I: pbuilder: network access will be disabled during build I: Current time: Thu May 18 01:41:35 -12 2023 I: pbuilder-time-stamp: 1684417295 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mecat2_0.0+git20200428.f54c542+ds-3.dsc] I: copying [./mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz] I: copying [./mecat2_0.0+git20200428.f54c542+ds-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Dec 5 09:18:18 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mecat2_0.0+git20200428.f54c542+ds-3.dsc: no acceptable signature found dpkg-source: info: extracting mecat2 in mecat2-0.0+git20200428.f54c542+ds dpkg-source: info: unpacking mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz dpkg-source: info: unpacking mecat2_0.0+git20200428.f54c542+ds-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying modify_makefiles.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1670899/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='bba406c687b948af99009c9e7bb17769' 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='1670899' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ZS82QeyF/pbuilderrc_piRK --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZS82QeyF/b1 --logfile b1/build.log mecat2_0.0+git20200428.f54c542+ds-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1670899/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 19.6 MB of archives. After unpacking 73.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 19.6 MB in 1s (26.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../30-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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 I: Building the package I: Running cd /build/mecat2-0.0+git20200428.f54c542+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mecat2_0.0+git20200428.f54c542+ds-3_source.changes dpkg-buildpackage: info: source package mecat2 dpkg-buildpackage: info: source version 0.0+git20200428.f54c542+ds-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j15 clean make[1]: Entering directory '/build/mecat2-0.0+git20200428.f54c542+ds' cd src && make clean make[2]: Entering directory '/build/mecat2-0.0+git20200428.f54c542+ds/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Building for 'Linux' '5.10.0-23-amd64' as 'amd64' Makefile:401: warning: overriding recipe for target '../Linux-amd64/bin/mecat2cns' Makefile:401: warning: ignoring old recipe for target '../Linux-amd64/bin/mecat2cns' Makefile:418: warning: overriding recipe for target 'clean_mecat2cns' Makefile:418: warning: ignoring old recipe for target 'clean_mecat2cns' rm -f ../Linux-amd64/bin/libhbn.a ../Linux-amd64/obj/libhbn.a/corelib/build_db.[doP] ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.[doP] ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.[doP] ../Linux-amd64/obj/libhbn.a/corelib/db_format.[doP] ../Linux-amd64/obj/libhbn.a/corelib/fasta.[doP] ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.[doP] ../Linux-amd64/obj/libhbn.a/corelib/kstring.[doP] ../Linux-amd64/obj/libhbn.a/corelib/line_reader.[doP] ../Linux-amd64/obj/libhbn.a/corelib/m4_record.[doP] ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.[doP] ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.[doP] ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seqdb.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.[doP] ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.[doP] ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.[doP] ../Linux-amd64/obj/libhbn.a/algo/chain_dp.[doP] ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.[doP] ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.[doP] ../Linux-amd64/obj/libhbn.a/algo/kalloc.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.[doP] ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.[doP] ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.[doP] ../Linux-amd64/obj/libhbn.a/algo/word_finder.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.[doP] rm -f ../Linux-amd64/bin/mecat2pcan ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.[doP] rm -f ../Linux-amd64/bin/mecat2map ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_options.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.[doP] ../Linux-amd64/obj/mecat2map/app/map/main.[doP] ../Linux-amd64/obj/mecat2map/app/map/mecat_results.[doP] rm -f ../Linux-amd64/bin/mecat2cns ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.[doP] rm -f ../Linux-amd64/bin/mecat2viewdb ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.[doP] rm -f ../Linux-amd64/bin/mecat2lcr ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.[doP] rm -f ../Linux-amd64/bin/mecat2splitreads ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.[doP] rm -f ../Linux-amd64/bin/mecat2trimbases ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.[doP] rm -f ../Linux-amd64/bin/mecat2pm4 ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.[doP] rm -f ../Linux-amd64/bin/mecat2extseqs ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.[doP] rm -f ../Linux-amd64/bin/libfsa.a ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/logger.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/utility.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.[doP] rm -f ../Linux-amd64/bin/fsa_ol_filter ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.[doP] rm -f ../Linux-amd64/bin/fsa_assemble ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.[doP] rm -f ../Linux-amd64/bin/fsa_ctg_bridge ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.[doP] rm -f ../Linux-amd64/bin/fsa_rd_stat ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.[doP] ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.