I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 24 17:05:36 +14 2021 I: pbuilder-time-stamp: 1632452736 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_0.10.15-5.dsc] I: copying [./sga_0.10.15.orig.tar.gz] I: copying [./sga_0.10.15-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.ldtdwn3b/trustedkeys.kbx': General error gpgv: Signature made Mon Dec 23 08:09:42 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./sga_0.10.15-5.dsc 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_0.10.15-5.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: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13079/tmp/hooks/D01_modify_environment starting debug: Running on jtx1c. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/13079/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/13079/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=f12adfa1dd0f461c94f90429a4d045d3 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=13079 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.IiOw6ridzx/pbuilderrc_OlsB --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.IiOw6ridzx/b2 --logfile b2/build.log sga_0.10.15-5.dsc' SUDO_GID=114 SUDO_UID=108 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash -rwxr-xr-x 1 root root 75880 Sep 23 2020 date -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd -rwxr-xr-x 1 root root 59912 Sep 23 2020 df -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 64212 Mar 3 2021 gzip -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln -rwxr-xr-x 1 root root 35068 Feb 8 2020 login -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Sep 24 17:06 sh -> bash lrwxrwxrwx 1 root root 4 Sep 21 23:26 sh.distrib -> dash -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync -rwxr-xr-x 1 root root 340872 Feb 17 2021 tar -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch -rwxr-xr-x 1 root root 22496 Sep 23 2020 true -rwxr-xr-x 1 root root 9636 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/13079/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team 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 (= 12), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, gawk, 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 ... 19398 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 (= 12); 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 gawk; however: Package gawk 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} gawk{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.1{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcurl3-gnutls{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libhts3{a} libice6{a} libicu67{a} libjbig0{a} libjpeg62-turbo{a} liblab-gamut1{a} libldap-2.4-2{a} liblocale-gettext-perl{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{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} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libsparsehash-dev{a} libssh2-1{a} libsub-override-perl{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libx11-6{a} libx11-data{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} 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} python3.9{a} python3.9-minimal{a} readline-common{a} samtools{a} sensible-utils{a} ucf{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-liberation 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, 119 newly installed, 0 to remove and 0 not upgraded. Need to get 40.7 MB of archives. After unpacking 125 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf gawk armhf 1:5.1.0-1 [568 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf liblocale-gettext-perl armhf 1.07-4+b1 [18.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libpython3.9-minimal armhf 3.9.2-1 [790 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf python3.9-minimal armhf 3.9.2-1 [1630 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf media-types all 4.0.0 [30.3 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf libmpdec3 armhf 2.5.1-1 [74.9 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libpython3.9-stdlib armhf 3.9.2-1 [1608 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf python3.9 armhf 3.9.2-1 [466 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf python3 armhf 3.9.2-3 [37.9 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf ucf all 3.0043 [74.0 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf python3-distutils all 3.9.2-1 [143 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf dh-python all 4.20201102+nmu1 [99.4 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf libpng16-16 armhf 1.6.37-3 [277 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [357 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf fonts-dejavu-core all 2.37-2 [1069 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf fontconfig-config all 2.13.1-4.2 [281 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf libfontconfig1 armhf 2.13.1-4.2 [329 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf fontconfig armhf 2.13.1-4.2 [415 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf libcdt5 armhf 2.42.2-5 [59.7 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf libcgraph6 armhf 2.42.2-5 [78.4 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [123 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf libjbig0 armhf 2.1-3.1+b2 [28.4 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf libwebp6 armhf 0.6.1-2.1 [226 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf libtiff5 armhf 4.2.0-1 [271 kB] Get: 64 http://deb.debian.org/debian bullseye/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 65 http://deb.debian.org/debian bullseye/main armhf libmd0 armhf 1.0.3-3 [27.4 kB] Get: 66 http://deb.debian.org/debian bullseye/main armhf libbsd0 armhf 0.11.3-1 [103 kB] Get: 67 http://deb.debian.org/debian bullseye/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf libxcb1 armhf 1.14-3 [136 kB] Get: 69 http://deb.debian.org/debian bullseye/main armhf libx11-data all 2:1.7.2-1 [311 kB] Get: 70 http://deb.debian.org/debian bullseye/main armhf libx11-6 armhf 2:1.7.2-1 [713 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf libxpm4 armhf 1:3.5.12-1 [44.0 kB] Get: 72 http://deb.debian.org/debian bullseye/main armhf libgd3 armhf 2.3.0-2 [119 kB] Get: 73 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf libgts-0.7-5 armhf 0.7.6+darcs121130-4+b1 [138 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf libpixman-1-0 armhf 0.40.0-1 [466 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf libxcb-render0 armhf 1.14-3 [110 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf libxcb-shm0 armhf 1.14-3 [101 kB] Get: 78 http://deb.debian.org/debian bullseye/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 80 http://deb.debian.org/debian bullseye/main armhf libcairo2 armhf 1.16.0-5 [615 kB] Get: 81 http://deb.debian.org/debian bullseye/main armhf libltdl7 armhf 2.4.6-15 [388 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf libfribidi0 armhf 1.0.8-2 [62.9 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf libgraphite2-3 armhf 1.3.14-1 [70.5 kB] Get: 84 http://deb.debian.org/debian bullseye/main armhf libharfbuzz0b armhf 2.7.4-1 [1427 kB] Get: 85 http://deb.debian.org/debian bullseye/main armhf libthai-data all 0.1.28-3 [170 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf libdatrie1 armhf 0.2.13-1 [39.4 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf libthai0 armhf 0.1.28-3 [50.9 kB] Get: 88 http://deb.debian.org/debian bullseye/main armhf libpango-1.0-0 armhf 1.46.2-3 [173 kB] Get: 89 http://deb.debian.org/debian bullseye/main armhf libpangoft2-1.0-0 armhf 1.46.2-3 [56.1 kB] Get: 90 http://deb.debian.org/debian bullseye/main armhf libpangocairo-1.0-0 armhf 1.46.2-3 [46.8 kB] Get: 91 http://deb.debian.org/debian bullseye/main armhf libpathplan4 armhf 2.42.2-5 [61.9 kB] Get: 92 http://deb.debian.org/debian bullseye/main armhf libgvc6 armhf 2.42.2-5 [597 kB] Get: 93 http://deb.debian.org/debian bullseye/main armhf libgvpr2 armhf 2.42.2-5 [185 kB] Get: 94 http://deb.debian.org/debian bullseye/main armhf liblab-gamut1 armhf 2.42.2-5 [220 kB] Get: 95 http://deb.debian.org/debian bullseye/main armhf x11-common all 1:7.7+22 [252 kB] Get: 96 