I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 12 21:09:48 -12 2020 I: pbuilder-time-stamp: 1597309788 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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_0.10.15-4.dsc] I: copying [./sga_0.10.15.orig.tar.gz] I: copying [./sga_0.10.15-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Sep 23 09:30:35 2018 -12 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_0.10.15-4.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_0.10.15-4.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4765/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4765' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.HfxT5wMb4z/pbuilderrc_pTNp --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.HfxT5wMb4z/b1 --logfile b1/build.log sga_0.10.15-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled16-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 12 20:26 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/4765/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: arm64 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 (>= 11~), libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, gawk, help2man, samtools, python, python-ruffus, python-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 ... 19168 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 (>= 11~); however: Package debhelper 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 python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on python-ruffus; however: Package python-ruffus is not installed. pbuilder-satisfydepends-dummy depends on python-pysam; however: Package python-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} bsdmainutils{a} debhelper{a} dh-autoreconf{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} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libcroco3{a} libcurl3-gnutls{a} libdatrie1{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} libgssapi-krb5-2{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libhts2{a} libice6{a} libicu63{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libltdl7{a} libmagic-mgc{a} libmagic1{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} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libsparsehash-dev{a} libssh2-1{a} libssl1.1{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} libxdot4{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} lsb-base{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python-pysam{a} python-ruffus{a} python2{a} python2-minimal{a} python2.7{a} python2.7-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 cwltool fonts-liberation krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libgts-bin libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 124 newly installed, 0 to remove and 0 not upgraded. Need to get 40.9 MB of archives. After unpacking 136 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 gawk arm64 1:4.2.1+dfsg-1 [628 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 liblocale-gettext-perl arm64 1.07-3+b4 [18.8 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 ucf all 3.0038+nmu1 [69.0 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libpng16-16 arm64 1.6.36-6 [287 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libfreetype6 arm64 2.9.1-3+deb10u1 [355 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 fontconfig-config all 2.13.1-2 [280 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 libfontconfig1 arm64 2.13.1-2 [343 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 fontconfig arm64 2.13.1-2 [405 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 libpixman-1-0 arm64 0.36.0-1 [436 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libxau6 arm64 1:1.0.8-1+b2 [19.3 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libxcb1 arm64 1.13.1-2 [135 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libx11-data all 2:1.6.7-1 [298 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libx11-6 arm64 2:1.6.7-1 [735 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 libxcb-render0 arm64 1.13.1-2 [108 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 libxcb-shm0 arm64 1.13.1-2 [99.3 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 libxext6 arm64 2:1.3.3-1+b2 [48.6 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 libcairo2 arm64 1.16.0-4 [644 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 libcdt5 arm64 2.40.1-6 [59.6 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 libcgraph6 arm64 2.40.1-6 [81.8 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 libjpeg62-turbo arm64 1:1.5.2-2+b1 [115 kB] Get: 72 http://deb.debian.org/debian buster/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 libwebp6 arm64 0.6.1-2 [233 kB] Get: 74 http://deb.debian.org/debian buster/main arm64 libtiff5 arm64 4.1.0+git191117-2~deb10u1 [259 kB] Get: 75 http://deb.debian.org/debian buster/main arm64 libxpm4 arm64 1:3.5.12-1 [43.9 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 libgd3 arm64 2.2.5-5.2 [125 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 libgts-0.7-5 arm64 0.7.6+darcs121130-4 [125 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 libltdl7 arm64 2.4.6-9 [389 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 libfribidi0 arm64 1.0.5-3.1+deb10u1 [63.6 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 libthai-data all 0.1.28-2 [170 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 libdatrie1 arm64 0.2.12-2 [38.6 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 