[doP] rm -f ../Linux-amd64/bin/mecat.pl rm -f ../Linux-amd64/bin/mecat.sh rm -f rm -f ../Linux-amd64/bin/Plgd/Grid.pm ../Linux-amd64/bin/Plgd/GridLsf.pm ../Linux-amd64/bin/Plgd/GridPbs.pm ../Linux-amd64/bin/Plgd/GridSge.pm ../Linux-amd64/bin/Plgd/GridSlurm.pm ../Linux-amd64/bin/Plgd/Project.pm ../Linux-amd64/bin/Plgd/Script.pm ../Linux-amd64/bin/Plgd/Utils.pm rm -rf ../Linux-amd64/bin/Plgd make[2]: Leaving directory '/build/mecat2-0.0+git20200428.f54c542+ds/src' make[1]: Leaving directory '/build/mecat2-0.0+git20200428.f54c542+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/mecat2-0.0+git20200428.f54c542+ds' cd src && make make[2]: Entering directory '/build/mecat2-0.0+git20200428.f54c542+ds/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Building for 'Linux' '5.10.0-23-amd64' as 'amd64' Makefile:401: warning: overriding recipe for target '../Linux-amd64/bin/mecat2cns' Makefile:401: warning: ignoring old recipe for target '../Linux-amd64/bin/mecat2cns' Makefile:418: warning: overriding recipe for target 'clean_mecat2cns' Makefile:418: warning: ignoring old recipe for target 'clean_mecat2cns' cp -pf pipeline/mecat.pl ../Linux-amd64/bin/mecat.pl chmod +x ../Linux-amd64/bin/mecat.pl cp -pf pipeline/mecat.sh ../Linux-amd64/bin/mecat.sh chmod +x ../Linux-amd64/bin/mecat.sh cp -pf pipeline/Plgd/Grid.pm ../Linux-amd64/bin/Plgd/Grid.pm cp -pf pipeline/Plgd/GridLsf.pm ../Linux-amd64/bin/Plgd/GridLsf.pm cp -pf pipeline/Plgd/GridPbs.pm ../Linux-amd64/bin/Plgd/GridPbs.pm cp -pf pipeline/Plgd/GridSge.pm ../Linux-amd64/bin/Plgd/GridSge.pm cp -pf pipeline/Plgd/GridSlurm.pm ../Linux-amd64/bin/Plgd/GridSlurm.pm cp -pf pipeline/Plgd/Project.pm ../Linux-amd64/bin/Plgd/Project.pm cp -pf pipeline/Plgd/Script.pm ../Linux-amd64/bin/Plgd/Script.pm cp -pf pipeline/Plgd/Utils.pm ../Linux-amd64/bin/Plgd/Utils.pm cc -o ../Linux-amd64/obj/libhbn.a/corelib/build_db.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/build_db.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/cmd_arg.c g++ -o ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/cstr_util.cpp cc -o ../Linux-amd64/obj/libhbn.a/corelib/db_format.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/db_format.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/fasta.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/fasta.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/gapped_candidate.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_aux.c corelib/hbn_aux.c: In function ‘hbn_get_cpu_count’: corelib/hbn_aux.c:357:9: warning: unused variable ‘allCPUNum_’ [-Wunused-variable] 357 | int allCPUNum_ = sysconf(_SC_NPROCESSORS_CONF); | ^~~~~~~~~~ cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_format.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_hit.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_package_version.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/kstring.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/kstring.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/line_reader.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/m4_record.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/name2id_map.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/partition_aux.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/raw_reads.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seqdb_summary.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seqdb.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seq_tag.c corelib/seq_tag.c:480:1: warning: ‘examine_ovlp_quality_perfect’ defined but not used [-Wunused-function] 480 | examine_ovlp_quality_perfect(int qoff, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ corelib/seq_tag.c:9:12: warning: ‘CircularSeq’ defined but not used [-Wunused-variable] 9 | static int CircularSeq = 0; | ^~~~~~~~~~~ corelib/seq_tag.c:7:12: warning: ‘RepeatSeq’ defined but not used [-Wunused-variable] 7 | static int RepeatSeq = 0; | ^~~~~~~~~ g++ -o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/seq_tag_report.cpp cc -o ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/small_object_alloc.c g++ -o ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/string2hsp.cpp cc -o ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/chain_dp.c algo/chain_dp.c: In function ‘find_best_kmer_match’: algo/chain_dp.c:164:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 164 | memset(t, 0, sizeof(int) * n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ algo/chain_dp.c: In function ‘chaining_find_candidates’: algo/chain_dp.c:257:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 257 | memset(t, 0, sizeof(int) * n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp algo/diff_gapalign.cpp algo/diff_gapalign.cpp:375:1: warning: ‘void dump_subseq(const u8*, int)’ defined but not used [-Wunused-function] 375 | dump_subseq(const u8* seq, int len) | ^~~~~~~~~~~ cc -o ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hash_list_bucket_sort.c cc -o ../Linux-amd64/obj/libhbn.a/algo/kalloc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/kalloc.c cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_extd2_sse.c cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_extz2_sse.c cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_wrapper.c cc -o ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hbn_lookup_table.c cc -o ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hbn_traceback_aux.c cc -o ../Linux-amd64/obj/libhbn.a/algo/word_finder.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/word_finder.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/c_ncbi_blast_aux.c g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/ncbi_blast_aux.