/src/SGA'
make[2]: Entering directory '/build/sga-0.10.15/src'
make[2]: Leaving directory '/build/sga-0.10.15/src'
make[1]: Leaving directory '/build/sga-0.10.15/src'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedirectory=src
dh_prep -O--sourcedirectory=src
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/sga-0.10.15'
dh_auto_install
cd src && make -j16 install DESTDIR=/build/sga-0.10.15/debian/sga AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/sga-0.10.15/src'
Making install in bin
make[3]: Entering directory '/build/sga-0.10.15/src/bin'
make[4]: Entering directory '/build/sga-0.10.15/src/bin'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/build/sga-0.10.15/debian/sga/usr/bin'
/usr/bin/install -c sga-bam2de sga-mergeDriver '/build/sga-0.10.15/debian/sga/usr/bin'
make[4]: Leaving directory '/build/sga-0.10.15/src/bin'
make[3]: Leaving directory '/build/sga-0.10.15/src/bin'
Making install in Thirdparty
make[3]: Entering directory '/build/sga-0.10.15/src/Thirdparty'
make[4]: Entering directory '/build/sga-0.10.15/src/Thirdparty'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/Thirdparty'
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Making install in Util
make[3]: Entering directory '/build/sga-0.10.15/src/Util'
make[4]: Entering directory '/build/sga-0.10.15/src/Util'
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make[4]: Leaving directory '/build/sga-0.10.15/src/Util'
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Making install in SQG
make[3]: Entering directory '/build/sga-0.10.15/src/SQG'
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make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/SQG'
make[3]: Leaving directory '/build/sga-0.10.15/src/SQG'
Making install in Bigraph
make[3]: Entering directory '/build/sga-0.10.15/src/Bigraph'
make[4]: Entering directory '/build/sga-0.10.15/src/Bigraph'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/Bigraph'
make[3]: Leaving directory '/build/sga-0.10.15/src/Bigraph'
Making install in Algorithm
make[3]: Entering directory '/build/sga-0.10.15/src/Algorithm'
make[4]: Entering directory '/build/sga-0.10.15/src/Algorithm'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/Algorithm'
make[3]: Leaving directory '/build/sga-0.10.15/src/Algorithm'
Making install in StringGraph
make[3]: Entering directory '/build/sga-0.10.15/src/StringGraph'
make[4]: Entering directory '/build/sga-0.10.15/src/StringGraph'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/StringGraph'
make[3]: Leaving directory '/build/sga-0.10.15/src/StringGraph'
Making install in Concurrency
make[3]: Entering directory '/build/sga-0.10.15/src/Concurrency'
make[4]: Entering directory '/build/sga-0.10.15/src/Concurrency'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/Concurrency'
make[3]: Leaving directory '/build/sga-0.10.15/src/Concurrency'
Making install in SuffixTools
make[3]: Entering directory '/build/sga-0.10.15/src/SuffixTools'
make[4]: Entering directory '/build/sga-0.10.15/src/SuffixTools'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/SuffixTools'
make[3]: Leaving directory '/build/sga-0.10.15/src/SuffixTools'
Making install in Scaffold
make[3]: Entering directory '/build/sga-0.10.15/src/Scaffold'
make[4]: Entering directory '/build/sga-0.10.15/src/Scaffold'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/Scaffold'
make[3]: Leaving directory '/build/sga-0.10.15/src/Scaffold'
Making install in GraphDiff
make[3]: Entering directory '/build/sga-0.10.15/src/GraphDiff'
make[4]: Entering directory '/build/sga-0.10.15/src/GraphDiff'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src/GraphDiff'
make[3]: Leaving directory '/build/sga-0.10.15/src/GraphDiff'
Making install in SGA
make[3]: Entering directory '/build/sga-0.10.15/src/SGA'
make[4]: Entering directory '/build/sga-0.10.15/src/SGA'
/bin/mkdir -p '/build/sga-0.10.15/debian/sga/usr/bin'
make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c sga '/build/sga-0.10.15/debian/sga/usr/bin'
make[4]: Leaving directory '/build/sga-0.10.15/src/SGA'
make[3]: Leaving directory '/build/sga-0.10.15/src/SGA'
make[3]: Entering directory '/build/sga-0.10.15/src'
make[4]: Entering directory '/build/sga-0.10.15/src'
make[4]: Nothing to be done for 'install-exec-am'.