http://deb.debian.org/debian bullseye/main armhf libice6 armhf 2:1.0.10-1 [51.9 kB] Get: 97 http://deb.debian.org/debian bullseye/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 98 http://deb.debian.org/debian bullseye/main armhf libxt6 armhf 1:1.2.0-1 [161 kB] Get: 99 http://deb.debian.org/debian bullseye/main armhf libxmu6 armhf 2:1.1.2-2+b3 [52.7 kB] Get: 100 http://deb.debian.org/debian bullseye/main armhf libxaw7 armhf 2:1.0.13-1.1 [167 kB] Get: 101 http://deb.debian.org/debian bullseye/main armhf graphviz armhf 2.42.2-5 [521 kB] Get: 102 http://deb.debian.org/debian bullseye/main armhf help2man armhf 1.48.1 [190 kB] Get: 103 http://deb.debian.org/debian bullseye/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-9 [141 kB] Get: 104 http://deb.debian.org/debian bullseye/main armhf libbamtools-dev armhf 2.5.1+dfsg-9 [195 kB] Get: 105 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 106 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 107 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 108 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB] Get: 109 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 110 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 111 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 112 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+b1 [306 kB] Get: 113 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB] Get: 114 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB] Get: 115 http://deb.debian.org/debian bullseye/main armhf libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 116 http://deb.debian.org/debian bullseye/main armhf python3-pysam armhf 0.15.4+ds-3+b2 [1381 kB] Get: 117 http://deb.debian.org/debian bullseye/main armhf python3-ruffus all 2.8.4-2 [152 kB] Get: 118 http://deb.debian.org/debian bullseye/main armhf samtools armhf 1.11-1 [519 kB] Get: 119 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Fetched 40.7 MB in 4s (9337 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_armhf.deb ... 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Unpacking libpython3.9-minimal:armhf (3.9.2-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.2.10-2_armhf.deb ... Unpacking libexpat1:armhf (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../python3.9-minimal_3.9.2-1_armhf.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:armhf (3.9.2-1) ... Setting up libexpat1:armhf (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20488 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:armhf. Preparing to unpack .../2-libmpdec3_2.5.1-1_armhf.deb ... Unpacking libmpdec3:armhf (2.5.1-1) ... Selecting previously unselected package libpython3.9-stdlib:armhf. Preparing to unpack .../3-libpython3.9-stdlib_3.9.2-1_armhf.deb ... Unpacking libpython3.9-stdlib:armhf (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../4-python3.9_3.9.2-1_armhf.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../5-libpython3-stdlib_3.9.2-3_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20885 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_armhf.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... 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Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../10-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../11-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../12-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... 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Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../22-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../23-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../24-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../25-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../26-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../27-python3-lib2to3_3.9.2-1_all.deb ... Unpacking python3-lib2to3 (3.9.2-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../28-python3-distutils_3.9.2-1_all.deb ... Unpacking python3-distutils (3.9.2-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../29-dh-python_4.20201102+nmu1_all.deb ... Unpacking dh-python (4.20201102+nmu1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../30-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../31-libpng16-16_1.6.37-3_armhf.deb ... Unpacking libpng16-16:armhf (1.6.37-3) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../32-libfreetype6_2.10.4+dfsg-1_armhf.deb ... Unpacking libfreetype6:armhf (2.10.4+dfsg-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../33-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../34-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../35-libfontconfig1_2.13.1-4.2_armhf.deb ... Unpacking libfontconfig1:armhf (2.13.1-4.2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../36-fontconfig_2.13.1-4.2_armhf.deb ... Unpacking fontconfig (2.13.1-4.2) ... Selecting previously unselected package libcdt5:armhf. Preparing to unpack .../37-libcdt5_2.42.2-5_armhf.deb ... Unpacking libcdt5:armhf (2.42.2-5) ... Selecting previously unselected package libcgraph6:armhf. Preparing to unpack .../38-libcgraph6_2.42.2-5_armhf.deb ... Unpacking libcgraph6:armhf (2.42.2-5) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../39-libjpeg62-turbo_1%3a2.0.6-4_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.0.6-4) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../40-libdeflate0_1.7-1_armhf.deb ... Unpacking libdeflate0:armhf (1.7-1) ... Selecting previously unselected package libjbig0:armhf. Preparing to unpack .../41-libjbig0_2.1-3.1+b2_armhf.deb ... Unpacking libjbig0:armhf (2.1-3.1+b2) ... Selecting previously unselected package libwebp6:armhf. Preparing to unpack .../42-libwebp6_0.6.1-2.1_armhf.deb ... Unpacking libwebp6:armhf (0.6.1-2.1) ... Selecting previously unselected package libtiff5:armhf. Preparing to unpack .../43-libtiff5_4.2.0-1_armhf.deb ... Unpacking libtiff5:armhf (4.2.0-1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../44-libxau6_1%3a1.0.9-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1) ... Selecting previously unselected package libmd0:armhf. Preparing to unpack .../45-libmd0_1.0.3-3_armhf.deb ... Unpacking libmd0:armhf (1.0.3-3) ... Selecting previously unselected package libbsd0:armhf. 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Unpacking libhts3:armhf (1.11-4) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../94-libncurses6_6.2+20201114-2_armhf.deb ... Unpacking libncurses6:armhf (6.2+20201114-2) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../95-libsparsehash-dev_2.0.3-2_all.deb ... Unpacking libsparsehash-dev (2.0.3-2) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../96-python3-pysam_0.15.4+ds-3+b2_armhf.deb ... Unpacking python3-pysam (0.15.4+ds-3+b2) ... Selecting previously unselected package python3-ruffus. Preparing to unpack .../97-python3-ruffus_2.8.4-2_all.deb ... Unpacking python3-ruffus (2.8.4-2) ... Selecting previously unselected package samtools. Preparing to unpack .../98-samtools_1.11-1_armhf.deb ... Unpacking samtools (1.11-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../99-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up libgraphite2-3:armhf (1.3.14-1) ... Setting up libpixman-1-0:armhf (0.40.0-1) ... Setting up libxau6:armhf (1:1.0.9-1) ... Setting up libpsl5:armhf (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7) ... Setting up libdatrie1:armhf (0.2.13-1) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up gawk (1:5.1.0-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:armhf (1.0.9-2+b2) ... Setting up liblab-gamut1:armhf (2.42.2-5) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:armhf (1.43.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up libdeflate0:armhf (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up m4 (1.4.18-5) ... Setting up file (1:5.39-3) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libjbig0:armhf (2.1-3.1+b2) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Setting up libgts-0.7-5:armhf (0.7.6+darcs121130-4+b1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libjpeg62-turbo:armhf (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libpathplan4:armhf (2.42.2-5) ... Setting up libncurses6:armhf (6.2+20201114-2) ... Setting up libfribidi0:armhf (1.0.8-2) ... Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-9) ... Setting up libpng16-16:armhf (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:armhf (0.6.1-2.1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libltdl7:armhf (2.4.6-15) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Setting up autoconf (2.69-14) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up libmd0:armhf (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libmpdec3:armhf (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libthai-data (0.1.28-3) ... Setting up libssh2-1:armhf (1.9.0-2) ... Setting up libcdt5:armhf (2.42.2-5) ... Setting up libcgraph6:armhf (2.42.2-5) ... Setting up libtiff5:armhf (4.2.0-1) ... Setting up libbsd0:armhf (0.11.3-1) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libpython3.9-stdlib:armhf (3.9.2-1) ... Setting up libpython3-stdlib:armhf (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libice6:armhf (2:1.0.10-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libxcb1:armhf (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:armhf (1.14-3) ... Setting up libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Setting up libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Setting up libxcb-shm0:armhf (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:armhf (0.1.28-3) ... Setting up libfreetype6:armhf (2.10.4+dfsg-1) ... Setting up libbamtools-dev:armhf (2.5.1+dfsg-9) ... Setting up ucf (3.0043) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libgvpr2:armhf (2.42.2-5) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libx11-6:armhf (2:1.7.2-1) ... Setting up libharfbuzz0b:armhf (2.7.4-1) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libhts3:armhf (1.11-4) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:armhf (2:1.3.3-1.1) ... Setting up python3 (3.9.2-3) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up libxt6:armhf (1:1.2.0-1) ... Setting up libfontconfig1:armhf (2.13.1-4.2) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxmu6:armhf (2:1.1.2-2+b3) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up libpango-1.0-0:armhf (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up libxaw7:armhf (2:1.0.13-1.1) ... Setting up libcairo2:armhf (1.16.0-5) ... Setting up libgd3:armhf (2.3.0-2) ... Setting up libpangoft2-1.0-0:armhf (1.46.2-3) ... Setting up libpangocairo-1.0-0:armhf (1.46.2-3) ... Setting up libgvc6 (2.42.2-5) ... Setting up graphviz (2.42.2-5) ... Setting up python3-ruffus (2.8.4-2) ... Processing triggers for libc-bin (2.31-13) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package hostname: Name or service not known I: Running cd /build/sga-0.10.15/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../sga_0.10.15-5_source.changes dpkg-buildpackage: info: source package sga dpkg-buildpackage: info: source version 0.10.15-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot 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 build dh build --with python3 --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src 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=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-bamtools=/usr/ checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... 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 google/sparse_hash_set usability... yes checking google/sparse_hash_set presence... yes checking for google/sparse_hash_set... yes checking for google/sparse_hash_set... (cached) yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking ext/hash_map usability... yes checking ext/hash_map presence... yes checking for ext/hash_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking ext/hash_set usability... yes checking ext/hash_set presence... yes checking for ext/hash_set... yes checking api/BamReader.h usability... yes checking api/BamReader.h presence... 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 -j4 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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o multiple_alignment.o multiple_alignment.cpp 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] 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 bcr.c: In function 'ld_restore': bcr.c:183:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | fread(&ld->max, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:186:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 186 | fread(&x, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:189:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 189 | fread(ld->a[i], 8, x, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MurmurHash3.o MurmurHash3.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; | ^~~~ 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 -fdebug-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o count_min_sketch.o count_min_sketch.cpp 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 Alphabet.cpp:101:84: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 101 | template<> const size_t AlphaCount64::maxValue = std::numeric_limits::max(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 /usr/include/c++/10/vector:72, from QualityVector.h:13, from QualityVector.cpp:13: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DNADouble&}; _Tp = DNADouble; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from QualityVector.h:13, from QualityVector.cpp:13: /usr/include/c++/10/bits/stl_vector.h: In member function 'void QualityVector::add(DNADouble)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from Quality.h:13, from Quality.cpp:9: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Quality.h:13, from Quality.cpp:9: /usr/include/c++/10/bits/stl_vector.h: In function 'DoubleVector Quality::uniformLogProbVector(double, size_t)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from Util.h:12, from Match.h:13, from MultiOverlap.h:13, from MultiOverlap.cpp:13: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MultiOverlap::MOData&}; _Tp = MultiOverlap::MOData; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Util.h:12, from Match.h:13, from MultiOverlap.h:13, from MultiOverlap.cpp:13: /usr/include/c++/10/bits/stl_vector.h: In member function 'void MultiOverlap::add(const string&, const Overlap&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 /usr/include/c++/10/bits/stl_vector.h: In member function 'void MultiOverlap::add(const MultiOverlap::MOData&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from Util.h:12, from Match.h:13, from MultiOverlap.h:13, from MultiOverlap.cpp:13: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AlphaCount&}; _Tp = AlphaCount; _Alloc = std::allocator >]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PUElem}; _Tp = PUElem; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PUElem}; _Tp = PUElem; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from MultiOverlap.cpp:10: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from MultiOverlap.cpp:10: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = MultiOverlap::MOData; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/algorithm:62, from MultiOverlap.cpp:10: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In member function 'void MultiOverlap::print(int, int)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Util.h:12, from Match.h:13, from MultiOverlap.h:13, from MultiOverlap.cpp:13: /usr/include/c++/10/bits/stl_vector.h: In member function 'std::string MultiOverlap::consensusConflict(double, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from VCFUtil.h:14, from VCFUtil.cpp:14: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const VCFRecord&}; _Tp = VCFRecord; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, from VCFUtil.h:14, from VCFUtil.cpp:14: /usr/include/c++/10/bits/stl_vector.h: In function 'VCFReturnCode VCFUtil::generateVCFFromCancerVariant(const string&, const string&, const string&, const string&, size_t, const string&, int, double, int, VCFVector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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::_copy(const EncodedString&) [with Codec = DNACodec]': ../Util/EncodedString.h:43:18: required from 'EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]' Vertex.cpp:34:46: 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/10/bits/stl_algo.h: In function '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 939 | __unique(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/list:63, from ../SuffixTools/BWTInterval.h:13, from OverlapBlock.h:14, from OverlapBlock.cpp:11: /usr/include/c++/10/bits/stl_list.h: In member function 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(std::__cxx11::list<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const OverlapBlock&}; _Tp = OverlapBlock; _Alloc = std::allocator]': /usr/include/c++/10/bits/stl_list.h:1909:8: note: parameter passing for argument of type 'std::__cxx11::list::iterator' changed in GCC 7.1 1909 | _M_insert(iterator __position, _Args&&... __args) | ^~~~~~~~~ In file included from /usr/include/c++/10/map:60, from ../SuffixTools/STGlobals.h:15, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapBlock.h:17, from OverlapBlock.cpp:11: /usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SearchSeed&}; _Tp = SearchSeed; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/list:63, from ../SuffixTools/BWTInterval.h:13, from OverlapBlock.h:14, from OverlapBlock.cpp:11: /usr/include/c++/10/bits/stl_list.h: In function 'OverlapBlockList resolveOverlap(const OverlapBlock&, const OverlapBlock&, const BWT*, const BWT*)': /usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 1212 | { this->_M_insert(end(), __x); } | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from ../SuffixTools/STGlobals.h:15, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapBlock.h:17, from OverlapBlock.cpp:11: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/list:64, from ../Util/Util.h:13, from ../Util/Alphabet.h:29, from ../SuffixTools/STGlobals.h:19, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/10/bits/list.tcc: In member function 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(std::__cxx11::list<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_iterator; = void; _Tp = OverlapBlock; _Alloc = std::allocator]': /usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::__cxx11::list::const_iterator' changed in GCC 7.1 133 | list<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 /usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 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 -fdebug-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 -fdebug-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 OverlapAlgorithm.cpp: In member function 'OverlapResult OverlapAlgorithm::overlapReadExact(const SeqRecord&, int, OverlapBlockList*) const': OverlapAlgorithm.cpp:150:87: note: parameter passing for argument of type 'std::__cxx11::list::const_iterator' changed in GCC 7.1 150 | oblSuffixFwd.insert(oblSuffixFwd.end(), oblFwdContain.begin(), oblFwdContain.end()); | ^ OverlapAlgorithm.cpp:150:87: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 OverlapAlgorithm.cpp:151:87: note: parameter passing for argument of type 'std::__cxx11::list::const_iterator' changed in GCC 7.1 151 | oblPrefixFwd.insert(oblPrefixFwd.end(), oblFwdContain.begin(), oblFwdContain.end()); | ^ OverlapAlgorithm.cpp:151:87: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 OverlapAlgorithm.cpp:152:87: note: parameter passing for argument of type 'std::__cxx11::list::const_iterator' changed in GCC 7.1 152 | oblSuffixRev.insert(oblSuffixRev.end(), oblRevContain.begin(), oblRevContain.end()); | ^ OverlapAlgorithm.cpp:152:87: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 OverlapAlgorithm.cpp:153:87: note: parameter passing for argument of type 'std::__cxx11::list::const_iterator' changed in GCC 7.1 153 | oblPrefixRev.insert(oblPrefixRev.end(), oblRevContain.begin(), oblRevContain.end()); | ^ OverlapAlgorithm.cpp:153:87: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SearchSeed; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from ../SuffixTools/STGlobals.h:15, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from ErrorCorrectProcess.h:14, from ErrorCorrectProcess.cpp:10: /usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 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 -fdebug-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 /usr/include/c++/10/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, ErrorCount>; _KeyOfValue = std::_Select1st, ErrorCount> >; _Compare = std::less >; _Alloc = std::allocator, ErrorCount> >]': /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, ErrorCount>, std::_Select1st, ErrorCount> >, std::less >, std::allocator, ErrorCount> > >::const_iterator' changed in GCC 7.1 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, ErrorCount>; _KeyOfValue = std::_Select1st, ErrorCount> >; _Compare = std::less >; _Alloc = std::allocator, ErrorCount> >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, ErrorCount>, std::_Select1st, ErrorCount> >, std::less >, std::allocator, ErrorCount> > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, ErrorCount>, std::_Select1st, ErrorCount> >, std::less >, std::allocator, ErrorCount> > >::const_iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/10/bits/stl_vector.h: In member function 'bool OverlapAlgorithm::findOverlapBlocksInexact(const string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1015:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1015 | return std::__unique(__first, __last, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1016 | __gnu_cxx::__ops::__iter_comp_iter(__binary_pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from ../SuffixTools/STGlobals.h:15, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from ErrorCorrectProcess.h:14, from ErrorCorrectProcess.cpp:10: /usr/include/c++/10/bits/stl_map.h: In member function 'void ErrorCorrectPostProcess::collectMetrics(const string&, const string&, const string&)': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, ErrorCount>, std::_Select1st, ErrorCount> >, std::less >, std::allocator, ErrorCount> > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, ErrorCount>, std::_Select1st, ErrorCount> >, std::less >, std::allocator, ErrorCount> > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from ../Util/Util.h:12, from FMMergeProcess.h:12, from FMMergeProcess.cpp:9: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BWTInterval&}; _Tp = BWTInterval; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from FMMergeProcess.h:13, from FMMergeProcess.cpp:9: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from FMMergeProcess.h:13, from FMMergeProcess.cpp:9: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BWTInterval; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from FMMergeProcess.h:13, from FMMergeProcess.cpp:9: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, from ../Util/Util.h:12, from FMMergeProcess.h:12, from FMMergeProcess.cpp:9: /usr/include/c++/10/bits/stl_vector.h: In member function 'FMMergeResult FMMergeProcess::process(const SequenceWorkItem&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from FMMergeProcess.h:13, from FMMergeProcess.cpp:9: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ LRAlignment.cpp: In function 'void LRAlignment::removeDuplicateCells(LRAlignment::LRStackEntry*, LRAlignment::LRHash&)': LRAlignment.cpp:560:34: warning: left shift count >= width of type [-Wshift-count-overflow] 560 | iter->second = i << 32 | p->G; | ~~^~~~~ LRAlignment.cpp:566:27: warning: left shift count >= width of type [-Wshift-count-overflow] 566 | hash[key] = i << 32 | p->G; | ~~^~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from ../Util/Util.h:12, from ReadCluster.h:13, from ReadCluster.