libthai0 arm64 0.1.28-2 [52.8 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 libpango-1.0-0 arm64 1.42.4-8~deb10u1 [179 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 libgraphite2-3 arm64 1.3.13-7 [75.8 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 libharfbuzz0b arm64 2.3.1-1 [1155 kB] Get: 86 http://deb.debian.org/debian buster/main arm64 libpangoft2-1.0-0 arm64 1.42.4-8~deb10u1 [65.7 kB] Get: 87 http://deb.debian.org/debian buster/main arm64 libpangocairo-1.0-0 arm64 1.42.4-8~deb10u1 [54.0 kB] Get: 88 http://deb.debian.org/debian buster/main arm64 libpathplan4 arm64 2.40.1-6 [61.9 kB] Get: 89 http://deb.debian.org/debian buster/main arm64 libxdot4 arm64 2.40.1-6 [57.0 kB] Get: 90 http://deb.debian.org/debian buster/main arm64 libgvc6 arm64 2.40.1-6 [590 kB] Get: 91 http://deb.debian.org/debian buster/main arm64 libgvpr2 arm64 2.40.1-6 [204 kB] Get: 92 http://deb.debian.org/debian buster/main arm64 lsb-base all 10.2019051400 [28.4 kB] Get: 93 http://deb.debian.org/debian buster/main arm64 x11-common all 1:7.7+19 [251 kB] Get: 94 http://deb.debian.org/debian buster/main arm64 libice6 arm64 2:1.0.9-2 [52.0 kB] Get: 95 http://deb.debian.org/debian buster/main arm64 liblab-gamut1 arm64 2.40.1-6 [220 kB] Get: 96 http://deb.debian.org/debian buster/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 97 http://deb.debian.org/debian buster/main arm64 libxt6 arm64 1:1.1.5-1+b3 [175 kB] Get: 98 http://deb.debian.org/debian buster/main arm64 libxmu6 arm64 2:1.1.2-2+b3 [57.8 kB] Get: 99 http://deb.debian.org/debian buster/main arm64 libxaw7 arm64 2:1.0.13-1+b2 [167 kB] Get: 100 http://deb.debian.org/debian buster/main arm64 graphviz arm64 2.40.1-6 [560 kB] Get: 101 http://deb.debian.org/debian buster/main arm64 help2man arm64 1.47.8 [177 kB] Get: 102 http://deb.debian.org/debian buster/main arm64 libbamtools2.5.1 arm64 2.5.1+dfsg-3 [149 kB] Get: 103 http://deb.debian.org/debian buster/main arm64 libbamtools-dev arm64 2.5.1+dfsg-3 [21.8 kB] Get: 104 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 105 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 106 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 107 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 108 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 109 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 110 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 111 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 112 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u2 [216 kB] Get: 113 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 114 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 115 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 116 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 117 http://deb.debian.org/debian buster/main arm64 libcurl3-gnutls arm64 7.64.0-4+deb10u1 [310 kB] Get: 118 http://deb.debian.org/debian buster/main arm64 libdeflate0 arm64 1.2-1 [51.4 kB] Get: 119 http://deb.debian.org/debian buster/main arm64 libhts2 arm64 1.9-11 [277 kB] Get: 120 http://deb.debian.org/debian buster/main arm64 libsparsehash-dev all 2.0.2-1 [76.9 kB] Get: 121 http://deb.debian.org/debian buster/main arm64 python-pysam arm64 0.15.2+ds-2 [1396 kB] Get: 122 http://deb.debian.org/debian buster/main arm64 python-ruffus all 2.8.1-4 [152 kB] Get: 123 http://deb.debian.org/debian buster/main arm64 samtools arm64 1.9-4 [424 kB] Get: 124 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 40.9 MB in 4s (10.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:arm64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_arm64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_arm64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:arm64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:arm64. Preparing to unpack .../14-libreadline7_7.0-5_arm64.deb ... Unpacking libreadline7:arm64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:arm64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:arm64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython2-stdlib:arm64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:arm64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython-stdlib:arm64 (2.7.16-1) ... Setting up libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20664 files and directories currently installed.) Preparing to unpack .../python_2.7.16-1_arm64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Setting up readline-common (7.0-5) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package gawk. (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 ... 20687 files and directories currently installed.) Preparing to unpack .../000-gawk_1%3a4.2.1+dfsg-1_arm64.deb ... Unpacking gawk (1:4.2.1+dfsg-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../001-liblocale-gettext-perl_1.07-3+b4_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../004-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../007-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../008-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../009-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../010-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../011-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../012-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../013-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../014-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../015-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../016-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../017-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../018-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../019-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../020-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../021-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../022-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../023-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../024-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../025-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../026-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 .../027-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../028-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../029-libpng16-16_1.6.36-6_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../030-libfreetype6_2.9.1-3+deb10u1_arm64.deb ... Unpacking libfreetype6:arm64 (2.9.1-3+deb10u1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../031-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../032-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../033-libfontconfig1_2.13.1-2_arm64.deb ... Unpacking libfontconfig1:arm64 (2.13.1-2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../034-fontconfig_2.13.1-2_arm64.deb ... Unpacking fontconfig (2.13.1-2) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../035-libpixman-1-0_0.36.0-1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.36.0-1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../036-libxau6_1%3a1.0.8-1+b2_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../037-libxdmcp6_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../038-libxcb1_1.13.1-2_arm64.deb ... Unpacking libxcb1:arm64 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../039-libx11-data_2%3a1.6.7-1_all.deb ... Unpacking libx11-data (2:1.6.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../040-libx11-6_2%3a1.6.7-1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.6.7-1) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../041-libxcb-render0_1.13.1-2_arm64.deb ... Unpacking libxcb-render0:arm64 (1.13.1-2) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../042-libxcb-shm0_1.13.1-2_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.13.1-2) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../043-libxext6_2%3a1.3.3-1+b2_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.3-1+b2) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../044-libxrender1_1%3a0.9.10-1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../045-libcairo2_1.16.0-4_arm64.deb ... Unpacking libcairo2:arm64 (1.16.0-4) ... Selecting previously unselected package libcdt5. Preparing to unpack .../046-libcdt5_2.40.1-6_arm64.deb ... Unpacking libcdt5 (2.40.1-6) ... Selecting previously unselected package libcgraph6. Preparing to unpack .../047-libcgraph6_2.40.1-6_arm64.deb ... Unpacking libcgraph6 (2.40.1-6) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../048-libjpeg62-turbo_1%3a1.5.2-2+b1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:1.5.2-2+b1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../049-libjbig0_2.1-3.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-3.1+b2) ... Selecting previously unselected package libwebp6:arm64. Preparing to unpack .../050-libwebp6_0.6.1-2_arm64.deb ... Unpacking libwebp6:arm64 (0.6.1-2) ... Selecting previously unselected package libtiff5:arm64. Preparing to unpack .../051-libtiff5_4.1.0+git191117-2~deb10u1_arm64.deb ... Unpacking libtiff5:arm64 (4.1.0+git191117-2~deb10u1) ... Selecting previously unselected package libxpm4:arm64. Preparing to unpack .../052-libxpm4_1%3a3.5.12-1_arm64.deb ... Unpacking libxpm4:arm64 (1:3.5.12-1) ... Selecting previously unselected package libgd3:arm64. Preparing to unpack .../053-libgd3_2.2.5-5.2_arm64.deb ... Unpacking libgd3:arm64 (2.2.5-5.2) ... Selecting previously unselected package libgts-0.7-5:arm64. Preparing to unpack .../054-libgts-0.7-5_0.7.6+darcs121130-4_arm64.deb ... Unpacking libgts-0.7-5:arm64 (0.7.6+darcs121130-4) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../055-libltdl7_2.4.6-9_arm64.deb ... Unpacking libltdl7:arm64 (2.4.6-9) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../056-libfribidi0_1.0.5-3.1+deb10u1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.5-3.1+deb10u1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../057-libthai-data_0.1.28-2_all.deb ... Unpacking libthai-data (0.1.28-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../058-libdatrie1_0.2.12-2_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.12-2) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../059-libthai0_0.1.28-2_arm64.deb ... Unpacking libthai0:arm64 (0.1.28-2) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../060-libpango-1.0-0_1.42.4-8~deb10u1_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.42.4-8~deb10u1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../061-libgraphite2-3_1.3.13-7_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.13-7) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../062-libharfbuzz0b_2.3.1-1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (2.3.1-1) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../063-libpangoft2-1.0-0_1.42.4-8~deb10u1_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.42.4-8~deb10u1) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../064-libpangocairo-1.0-0_1.42.4-8~deb10u1_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.42.4-8~deb10u1) ... Selecting previously unselected package libpathplan4. Preparing to unpack .../065-libpathplan4_2.40.1-6_arm64.deb ... Unpacking libpathplan4 (2.40.1-6) ... Selecting previously unselected package libxdot4. Preparing to unpack .../066-libxdot4_2.40.1-6_arm64.deb ... Unpacking libxdot4 (2.40.1-6) ... Selecting previously unselected package libgvc6. 