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make[4]: Leaving directory '/build/sga-0.10.15/src'
make[3]: Leaving directory '/build/sga-0.10.15/src'
make[2]: Leaving directory '/build/sga-0.10.15/src'
cp -a src/bin/sga-bam2de.pl debian/sga/usr/bin/sga-bam2de
cp -a src/bin/sga-astat.py debian/sga/usr/bin/sga-astat
make[1]: Leaving directory '/build/sga-0.10.15'
dh_install -O--sourcedirectory=src
dh_installdocs -O--sourcedirectory=src
dh_installchangelogs -O--sourcedirectory=src
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/sga-0.10.15'
dh_installexamples
mkdir -p debian/sga/usr/share/doc/sga/examples
sed -e 's?^\(SGA_BIN=sga\).*?\1?' \
-e 's?^.*/bin/sga-align?sga-align?' \
-e 's?^.*/bin/sga-bam2de.pl?sga-bam2de?' \
-e 's?^.*/bin/sga-astat.py?sga-astat?' \
src/examples/sga-celegans.sh > debian/sga/usr/share/doc/sga/examples/sga-celegans.sh
make[1]: Leaving directory '/build/sga-0.10.15'
debian/rules override_dh_installman
make[1]: Entering directory '/build/sga-0.10.15'
dh_installman
mkdir -p /build/sga-0.10.15/debian/sga/usr/share/man/man1/
PATH=/usr/lib/abyss:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \
help2man \
--version-string="0.10.15" \
--no-info \
--name "Make a distance estimate file from a bam file of reads aligned to contigs" \
--output /build/sga-0.10.15/debian/sga/usr/share/man/man1//sga-bam2de.1 \
/build/sga-0.10.15/debian/sga/usr/bin/sga-bam2de
help2man \
--no-info \
--version-string="0.10.15" \
--name="String Graph Assembler: de novo genome assembler that uses string graphs" \
--output /build/sga-0.10.15/debian/sga/usr/share/man/man1//sga.1 \
/build/sga-0.10.15/debian/sga/usr/bin/sga
help2man \
--no-info\
--version-string="0.10.15" \
--name="generate sga merge commands from a list of files" \
--output /build/sga-0.10.15/debian/sga/usr/share/man/man1//sga-mergeDriver.1 \
/build/sga-0.10.15/debian/sga/usr/bin/sga-mergeDriver
make[1]: Leaving directory '/build/sga-0.10.15'
dh_python3 -O--sourcedirectory=src
dh_installsystemduser -O--sourcedirectory=src
dh_perl -O--sourcedirectory=src
dh_link -O--sourcedirectory=src
dh_strip_nondeterminism -O--sourcedirectory=src
dh_compress -O--sourcedirectory=src
dh_fixperms -O--sourcedirectory=src
dh_missing -O--sourcedirectory=src
dh_dwz -a -O--sourcedirectory=src
dh_strip -a -O--sourcedirectory=src
dh_makeshlibs -a -O--sourcedirectory=src
dh_shlibdeps -a -O--sourcedirectory=src
dh_installdeb -O--sourcedirectory=src
dh_gencontrol -O--sourcedirectory=src
dh_md5sums -O--sourcedirectory=src
dh_builddeb -O--sourcedirectory=src
dpkg-deb: building package 'sga' in '../sga_0.10.15-7_amd64.deb'.
dpkg-deb: building package 'sga-dbgsym' in '../sga-dbgsym_0.10.15-7_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../sga_0.10.15-7_amd64.buildinfo
dpkg-genchanges --build=binary -O../sga_0.10.15-7_amd64.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/986957 and its subdirectories
I: Current time: Fri Jun 21 18:49:30 -12 2024
I: pbuilder-time-stamp: 1719038971
Sun May 21 00:26:23 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Sun May 21 00:26:23 UTC 2023 I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Sun May 21 00:32:34 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Sun May 21 00:32:34 UTC 2023 I: sga_0.10.15-7_amd64.changes:
Format: 1.8
Date: Fri, 17 Sep 2021 15:56:21 +0200
Source: sga
Binary: sga sga-dbgsym
Architecture: amd64
Version: 0.10.15-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
sga - de novo genome assembler that uses string graphs
Changes:
sga (0.10.15-7) unstable; urgency=medium
.
* Fix watchfile to detect new versions on github (routine-update)
* Standards-Version: 4.6.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Include ${perl:Depends}
Checksums-Sha1:
12f99c478d28f24495cc415708b4404ce11695e0 15661936 sga-dbgsym_0.10.15-7_amd64.deb
bb38f2dac10a7f92cd90df75e56584f7c7962995 8182 sga_0.10.15-7_amd64.buildinfo
f84e53e9a7d3b693527d1b37b585384c8d88155d 830820 sga_0.10.15-7_amd64.deb
Checksums-Sha256:
e3729caf39b209daa77f63750924073c50a24762f29c944221233d38f7fd06d2 15661936 sga-dbgsym_0.10.15-7_amd64.deb
407541a6ff7178d5b7c7f08376d772a3b3b814aad4061a6ed904314cf099ac51 8182 sga_0.10.15-7_amd64.buildinfo
113b177664fb62ea4678b6b84195a3d64f4afd00e28edec49b1412968cf54d37 830820 sga_0.10.15-7_amd64.deb
Files:
ddeb04288eb81de8568a46d45c1d7a03 15661936 debug optional sga-dbgsym_0.10.15-7_amd64.deb
cadd3f556f67eb1f5463afc6d393da61 8182 science optional sga_0.10.15-7_amd64.buildinfo
3d3e794916c60723081e7fb275aa5837 830820 science optional sga_0.10.15-7_amd64.deb
Sun May 21 00:32:35 UTC 2023 I: diffoscope 242 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.EV9fxeni/sga_0.10.15-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.EV9fxeni/sga_0.10.15-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.EV9fxeni/sga_0.10.15-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.EV9fxeni/b1/sga_0.10.15-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.EV9fxeni/b2/sga_0.10.15-7_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.519s)
0.519s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.194s)
0.194s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.001s)
0.001s 1 call specialize
Sun May 21 00:32:37 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Sun May 21 00:32:37 UTC 2023 I: sga from bookworm built successfully and reproducibly on amd64.
Sun May 21 00:32:38 UTC 2023 I: Submitting .buildinfo files to external archives:
Sun May 21 00:32:38 UTC 2023 I: Submitting 12K b1/sga_0.10.15-7_amd64.buildinfo.asc
Sun May 21 00:32:39 UTC 2023 I: Submitting 12K b2/sga_0.10.15-7_amd64.buildinfo.asc
Sun May 21 00:32:40 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun May 21 00:32:40 UTC 2023 I: Done submitting .buildinfo files.
Sun May 21 00:32:40 UTC 2023 I: Removing signed sga_0.10.15-7_amd64.buildinfo.asc files:
removed './b1/sga_0.10.15-7_amd64.buildinfo.asc'
removed './b2/sga_0.10.15-7_amd64.buildinfo.asc'