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/blast_args.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/cmdline_flags.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/format_flags.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_allow.cpp ncbi_blast/cmdline_args/ncbiargs_allow.cpp:85:15: warning: ‘std::string ncbi::s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass)’ defined but not used [-Wunused-function] 85 | static string s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass symbol_class) | ^~~~~~~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_desc.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_types.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr_util.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/str_cmp.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/numeric_str_interconv.cpp ncbi_blast/str_util/numeric_str_interconv.cpp: In function ‘ncbi::SIZE_TYPE ns_hbnstr::DoubleToString_Ecvt(double, unsigned int, char*, ncbi::SIZE_TYPE, int*, int*)’: ncbi_blast/str_util/numeric_str_interconv.cpp:2175:20: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 0 and 15 bytes from a string of length 31 [-Wstringop-truncation] 2175 | strncpy(buffer,digits,digits_len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/str_util.cpp cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_encoding.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_hits.c ncbi_blast/setup/blast_hits.c:3897:1: warning: ‘s_TrimResultsByTotalHSPLimitEx’ defined but not used [-Wunused-function] 3897 | s_TrimResultsByTotalHSPLimitEx(BlastHSPResults* results, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbi_blast/setup/blast_hits.c:3815:1: warning: ‘s_TrimResultsByTotalHSPLimit’ defined but not used [-Wunused-function] 3815 | s_TrimResultsByTotalHSPLimit(BlastHSPResults* results, Uint4 total_hsp_limit) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbi_blast/setup/blast_hits.c:3580:12: warning: ‘s_SortHspWrapRawScore’ defined but not used [-Wunused-function] 3580 | static int s_SortHspWrapRawScore(const void *x, const void *y) | ^~~~~~~~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_message.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_options.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_stat.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_parameters.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_program.c g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/setup/blast_types.cpp cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/boost_erf.c g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/setup/hsp2string.cpp cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/ncbi_math.c In file included from ncbi_blast/setup/ncbi_math.c:498: ncbi_blast/setup/ncbi_erf.c: In function ‘s_IEEE754_Exp’: ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 40 | #define __LO(x) *(int*)&x | ^ ncbi_blast/setup/ncbi_erf.c:140:34: note: in expansion of macro ‘__LO’ 140 | if(((hx&0xfffff)|__LO(x))!=0) | ^~~~ ncbi_blast/setup/ncbi_erf.c: In function ‘BLAST_Erf’: ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 40 | #define __LO(x) *(int*)&x | ^ ncbi_blast/setup/ncbi_erf.c:401:9: note: in expansion of macro ‘__LO’ 401 | __LO(z) = 0; | ^~~~ ncbi_blast/setup/ncbi_erf.c: In function ‘BLAST_ErfC’: ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 40 | #define __LO(x) *(int*)&x | ^ ncbi_blast/setup/ncbi_erf.c:462:13: note: in expansion of macro ‘__LO’ 462 | __LO(z) = 0; | ^~~~ cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_query_info.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_sequence_blk.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/gapinfo.c ar rv ../Linux-amd64/bin/libhbn.a ../Linux-amd64/obj/libhbn.a/corelib/build_db.o ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o ../Linux-amd64/obj/libhbn.a/corelib/db_format.o ../Linux-amd64/obj/libhbn.a/corelib/fasta.o ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o ../Linux-amd64/obj/libhbn.a/corelib/kstring.o ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o ../Linux-amd64/obj/libhbn.a/algo/kalloc.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o ../Linux-amd64/obj/libhbn.a/algo/word_finder.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o ar: creating ../Linux-amd64/bin/libhbn.a a - ../Linux-amd64/obj/libhbn.a/corelib/build_db.o a - ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o a - ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o a - ../Linux-amd64/obj/libhbn.a/corelib/db_format.o a - ../Linux-amd64/obj/libhbn.a/corelib/fasta.o a - ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o a - ../Linux-amd64/obj/libhbn.a/corelib/kstring.o a - ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o a - ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o a - ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o a - ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o a - ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o a - ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o a - ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o a - ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o a - ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o a - ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o a - ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o a - ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o a - ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o a - ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o a - ../Linux-amd64/obj/libhbn.a/algo/kalloc.o a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o a - ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o a - ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o a - ../Linux-amd64/obj/libhbn.a/algo/word_finder.