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Unpacking libsm6:arm64 (2:1.2.3-1) ... Selecting previously unselected package libxt6:arm64. Preparing to unpack .../074-libxt6_1%3a1.1.5-1+b3_arm64.deb ... Unpacking libxt6:arm64 (1:1.1.5-1+b3) ... Selecting previously unselected package libxmu6:arm64. Preparing to unpack .../075-libxmu6_2%3a1.1.2-2+b3_arm64.deb ... Unpacking libxmu6:arm64 (2:1.1.2-2+b3) ... Selecting previously unselected package libxaw7:arm64. Preparing to unpack .../076-libxaw7_2%3a1.0.13-1+b2_arm64.deb ... Unpacking libxaw7:arm64 (2:1.0.13-1+b2) ... Selecting previously unselected package graphviz. Preparing to unpack .../077-graphviz_2.40.1-6_arm64.deb ... Unpacking graphviz (2.40.1-6) ... Selecting previously unselected package help2man. Preparing to unpack .../078-help2man_1.47.8_arm64.deb ... Unpacking help2man (1.47.8) ... Selecting previously unselected package libbamtools2.5.1:arm64. Preparing to unpack .../079-libbamtools2.5.1_2.5.1+dfsg-3_arm64.deb ... Unpacking libbamtools2.5.1:arm64 (2.5.1+dfsg-3) ... Selecting previously unselected package libbamtools-dev:arm64. Preparing to unpack .../080-libbamtools-dev_2.5.1+dfsg-3_arm64.deb ... Unpacking libbamtools-dev:arm64 (2.5.1+dfsg-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../081-libkeyutils1_1.6-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6-6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../082-libkrb5support0_1.17-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.17-3) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../083-libk5crypto3_1.17-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.17-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../084-libkrb5-3_1.17-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../085-libgssapi-krb5-2_1.17-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.17-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../086-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../087-libsasl2-2_2.1.27+dfsg-1+deb10u1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../088-libldap-common_2.4.47+dfsg-3+deb10u2_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libldap-2.4-2:arm64. Preparing to unpack .../089-libldap-2.4-2_2.4.47+dfsg-3+deb10u2_arm64.deb ... Unpacking libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../090-libnghttp2-14_1.36.0-2+deb10u1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../091-libpsl5_0.20.2-2_arm64.deb ... Unpacking libpsl5:arm64 (0.20.2-2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../092-librtmp1_2.4+20151223.gitfa8646d.1-2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../093-libssh2-1_1.8.0-2.1_arm64.deb ... Unpacking libssh2-1:arm64 (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:arm64. Preparing to unpack .../094-libcurl3-gnutls_7.64.0-4+deb10u1_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.64.0-4+deb10u1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../095-libdeflate0_1.2-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.2-1) ... Selecting previously unselected package libhts2:arm64. Preparing to unpack .../096-libhts2_1.9-11_arm64.deb ... Unpacking libhts2:arm64 (1.9-11) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../097-libsparsehash-dev_2.0.2-1_all.deb ... Unpacking libsparsehash-dev (2.0.2-1) ... Selecting previously unselected package python-pysam. Preparing to unpack .../098-python-pysam_0.15.2+ds-2_arm64.deb ... Unpacking python-pysam (0.15.2+ds-2) ... Selecting previously unselected package python-ruffus. Preparing to unpack .../099-python-ruffus_2.8.1-4_all.deb ... Unpacking python-ruffus (2.8.1-4) ... Selecting previously unselected package samtools. Preparing to unpack .../100-samtools_1.9-4_arm64.deb ... Unpacking samtools (1.9-4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../101-zlib1g-dev_1%3a1.2.11.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up libexpat1:arm64 (2.2.6-2+deb10u1) ... Setting up libpipeline1:arm64 (1.5.1-2) ... Setting up libxdot4 (2.40.1-6) ... Setting up libgraphite2-3:arm64 (1.3.13-7) ... Setting up libpixman-1-0:arm64 (0.36.0-1) ... Setting up lsb-base (10.2019051400) ... Setting up libxau6:arm64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:arm64 (1.6-6) ... Setting up libpsl5:arm64 (0.20.2-2) ... Setting up mime-support (3.62) ... Setting up libdatrie1:arm64 (0.2.12-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up gawk (1:4.2.1+dfsg-1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up liblab-gamut1 (2.40.1-6) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.36.0-2+deb10u1) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up libdeflate0:arm64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up m4 (1.4.18-2) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libsparsehash-dev (2.0.2-1) ... Setting up libjbig0:arm64 (2.1-3.1+b2) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up libkrb5support0:arm64 (1.17-3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up libgts-0.7-5:arm64 (0.7.6+darcs121130-4) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:arm64 (1:1.5.2-2+b1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libpathplan4 (2.40.1-6) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libfribidi0:arm64 (1.0.5-3.1+deb10u1) ... Setting up libbamtools2.5.1:arm64 (2.5.1+dfsg-3) ... Setting up libpng16-16:arm64 (1.6.36-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:arm64 (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libk5crypto3:arm64 (1.17-3) ... Setting up libltdl7:arm64 (2.4.6-9) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up autoconf (2.69-11) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libthai-data (0.1.28-2) ... Setting up libssh2-1:arm64 (1.8.0-2.1) ... Setting up libcdt5 (2.40.1-6) ... Setting up libkrb5-3:arm64 (1.17-3) ... Setting up libcgraph6 (2.40.1-6) ... Setting up libtiff5:arm64 (4.1.0+git191117-2~deb10u1) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libice6:arm64 (2:1.0.9-2) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libxcb1:arm64 (1.13.1-2) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up libxcb-render0:arm64 (1.13.1-2) ... Setting up libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u2) ... Setting up libxcb-shm0:arm64 (1.13.1-2) ... Setting up python2 (2.7.16-1) ... Setting up help2man (1.47.8) ... Setting up libthai0:arm64 (0.1.28-2) ... Setting up libpython-stdlib:arm64 (2.7.16-1) ... Setting up libfreetype6:arm64 (2.9.1-3+deb10u1) ... Setting up libbamtools-dev:arm64 (2.5.1+dfsg-3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:arm64 (1.17-3) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libgvpr2 (2.40.1-6) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libx11-6:arm64 (2:1.6.7-1) ... Setting up libharfbuzz0b:arm64 (2.3.1-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up python (2.7.16-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libxpm4:arm64 (1:3.5.12-1) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:arm64 (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:arm64 (7.64.0-4+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxt6:arm64 (1:1.1.5-1+b3) ... Setting up libfontconfig1:arm64 (2.13.1-2) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxmu6:arm64 (2:1.1.2-2+b3) ... Setting up libhts2:arm64 (1.9-11) ... Setting up po-debconf (1.0.21) ... Setting up libpango-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up libxaw7:arm64 (2:1.0.13-1+b2) ... Setting up libcairo2:arm64 (1.16.0-4) ... Setting up samtools (1.9-4) ... Setting up libgd3:arm64 (2.2.5-5.2) ... Setting up libpangoft2-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up libpangocairo-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up python-pysam (0.15.2+ds-2) ... Setting up libgvc6 (2.40.1-6) ... Setting up graphviz (2.40.1-6) ... Setting up python-ruffus (2.8.1-4) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.1.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/sga-0.10.15/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package sga dpkg-buildpackage: info: source version 0.10.15-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules build dh build --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=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-bamtools=/usr/ configure: WARNING: unrecognized options: --disable-maintainer-mode 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... no checking unordered_map presence... yes configure: WARNING: unordered_map: present but cannot be compiled configure: WARNING: unordered_map: check for missing prerequisite headers? configure: WARNING: unordered_map: see the Autoconf documentation configure: WARNING: unordered_map: section "Present But Cannot Be Compiled" configure: WARNING: unordered_map: proceeding with the compiler's result configure: WARNING: ## -------------------------------- ## configure: WARNING: ## Report this to js18@sanger.ac.uk ## configure: WARNING: ## -------------------------------- ## checking for unordered_map... no 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... no checking unordered_set presence... yes configure: WARNING: unordered_set: present but cannot be compiled configure: WARNING: unordered_set: check for missing prerequisite headers? configure: WARNING: unordered_set: see the Autoconf documentation configure: WARNING: unordered_set: section "Present But Cannot Be Compiled" configure: WARNING: unordered_set: proceeding with the compiler's result configure: WARNING: ## -------------------------------- ## configure: WARNING: ## Report this to js18@sanger.ac.uk ## configure: WARNING: ## -------------------------------- ## checking for unordered_set... no 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 configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/sga-0.10.15' dh_auto_build -O--sourcedirectory=src cd src && make -j8 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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o multiple_alignment.o multiple_alignment.cpp gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o bcr.o bcr.c g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o MurmurHash3.o MurmurHash3.