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ClusterNode&}; _Tp = ClusterNode; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from ReadCluster.h:14, from ReadCluster.cpp:10: /usr/include/c++/10/bits/stl_algo.h: In function '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 939 | __unique(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from ReadCluster.cpp:10: ReadCluster.h: In member function 'ClusterNode ReadCluster::addSeed(const string&, bool)': ReadCluster.h:17:8: warning: 'emptyNode.ClusterNode::fwdCanonicalID' may be used uninitialized in this function [-Wmaybe-uninitialized] 17 | struct ClusterNode | ^~~~~~~~~~~ ReadCluster.h:17:8: warning: 'emptyNode.ClusterNode::isReverseInterval' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from ReadCluster.h:14, from ReadCluster.cpp:10: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from ReadCluster.h:14, from ReadCluster.cpp:10: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ClusterNode; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from ReadCluster.h:14, from ReadCluster.cpp:10: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from LRAlignment.h:13, from LRAlignment.cpp:10: /usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = LRAlignment::LRHit; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In member function 'ClusterNodeVector ReadCluster::getOutput() const': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1015:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1015 | return std::__unique(__first, __last, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1016 | __gnu_cxx::__ops::__iter_comp_iter(__binary_pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 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 -fdebug-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 /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LRAlignment::LRCell&}; _Tp = LRAlignment::LRCell; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LRAlignment::LRHit&}; _Tp = LRAlignment::LRHit; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from LRAlignment.h:13, from LRAlignment.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In function 'void LRAlignment::saveTerminalHits(const SuffixArray*, const SampledSuffixArray*, const BWT*, LRAlignment::LRStackEntry*, int, LRAlignment::LRHitVector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function 'void LRAlignment::saveAllHits(const SuffixArray*, const SampledSuffixArray*, const BWT*, LRAlignment::LRStackEntry*, int, LRAlignment::LRHitVector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../Util/Util.h:12, from ReadCluster.h:13, from ReadCluster.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In member function 'void ReadCluster::run(size_t, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from LRAlignment.h:13, from LRAlignment.cpp:10: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from LRAlignment.h:13, from LRAlignment.cpp:10: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LRAlignment::LRHit; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from LRAlignment.h:13, from LRAlignment.cpp:10: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'int LRAlignment::resolveDuplicateHits(const BWT*, const SampledSuffixArray*, LRAlignment::LRHitVector&, int)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from LRAlignment.h:13, from LRAlignment.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In function 'void LRAlignment::bwaswAlignment(const string&, const BWT*, const SampledSuffixArray*, const LRAlignment::LRParams&, LRAlignment::LRHitVector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 1665 | _M_range_insert(__pos, __first, __last, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 1666 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 1665 | _M_range_insert(__pos, __first, __last, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 1666 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 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 -fdebug-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 /usr/include/c++/10/bits/stl_vector.h: In function 'int LRAlignment::resolveDuplicateHitsByID(const BWT*, const SampledSuffixArray*, LRAlignment::LRHitVector&, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from LRAlignment.h:13, from LRAlignment.cpp:10: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ KmerOverlaps.cpp:60:12: warning: width of 'KmerMatch::index' exceeds its type 60 | size_t index:47; | ^~~~~ In file included from /usr/include/c++/10/vector:72, from ../Thirdparty/multiple_alignment.h:30, from KmerOverlaps.h:13, from KmerOverlaps.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ApproxSeed&}; _Tp = ApproxSeed; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from ../Thirdparty/multiple_alignment.h:30, from KmerOverlaps.h:13, from KmerOverlaps.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In function 'void _approximateSeededMatch(const string&, int, double, int, int, bool, const BWTIndexSet&, SequenceOverlapPairVector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from STGlobals.h:13, from STCommon.h:11, from SuffixArray.h:11, from SuffixArray.cpp:9: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SAElem&}; _Tp = SAElem; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from STGlobals.h:13, from STCommon.h:11, from SuffixArray.h:11, from SuffixArray.cpp:9: /usr/include/c++/10/bits/stl_vector.h: In member function 'void SuffixArray::removeReads(const NumericIDSet&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from STGlobals.h:14, from STCommon.h:11, from InverseSuffixArray.h:12, from InverseSuffixArray.cpp:10: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from STGlobals.h:14, from STCommon.h:11, from InverseSuffixArray.h:12, from InverseSuffixArray.cpp:10: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from STGlobals.h:13, from STCommon.h:11, from InverseSuffixArray.h:12, from InverseSuffixArray.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from STGlobals.h:13, from STCommon.h:11, from InverseSuffixArray.h:12, from InverseSuffixArray.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In member function 'void InverseSuffixArray::validate() const': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from STGlobals.h:14, from STCommon.h:11, from InverseSuffixArray.h:12, from InverseSuffixArray.cpp:10: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 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::_copy(const EncodedString&) [with Codec = DNACodec]': ../Util/EncodedString.h:43:18: required from 'EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]' /usr/include/c++/10/ext/new_allocator.h:150:4: required from 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString]' /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; std::allocator_traits >::allocator_type = std::allocator >]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString}; _Tp = EncodedString; _Alloc = std::allocator >]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = EncodedString; _Alloc = std::allocator >; std::vector<_Tp, _Alloc>::value_type = EncodedString]' BWTDiskConstruction.cpp:252:56: 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../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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from STGlobals.h:13, from STCommon.h:11, from SuffixArray.h:11, from BWTDiskConstruction.h:18, from BWTDiskConstruction.cpp:12: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MergeItem&}; _Tp = MergeItem; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from STGlobals.h:13, from STCommon.h:11, from SuffixArray.h:11, from BWTDiskConstruction.h:18, from BWTDiskConstruction.cpp:12: /usr/include/c++/10/bits/stl_vector.h: In function 'MergeVector computeInitialSAIS(const BWTDiskParameters&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../Util/Util.h:12, from SAReader.h:12, from SAReader.cpp:9: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SAElem&}; _Tp = SAElem; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../Util/Util.h:12, from SAReader.h:12, from SAReader.cpp:9: /usr/include/c++/10/bits/stl_vector.h: In member function 'void SAReader::readElems(SAElemVector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 /usr/include/c++/10/bits/stl_vector.h: In function 'MergeVector computeInitialBCR(const BWTDiskParameters&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../Util/Util.h:12, from RankProcess.h:13, from RankProcess.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../Util/Util.h:12, from RankProcess.h:13, from RankProcess.