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o cc -o ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2pcan app/mecat2pcan/pcan.c cc -o ../Linux-amd64/bin/mecat2pcan -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/map app/map/cmdline_args.cpp app/map/cmdline_args.cpp:74:20: warning: ‘ncbi::kGroupExtension’ defined but not used [-Wunused-variable] 74 | static const char* kGroupExtension = "Extension options"; | ^~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_align_one_volume.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_build_seqdb.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_extend_subseq_hit.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_find_subseq_hit.c In function ‘group_subject_init_hits’, inlined from ‘find_candidate_subject_subseqs’ at app/map/hbn_find_subseq_hit.c:151:22: app/map/hbn_find_subseq_hit.c:39:51: warning: argument 1 range [18446743953450467328, 18446744073709551560] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 39 | HbnInitHit* tmp_init_hit_array = (HbnInitHit*)malloc(sizeof(HbnInitHit) * init_hit_count); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from app/map/../../ncbi_blast/setup/../../corelib/kstring.h:29, from app/map/../../ncbi_blast/setup/../../corelib/hbn_aux.h:11, from app/map/../../ncbi_blast/setup/../c_ncbi_blast_aux.h:4, from app/map/../../ncbi_blast/setup/blast_message.h:40, from app/map/../../ncbi_blast/setup/blast_options.h:46, from app/map/hbn_options.h:4, from app/map/hbn_find_subseq_hit.h:4, from app/map/hbn_find_subseq_hit.c:1: /usr/include/stdlib.h: In function ‘find_candidate_subject_subseqs’: /usr/include/stdlib.h:553:14: note: in a call to allocation function ‘malloc’ declared here 553 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_job_control.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_options.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_subseq_hit.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_task_struct.c cc -o ../Linux-amd64/obj/mecat2map/app/map/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/main.c cc -o ../Linux-amd64/obj/mecat2map/app/map/mecat_results.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/mecat_results.c g++ -o ../Linux-amd64/bin/mecat2map -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.o ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.o ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.o ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.o ../Linux-amd64/obj/mecat2map/app/map/hbn_options.o ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.o ../Linux-amd64/obj/mecat2map/app/map/main.o ../Linux-amd64/obj/mecat2map/app/map/mecat_results.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_aux.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_one_part.c g++ -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_one_read.cpp app/mecat2cns/cns_one_read.cpp: In function ‘BOOL meap_consensus_one_segment(FCCnsData*, int*, int*, int, int, kstring_t*)’: app/mecat2cns/cns_one_read.cpp:34:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 34 | if (ks_size(*cns_seq) < min_size) return FALSE; In file included from app/mecat2cns/cns_one_read.h:4, from app/mecat2cns/cns_one_read.cpp:1: app/mecat2cns/cns_one_read.cpp: In function ‘void consensus_one_read(CnsThreadData*, int)’: app/mecat2cns/cns_one_read.cpp:242:32: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 242 | hbn_assert(read_length == kv_size(*fwd_read_v)); app/mecat2cns/../../corelib/hbn_aux.h:115:15: note: in definition of macro ‘__hbn_assert’ 115 | if (!(expr)) { \ | ^~~~ app/mecat2cns/cns_one_read.cpp:242:9: note: in expansion of macro ‘hbn_assert’ 242 | hbn_assert(read_length == kv_size(*fwd_read_v)); | ^~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_options.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns_align_tag.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns_aux.c app/mecat2cns/fccns_aux.c: In function ‘consensus_backbone_segment’: app/mecat2cns/fccns_aux.c:137:9: warning: variable ‘g_best_ck’ set but not used [-Wunused-but-set-variable] 137 | int g_best_ck = 0; | ^~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/hbn_task_struct.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/main.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/raw_reads_reader.c g++ -o ../Linux-amd64/bin/mecat2cns -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/hbndb app/hbndb/viewhbndb.c cc -o ../Linux-amd64/bin/mecat2viewdb -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/largest_cover_range.c cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/main.c cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/common/range_list.c cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/common/m4_aux.c g++ -o ../Linux-amd64/bin/mecat2lcr -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/main.c cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/split_reads.c cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/range_list.c cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/m4_aux.c g++ -o ../Linux-amd64/bin/mecat2splitreads -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/3_trim_bases app/mecat2trim/3_trim_bases/main.c cc -o ../Linux-amd64/bin/mecat2trimbases -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2pm4 app/mecat2pm4/main.c cc -o ../Linux-amd64/bin/mecat2pm4 -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2extseqs -Iapp/mecat2extseqs/libboost app/mecat2extseqs/main.c cc -o ../Linux-amd64/bin/mecat2extseqs -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/argument_parser.cpp cc -o ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/fsa app/fsa/getopt.c g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/logger.