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o count_min_sketch.o count_min_sketch.cpp MurmurHash3.cpp: In function 'void MurmurHash3_x86_32(const void*, int, uint32_t, void*)': MurmurHash3.cpp:132:14: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: k1 ^= tail[2] << 16; ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:133:3: note: here case 2: k1 ^= tail[1] << 8; ^~~~ MurmurHash3.cpp:133:14: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: k1 ^= tail[1] << 8; ~~~^~~~~~~~~~~~~~~ MurmurHash3.cpp:134:3: note: here 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=] case 15: k4 ^= tail[14] << 16; ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:208:3: note: here case 14: k4 ^= tail[13] << 8; ^~~~ MurmurHash3.cpp:208:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 14: k4 ^= tail[13] << 8; ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:209:3: note: here case 13: k4 ^= tail[12] << 0; ^~~~ MurmurHash3.cpp:210:56: warning: this statement may fall through [-Wimplicit-fallthrough=] k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4; ~~~^~~~~ MurmurHash3.cpp:212:3: note: here case 12: k3 ^= tail[11] << 24; ^~~~ MurmurHash3.cpp:212:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 12: k3 ^= tail[11] << 24; ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:213:3: note: here case 11: k3 ^= tail[10] << 16; ^~~~ MurmurHash3.cpp:213:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 11: k3 ^= tail[10] << 16; ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:214:3: note: here case 10: k3 ^= tail[ 9] << 8; ^~~~ MurmurHash3.cpp:214:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 10: k3 ^= tail[ 9] << 8; ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:215:3: note: here case 9: k3 ^= tail[ 8] << 0; ^~~~ MurmurHash3.cpp:216:56: warning: this statement may fall through [-Wimplicit-fallthrough=] k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3; ~~~^~~~~ MurmurHash3.cpp:218:3: note: here case 8: k2 ^= tail[ 7] << 24; ^~~~ MurmurHash3.cpp:218:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 8: k2 ^= tail[ 7] << 24; ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:219:3: note: here case 7: k2 ^= tail[ 6] << 16; ^~~~ MurmurHash3.cpp:219:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 7: k2 ^= tail[ 6] << 16; ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:220:3: note: here case 6: k2 ^= tail[ 5] << 8; ^~~~ MurmurHash3.cpp:220:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 6: k2 ^= tail[ 5] << 8; ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:221:3: note: here case 5: k2 ^= tail[ 4] << 0; ^~~~ MurmurHash3.cpp:222:56: warning: this statement may fall through [-Wimplicit-fallthrough=] k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2; ~~~^~~~~ MurmurHash3.cpp:224:3: note: here case 4: k1 ^= tail[ 3] << 24; ^~~~ MurmurHash3.cpp:224:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 4: k1 ^= tail[ 3] << 24; ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:225:3: note: here case 3: k1 ^= tail[ 2] << 16; ^~~~ MurmurHash3.cpp:225:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: k1 ^= tail[ 2] << 16; ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:226:3: note: here case 2: k1 ^= tail[ 1] << 8; ^~~~ MurmurHash3.cpp:226:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: k1 ^= tail[ 1] << 8; ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:227:3: note: here 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=] case 15: k2 ^= uint64_t(tail[14]) << 48; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:297:3: note: here case 14: k2 ^= uint64_t(tail[13]) << 40; ^~~~ MurmurHash3.cpp:297:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 14: k2 ^= uint64_t(tail[13]) << 40; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:298:3: note: here case 13: k2 ^= uint64_t(tail[12]) << 32; ^~~~ MurmurHash3.cpp:298:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 13: k2 ^= uint64_t(tail[12]) << 32; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:299:3: note: here case 12: k2 ^= uint64_t(tail[11]) << 24; ^~~~ MurmurHash3.cpp:299:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 12: k2 ^= uint64_t(tail[11]) << 24; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:300:3: note: here case 11: k2 ^= uint64_t(tail[10]) << 16; ^~~~ MurmurHash3.cpp:300:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 11: k2 ^= uint64_t(tail[10]) << 16; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:301:3: note: here case 10: k2 ^= uint64_t(tail[ 9]) << 8; ^~~~ MurmurHash3.cpp:301:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 10: k2 ^= uint64_t(tail[ 9]) << 8; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:302:3: note: here case 9: k2 ^= uint64_t(tail[ 8]) << 0; ^~~~ MurmurHash3.cpp:303:56: warning: this statement may fall through [-Wimplicit-fallthrough=] k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2; ~~~^~~~~ MurmurHash3.cpp:305:3: note: here case 8: k1 ^= uint64_t(tail[ 7]) << 56; ^~~~ MurmurHash3.cpp:305:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 8: k1 ^= uint64_t(tail[ 7]) << 56; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:306:3: note: here case 7: k1 ^= uint64_t(tail[ 6]) << 48; ^~~~ MurmurHash3.cpp:306:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 7: k1 ^= uint64_t(tail[ 6]) << 48; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:307:3: note: here case 6: k1 ^= uint64_t(tail[ 5]) << 40; ^~~~ MurmurHash3.cpp:307:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 6: k1 ^= uint64_t(tail[ 5]) << 40; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:308:3: note: here case 5: k1 ^= uint64_t(tail[ 4]) << 32; ^~~~ MurmurHash3.cpp:308:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 5: k1 ^= uint64_t(tail[ 4]) << 32; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:309:3: note: here case 4: k1 ^= uint64_t(tail[ 3]) << 24; ^~~~ MurmurHash3.cpp:309:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 4: k1 ^= uint64_t(tail[ 3]) << 24; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:310:3: note: here case 3: k1 ^= uint64_t(tail[ 2]) << 16; ^~~~ MurmurHash3.cpp:310:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 3: k1 ^= uint64_t(tail[ 2]) << 16; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:311:3: note: here case 2: k1 ^= uint64_t(tail[ 1]) << 8; ^~~~ MurmurHash3.cpp:311:15: warning: this statement may fall through [-Wimplicit-fallthrough=] case 2: k1 ^= uint64_t(tail[ 1]) << 8; ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:312:3: note: here case 1: k1 ^= uint64_t(tail[ 0]) << 0; ^~~~ bcr.c: In function 'ld_restore': bcr.c:183:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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] fread(&x, sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:189:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(ld->a[i], 8, x, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ overlapper.cpp:37:64: warning: missing initializer for member 'OverlapperParams::gap_s1_start' [-Wmissing-field-initializers] 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] 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] 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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libutil_a-ReadTable.o `test -f 'ReadTable.cpp' || echo './'`ReadTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libutil_a-Quality.o `test -f 'Quality.cpp' || echo './'`Quality.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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libutil_a-BitVector.o `test -f 'BitVector.cpp' || echo './'`BitVector.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libutil_a-KmerDistribution.o `test -f 'KmerDistribution.cpp' || echo './'`KmerDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libutil_a-MultiAlignment.o `test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libutil_a-VCFUtil.o `test -f 'VCFUtil.cpp' || echo './'`VCFUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libutil_a-BloomFilter.o `test -f 'BloomFilter.cpp' || echo './'`BloomFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp rm -f libutil.a ar cru libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-SGAStats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o libutil_a-VariantIndex.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libutil.a make[3]: Leaving directory '/build/sga-0.10.15/src/Util' Making all in SQG make[3]: Entering directory '/build/sga-0.10.15/src/SQG' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libbigraph_a-EdgeDesc.o `test -f 'EdgeDesc.cpp' || echo './'`EdgeDesc.cpp 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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libalgorithm_a-QCProcess.o `test -f 'QCProcess.cpp' || echo './'`QCProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libalgorithm_a-DPAlignment.o `test -f 'DPAlignment.cpp' || echo './'`DPAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libalgorithm_a-ConnectProcess.o `test -f 'ConnectProcess.cpp' || echo './'`ConnectProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libalgorithm_a-LRAlignment.o `test -f 'LRAlignment.cpp' || echo './'`LRAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libalgorithm_a-StringThreader.o `test -f 'StringThreader.cpp' || echo './'`StringThreader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libalgorithm_a-ExtensionDP.o `test -f 'ExtensionDP.cpp' || echo './'`ExtensionDP.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libalgorithm_a-GapFillProcess.o `test -f 'GapFillProcess.cpp' || echo './'`GapFillProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libalgorithm_a-VariationBuilderCommon.o `test -f 'VariationBuilderCommon.cpp' || echo './'`VariationBuilderCommon.cpp 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] struct ClusterNode ^~~~~~~~~~~ ReadCluster.h:17:8: warning: 'emptyNode.ClusterNode::isReverseInterval' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 -std=c++98 -O3 -c -o libalgorithm_a-KmerOverlaps.o `test -f 'KmerOverlaps.cpp' || echo './'`KmerOverlaps.cpp 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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libsuffixtools_a-BWTAlgorithms.o `test -f 'BWTAlgorithms.cpp' || echo './'`BWTAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libsuffixtools_a-BWTDiskConstruction.o `test -f 'BWTDiskConstruction.cpp' || echo './'`BWTDiskConstruction.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libsuffixtools_a-BWTReader.o `test -f 'BWTReader.cpp' || echo './'`BWTReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libsuffixtools_a-GapArray.o `test -f 'GapArray.cpp' || echo './'`GapArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libsuffixtools_a-SBWT.o `test -f 'SBWT.cpp' || echo './'`SBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libsuffixtools_a-RLBWT.o `test -f 'RLBWT.cpp' || echo './'`RLBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libsuffixtools_a-BWTWriterBinary.o `test -f 'BWTWriterBinary.cpp' || echo './'`BWTWriterBinary.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libsuffixtools_a-PopulationIndex.o `test -f 'PopulationIndex.cpp' || echo './'`PopulationIndex.cpp 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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libscaffold_a-ScaffoldSearch.o `test -f 'ScaffoldSearch.cpp' || echo './'`ScaffoldSearch.