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In member function 'RankResult RankProcess::process(const SequenceWorkItem&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 /usr/include/c++/10/bits/stl_vector.h: In function 'void buildBWTDisk(const BWTDiskParameters&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from STGlobals.h:14, from STCommon.h:11, from SAWriter.h:13, from BWTCABauerCoxRosone.h:12, from BWTCABauerCoxRosone.cpp:9: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BWTCA::BCRElem; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from STGlobals.h:14, from STCommon.h:11, from SAWriter.h:13, from BWTCABauerCoxRosone.h:12, from BWTCABauerCoxRosone.cpp:9: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void BWTCA::runBauerCoxRosone(const DNAEncodedStringVector*, const string&, const string&)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from ../Bigraph/GraphCommon.h:13, from ScaffoldLink.h:14, from ScaffoldRecord.h:14, from ScaffoldRecord.cpp:11: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ScaffoldLink&}; _Tp = ScaffoldLink; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from ../Bigraph/GraphCommon.h:13, from ScaffoldLink.h:14, from ScaffoldRecord.h:14, from ScaffoldRecord.cpp:11: /usr/include/c++/10/bits/stl_vector.h: In member function 'void ScaffoldRecord::addLink(const ScaffoldLink&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void ScaffoldRecord::parse(const string&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from ../Bigraph/Bigraph.h:14, from ScaffoldVertex.h:12, from ScaffoldGroup.h:13, from ScaffoldGroup.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LinkVertexPair&}; _Tp = LinkVertexPair; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../Bigraph/Bigraph.h:14, from ScaffoldVertex.h:12, from ScaffoldGroup.h:13, from ScaffoldGroup.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In member function 'void ScaffoldGroup::addLink(const ScaffoldLink&, ScaffoldVertex*)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void ScaffoldGroup::computeBestOrdering()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../Bigraph/Bigraph.h:14, from ScaffoldVertex.h:12, from ScaffoldGroup.h:13, from ScaffoldGroup.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ScaffoldLink&}; _Tp = ScaffoldLink; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../Bigraph/Bigraph.h:14, from ScaffoldVertex.h:12, from ScaffoldGroup.h:13, from ScaffoldGroup.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In member function 'void ScaffoldGroup::getLinearLinks(LinkVector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 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::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::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl; | ^~~ DindelUtil.cpp: In function 'DindelReturnCode DindelUtil::runDindelPairMatePair(const 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 DindelRealignWindow::computeHaplotypePairLikelihoods(std::vector&, std::unordered_map, std::__cxx11::list >&, const std::vector >&)': DindelRealignWindow.cpp:2589:12: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 2589 | for (int h1=0;h1&, const std::vector >&, double, int)': DindelRealignWindow.cpp:2743:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 2743 | for (size_t x=0;x&, const std::vector >&, double, int)': DindelRealignWindow.cpp:2906:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 2906 | for (size_t x=0;x::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {DindelRead}; _Tp = DindelRead; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {DindelRead}; _Tp = DindelRead; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 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; | ^~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/vector:72, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DindelVariant&}; _Tp = DindelVariant; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 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 -fdebug-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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector WindowFile::getNextWindow()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from ../SuffixTools/BWTIndexSet.h:14, from HapgenUtil.h:14, from HapgenUtil.cpp:12: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BWTInterval&}; _Tp = BWTInterval; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LocalAlignmentResult&}; _Tp = LocalAlignmentResult; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const VCFRecord&}; _Tp = VCFRecord; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from ../SuffixTools/BWTIndexSet.h:14, from HapgenUtil.h:14, from HapgenUtil.cpp:12: /usr/include/c++/10/bits/stl_vector.h: In function 'LocalAlignmentResultVector HapgenUtil::alignReadsLocally(const string&, const SeqItemVector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from ../SuffixTools/BWTIndexSet.h:14, from HapgenUtil.h:14, from HapgenUtil.cpp:12: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LocalAlignmentResult}; _Tp = LocalAlignmentResult; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In function 'bool HapgenUtil::checkAlignmentsAreConsistent(const string&, const StringVector&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void DindelRealignWindow::setAddReadsSingleReadMultiSample(int, int, const std::vector >&, std::vector >&, std::vector&, int, int, std::vector&, std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::unordered_map, std::__cxx11::list >&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {DindelRealignWindowResult::HaplotypeProperties}; _Tp = DindelRealignWindowResult::HaplotypeProperties; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {DindelRealignWindowResult::HaplotypeProperties}; _Tp = DindelRealignWindowResult::HaplotypeProperties; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from ../SuffixTools/BWTIndexSet.h:14, from HapgenUtil.h:14, from HapgenUtil.cpp:12: /usr/include/c++/10/bits/stl_vector.h: In function 'bool HapgenUtil::extractHaplotypeReads(const StringVector&, const BWTIndexSet&, int, bool, size_t, int64_t, SeqRecordVector*, SeqRecordVector*)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 In file included from /usr/include/c++/10/vector:67, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/10/bits/stl_vector.h: In member function 'void DindelRealignWindowResult::Inference::outputAsVCF(const DindelVariant&, const DindelRealignWindowResult&, VCFCollection&, const ReadTable*) const': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void DindelRealignWindow::computeProjectedMappingQuality()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from DindelRealignWindow.cpp:24: /usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = DindelVariant; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/map:61, from DindelRealignWindow.cpp:24: /usr/include/c++/10/bits/stl_map.h: In member function 'void DindelRealignWindow::addDiploidGenotypes(DindelRealignWindowResult&, const std::vector&, const std::vector >&)': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {DindelHaplotype}; _Tp = DindelHaplotype; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/10/bits/stl_vector.h: In member function 'void DindelHaplotype::extractVariants()': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/10/bits/vector.tcc: In constructor 'DindelMultiHaplotype::DindelMultiHaplotype(const std::vector&, const string&, size_t)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DindelRead&}; _Tp = DindelRead; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/10/bits/stl_vector.h: In member function 'void DindelRealignWindow::showHaplotypeOnlyReadsSingleRead(int, const std::vector >&, int, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function 'void DindelRealignWindow::showHaplotypeOnlyReadsMatePairs(int, const std::vector >&, int, int)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 index.cpp: In function 'void parseIndexOptions(int, char**)': index.cpp:276:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 276 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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::_copy(const EncodedString&) [with Codec = DNACodec]': ../Util/EncodedString.h:43:18: required from 'EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]' /usr/include/c++/10/ext/new_allocator.h:150:4: required from 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString]' /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; std::allocator_traits >::allocator_type = std::allocator >]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString}; _Tp = EncodedString; _Alloc = std::allocator >]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = EncodedString; _Alloc = std::allocator >; std::vector<_Tp, _Alloc>::value_type = EncodedString]' index.cpp:130:45: 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); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ overlap.cpp: In function 'void parseOverlapOptions(int, char**)': overlap.cpp:327:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 327 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ assemble.cpp: In function 'void parseAssembleOptions(int, char**)': assemble.cpp:234:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 234 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 correct.cpp: In function 'void parseCorrectOptions(int, char**)': correct.cpp:330:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 330 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ preprocess.cpp: In function 'void parsePreprocessOptions(int, char**)': preprocess.cpp:616:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 616 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ oview.cpp: In function 'void parseOviewOptions(int, char**)': oview.cpp:202:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 202 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 merge.cpp: In function 'void parseMergeOptions(int, char**)': merge.cpp:173:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 173 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 rmdup.cpp: In function 'void parseRmdupOptions(int, char**)': rmdup.cpp:348:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 348 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ subgraph.cpp: In function 'void parseSubgraphOptions(int, char**)': subgraph.cpp:169:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 169 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 -fdebug-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 scaffold.cpp: In function 'void parseScaffoldOptions(int, char**)': scaffold.cpp:189:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 189 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ scaffold2fasta.cpp: In function 'void parseScaffold2fastaOptions(int, char**)': scaffold2fasta.cpp:196:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 196 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 -fdebug-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 connect.cpp: In function 'void parseConnectOptions(int, char**)': connect.cpp:465:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 465 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ walk.cpp: In function 'void parseWalkOptions(int, char**)': walk.cpp:323:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 323 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ filter.cpp: In function 'void parseFilterOptions(int, char**)': filter.cpp:217:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 217 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 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 -fdebug-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 -fdebug-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 kmer-count.cpp: In function 'void parseKmerCountOptions(int, char**)': kmer-count.cpp:63:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 63 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ stats.cpp: In function 'void parseStatsOptions(int, char**)': stats.cpp:171:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 171 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ fm-merge.cpp: In function 'void parseFMMergeOptions(int, char**)': fm-merge.cpp:164:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 164 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 gmap.cpp: In function 'void parseGmapOptions(int, char**)': gmap.cpp:303:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 303 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ gen-ssa.cpp: In function 'void parseGenSSAOptions(int, char**)': gen-ssa.cpp:108:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 108 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ filterBAM.cpp: In function 'void parseFilterBAMOptions(int, char**)': filterBAM.cpp:438:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 438 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cluster.cpp: In function 'void parseClusterOptions(int, char**)': cluster.cpp:292:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 292 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 -fdebug-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 bwt2fa.cpp: In function 'void parseBWT2FAOptions(int, char**)': bwt2fa.cpp:96:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 96 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 graph-diff.cpp: In function 'void parseGraphDiffOptions(int, char**)': graph-diff.cpp:493:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 493 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 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 'unsigned int'} [-Wsign-compare] 214 | if(end > chr.seq.length()) | ~~~~^~~~~~~~~~~~~~~~~~ graph-concordance.cpp: In function 'void parseGraphConcordanceOptions(int, char**)': graph-concordance.cpp:437:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 437 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ gapfill.cpp: In function 'void parseGapFillOptions(int, char**)': gapfill.cpp:148:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 148 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 overlap-long.cpp: In function 'void parseOverlapLongOptions(int, char**)': overlap-long.cpp:338:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 338 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ variant-detectability.cpp: In function 'void parseVarDetectOptions(int, char**)': variant-detectability.cpp:205:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 205 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:170:3: 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::Ch rapidjson::UTF8::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:183:3: 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::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:189:3: 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::Put(OutputByteStream&, rapidjson::UTF8::Ch)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:195:3: 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::Encode(OutputStream&, unsigned int)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:219:3: 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::Decode(InputStream&, unsigned int*)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:234:3: 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::Validate(InputStream&, OutputStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:252:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 252 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:253:3: 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::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:271:3: 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::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:278:3: 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::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:286:3: 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::Put(OutputByteStream&, CharType)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:292:3: 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::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:303:3: 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::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:310:3: 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::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:318:3: 