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/read_store.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/sequence.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/utility.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fasta_reader.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fastq_reader.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_store.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/simple_align.cpp app/fsa/simple_align.cpp: In member function ‘SimpleAlign::Result SimpleAlign::Align(const std::string&, const std::string&, int, bool)’: app/fsa/simple_align.cpp:153:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 153 | if ( node.x + node.len >= query.size() || node.y + node.len >= target_.size()) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ app/fsa/simple_align.cpp:153:75: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 153 | if ( node.x + node.len >= query.size() || node.y + node.len >= target_.size()) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_filter.cpp app/fsa/overlap_filter.cpp: In member function ‘void OverlapFilter::FilterLocalStep(Seq::Id, const std::unordered_map&)’: app/fsa/overlap_filter.cpp:413:18: warning: unused variable ‘loc’ [-Wunused-variable] 413 | auto loc = o.Location(max_overhang_); | ^~~ app/fsa/overlap_filter.cpp:447:22: warning: unused variable ‘loc’ [-Wunused-variable] 447 | auto loc = o.Location(max_overhang_); | ^~~ g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_stat.cpp ar rv ../Linux-amd64/bin/libfsa.a ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o ar: creating ../Linux-amd64/bin/libfsa.a a - ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o g++ -o ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_ol_filter.cpp g++ -o ../Linux-amd64/bin/fsa_ol_filter -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_assemble.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/assembly.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/graph.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/string_graph.cpp app/fsa/string_graph.cpp: In member function ‘std::vector StringNode::GetAllOutNodes()’: app/fsa/string_graph.cpp:39:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 39 | return std::move(nodes); | ~~~~~~~~~^~~~~~~ app/fsa/string_graph.cpp:39:21: note: remove ‘std::move’ call app/fsa/string_graph.cpp: In member function ‘std::vector StringNode::GetAllInNodes()’: app/fsa/string_graph.cpp:49:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 49 | return std::move(nodes); | ~~~~~~~~~^~~~~~~ app/fsa/string_graph.cpp:49:21: note: remove ‘std::move’ call g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/path_graph.cpp g++ -o ../Linux-amd64/bin/fsa_assemble -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.o ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.o ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.o ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.o ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_ctg_bridge.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_bridge.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_graph.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_link.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_link_store.cpp g++ -o ../Linux-amd64/bin/fsa_ctg_bridge -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_rd_stat.cpp g++ -o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/read_stat.cpp g++ -o ../Linux-amd64/bin/fsa_rd_stat -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp make[2]: Leaving directory '/build/mecat2-0.0+git20200428.f54c542+ds/src' make[1]: Leaving directory '/build/mecat2-0.0+git20200428.f54c542+ds' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/mecat2/ debian/rules override_dh_install make[1]: Entering directory '/build/mecat2-0.0+git20200428.f54c542+ds' dh_install sed 's/\#\!\/usr\/bin\/env perl/\#\!\/usr\/bin\/perl/' \ debian/mecat2/usr/bin/mecat.pl > debian/mecat2/usr/bin/mecat rm -f debian/mecat2/usr/bin/mecat.pl make[1]: Leaving directory '/build/mecat2-0.0+git20200428.f54c542+ds' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/mecat2/usr/bin/fsa_assemble: .debug_info section not present dwz: debian/mecat2/usr/bin/fsa_ctg_bridge: .debug_info section not present dwz: debian/mecat2/usr/bin/fsa_ol_filter: .debug_info section not present dwz: debian/mecat2/usr/bin/fsa_rd_stat: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2cns: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2extseqs: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2lcr: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2map: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2pcan: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2pm4: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2splitreads: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2trimbases: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2viewdb: .debug_info section not present dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mecat2-dbgsym' in '../mecat2-dbgsym_0.0+git20200428.f54c542+ds-3_amd64.deb'. dpkg-deb: building package 'mecat2' in '../mecat2_0.0+git20200428.f54c542+ds-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../mecat2_0.0+git20200428.f54c542+ds-3_amd64.buildinfo dpkg-genchanges --build=binary -O../mecat2_0.0+git20200428.f54c542+ds-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1670899 and its subdirectories I: Current time: Thu May 18 01:51:45 -12 2023 I: pbuilder-time-stamp: 1684417905