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libscaffold_a-ScaffoldWalk.o `test -f 'ScaffoldWalk.cpp' || echo './'`ScaffoldWalk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libgraphdiff_a-OverlapHaplotypeBuilder.o `test -f 'OverlapHaplotypeBuilder.cpp' || echo './'`OverlapHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libgraphdiff_a-StringHaplotypeBuilder.o `test -f 'StringHaplotypeBuilder.cpp' || echo './'`StringHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -std=c++98 -O3 -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o `test -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'`PairedDeBruijnHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libgraphdiff_a-HapgenUtil.o `test -f 'HapgenUtil.cpp' || echo './'`HapgenUtil.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] 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' for (std::list::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl; ^~~ DindelRealignWindow.cpp: In member function 'void DindelRealignWindow::computeHaplotypePairLikelihoods(std::vector&, std::tr1::unordered_map, std::__cxx11::list >&, const std::vector >&)': DindelRealignWindow.cpp:2589:12: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (int h1=0;h1&, const std::vector >&, double, int)': DindelRealignWindow.cpp:2743:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (size_t x=0;x&, const std::vector >&, double, int)': DindelRealignWindow.cpp:2906:13: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (size_t x=0;x 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] for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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] 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] 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:170:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:183:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:189:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:195:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:219:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:234:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:252:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:253:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:271:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:278:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:286:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:292:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:303:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:310:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:318:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:324:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:348:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:355:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:363:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:375:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:382:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:392:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:398:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:411:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:418:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:428:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' 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] RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro 'RAPIDJSON_DO_JOIN2' #define RAPIDJSON_DO_JOIN2(X, Y) X##Y ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro 'RAPIDJSON_DO_JOIN' #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:2: note: in expansion of macro 'RAPIDJSON_JOIN' RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:434:3: note: in expansion of macro 'RAPIDJSON_STATIC_ASSERT' RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 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] 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 -std=c++98 -O3 -c -o sga-rewrite-evidence-bam.o `test -f 'rewrite-evidence-bam.cpp' || echo './'`rewrite-evidence-bam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o sga-somatic-variant-filters.o `test -f 'somatic-variant-filters.cpp' || echo './'`somatic-variant-filters.cpp 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] 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 -std=c++98 -O3 -c -o sga-haplotype-filter.o `test -f 'haplotype-filter.cpp' || echo './'`haplotype-filter.cpp 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] 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 -std=c++98 -O3 -c -o sga-OverlapCommon.o `test -f 'OverlapCommon.cpp' || echo './'`OverlapCommon.cpp 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] for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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] for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -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 -j8 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 --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 -j8 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 \ 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_installinit -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_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src 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_0.10.15-4_arm64.deb'. dpkg-deb: building package 'sga' in '../sga_0.10.15-4_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sga_0.10.15-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4765 and its subdirectories I: Current time: Wed Aug 12 21:15:38 -12 2020 I: pbuilder-time-stamp: 1597310138