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::Put(OutputByteStream&, CharType)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:324:3: 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::Encode(OutputStream&, unsigned int)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:348:3: 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::Decode(InputStream&, unsigned int*)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:355:3: 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::Validate(InputStream&, OutputStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:363:3: 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::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:375:3: 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::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:382:3: 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::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:392:3: 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::Put(OutputByteStream&, CharType)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:398:3: 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::TakeBOM(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:411:3: 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::Take(InputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:418:3: 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::PutBOM(OutputByteStream&)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:428:3: 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::Put(OutputByteStream&, CharType)': ../Thirdparty/rapidjson/rapidjson.h:115:17: 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:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:434:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 434 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ rewrite-evidence-bam.cpp: In function 'void parseRewriteEvidenceBAMOptions(int, char**)': rewrite-evidence-bam.cpp:158:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 158 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ preqc.cpp: In function 'void parsePreQCOptions(int, char**)': preqc.cpp:2090:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 2090 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 -fdebug-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 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 -fdebug-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 -fdebug-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 /usr/include/c++/10/queue:62, from preqc.cpp:14: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from preqc.h:14, from preqc.cpp:16: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ haplotype-filter.cpp: In function 'void parseHaplotypeFilterOptions(int, char**)': haplotype-filter.cpp:1066:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 1066 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ somatic-variant-filters.cpp: In function 'void parseSomaticVariantFiltersOptions(int, char**)': somatic-variant-filters.cpp:794:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 794 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/BWTAlgorithms.h:12, from somatic-variant-filters.cpp:16: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/BWTAlgorithms.h:12, from somatic-variant-filters.cpp:16: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../Util/Util.h:12, from haplotype-filter.cpp:14: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ../Util/Util.h:12, from haplotype-filter.cpp:14: /usr/include/c++/10/bits/stl_vector.h: In function 'std::vector loadSampleDepthsFromFile(std::string)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'double median(std::vector) [with T = double]': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/queue:61, from preqc.cpp:14: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/c++/10/queue:61, from preqc.cpp:14: /usr/include/c++/10/bits/stl_vector.h: In function 'void generate_gc_distribution(JSONWriter*, const BWTIndexSet&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../Util/Util.h:12, from somatic-variant-filters.cpp:14: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In function 'CoverageStats getVariantCoverage(BamTools::BamReader*, const VCFRecord&, const ReadTable*)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/queue:61, from preqc.cpp:14: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from preqc.h:14, from preqc.cpp:16: /usr/include/c++/10/bits/stl_algo.h: In function '_Z25generate_duplication_ratePN9rapidjson12PrettyWriterINS_10FileStreamENS_4UTF8IcEES3_NS_19MemoryPoolAllocatorINS_12CrtAllocatorEEEEERK11BWTIndexSet._omp_fn.0': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/c++/10/queue:61, from preqc.cpp:14: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ preqc.cpp:1191:13: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 1191 | #pragma omp parallel for | ^~~ preqc.cpp:1191:13: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 g++ -Wall -Wextra -Wno-unknown-pragmas -g -O2 -fdebug-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' make[3]: Entering 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' make[1]: Leaving directory '/build/sga-0.10.15/src' dh_auto_test -O--sourcedirectory=src cd src && make -j4 check 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'. make[2]: Leaving directory '/build/sga-0.10.15/src/Thirdparty' Making check in Util make[2]: Entering directory '/build/sga-0.10.15/src/Util' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-0.10.15/src/Util' 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 fakeroot debian/rules binary dh binary --with python3 --sourcedirectory=src 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 -j4 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'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-0.10.15/src/Thirdparty' make[3]: Leaving directory '/build/sga-0.10.15/src/Thirdparty' 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' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-0.10.15/src/Util' make[3]: Leaving directory '/build/sga-0.10.15/src/Util' Making install in SQG make[3]: Entering directory '/build/sga-0.10.15/src/SQG' make[4]: Entering directory '/build/sga-0.10.15/src/SQG' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. 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'. make[4]: Nothing to be done for 'install-data-am'. 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'. make[4]: Nothing to be done for 'install-data-am'. 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'. make[4]: Nothing to be done for 'install-data-am'. 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'. make[4]: Nothing to be done for 'install-data-am'. 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'. make[4]: Nothing to be done for 'install-data-am'. 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'. make[4]: Nothing to be done for 'install-data-am'. 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'. make[4]: Nothing to be done for 'install-data-am'. 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' 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 '/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'. make[4]: Nothing to be done for 'install-data-am'. 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:/i/capture/the/path \ 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_installinit -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 -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: debian/sga/usr/bin/sga contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dpkg-gencontrol: warning: package sga: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package sga: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'sga-dbgsym' in '../sga-dbgsym_0.10.15-5_armhf.deb'. dpkg-deb: building package 'sga' in '../sga_0.10.15-5_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sga_0.10.15-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/13079/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/13079/tmp/hooks/B01_cleanup finished 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/13079 and its subdirectories I: Current time: Fri Sep 24 17:15:44 +14 2021 I: pbuilder-time-stamp: 1632453344