Diff of the two buildlogs: -- --- b1/build.log 2021-12-30 21:19:35.669958099 +0000 +++ b2/build.log 2021-12-30 21:22:13.069041254 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 30 09:16:54 -12 2021 -I: pbuilder-time-stamp: 1640899014 +I: Current time: Thu Feb 2 17:42:37 +14 2023 +I: pbuilder-time-stamp: 1675309357 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./pbseqlib_5.3.4+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.cvZ5QeyD/trustedkeys.kbx': General error -gpgv: Signature made Mon Nov 16 00:52:04 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.OoNu0MqF/trustedkeys.kbx': General error +gpgv: Signature made Tue Nov 17 02:52:04 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ dpkg-source: info: applying static+shared_lib.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1697420/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/826658/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/826658/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/826658/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,-fixfilepath parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6edd3395f7e54ac7866af6f2a93fb1b9' - 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='1697420' - PS1='# ' - PS2='> ' + INVOCATION_ID=13d9179507a54e918687d000edebb858 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=826658 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.wHzfHRc2Vk/pbuilderrc_5jnq --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wHzfHRc2Vk/b1 --logfile b1/build.log pbseqlib_5.3.4+dfsg-3.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.wHzfHRc2Vk/pbuilderrc_LItK --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wHzfHRc2Vk/b2 --logfile b2/build.log pbseqlib_5.3.4+dfsg-3.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more - -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 20 21:24 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/1697420/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 2021 more + -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount + -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Feb 2 17:42 sh -> bash + lrwxrwxrwx 1 root root 4 Jan 24 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 2021 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/826658/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -319,7 +353,7 @@ Get: 97 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 meson all 0.56.2-1 [437 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] -Fetched 61.0 MB in 2s (38.6 MB/s) +Fetched 61.0 MB in 1s (83.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) @@ -735,7 +769,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/pbseqlib-5.3.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pbseqlib_5.3.4+dfsg-3_source.changes +hostname: Name or service not known +I: Running cd /build/pbseqlib-5.3.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pbseqlib_5.3.4+dfsg-3_source.changes dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.4+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -797,13 +832,14 @@ Option buildtype is: plain [default: release] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build - cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j15 -v + cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j16 -v [1/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp ../hdf/HDFAttributable.cpp: In member function ‘int HDFAttributable::ContainsAttribute(const string&)’: ../hdf/HDFAttributable.cpp:48:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 48 | } catch (H5::Exception e) { | ^ -[2/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp +[2/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp +[3/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp ../hdf/HDFData.cpp: In member function ‘int HDFData::BaseInitializeDataset(H5::Group&, const string&)’: ../hdf/HDFData.cpp:37:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 37 | dataset = hdfFile.openDataSet(_datasetName.c_str()); @@ -824,7 +860,9 @@ /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ -[3/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp +[4/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp +[5/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp +[6/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: ../hdf/HDFFile.cpp:23:33: warning: catching polymorphic type ‘class H5::FileIException’ by value [-Wcatch-value=] 23 | } catch (FileIException e) { @@ -855,7 +893,7 @@ ../hdf/HDFFile.cpp:35:33: warning: catching polymorphic type ‘class H5::FileIException’ by value [-Wcatch-value=] 35 | } catch (FileIException fileException) { | ^~~~~~~~~~~~~ -[4/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp +[7/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp ../hdf/HDFGroup.cpp: In member function ‘int HDFGroup::Initialize(H5::Group&, std::string)’: ../hdf/HDFGroup.cpp:18:47: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 18 | group = fg.openGroup(groupName.c_str()); @@ -866,9 +904,7 @@ /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ -[5/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp -[6/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp -[7/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp +[8/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp ../hdf/BufferedHDF2DArray.cpp: In member function ‘void BufferedHDF2DArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]’: ../hdf/BufferedHDF2DArray.cpp:79:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 79 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ @@ -960,7 +996,6 @@ /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ -[8/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp [9/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::Create(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.cpp:9:92: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] @@ -1876,7 +1911,23 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[11/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp +[11/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp +[12/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp +In file included from ../hdf/BufferedHDFArray.hpp:217, + from ../hdf/HDFArray.hpp:9, + from ../hdf/HDFAlnGroupGroup.hpp:6, + from ../hdf/HDFAlnGroupGroup.cpp:1: +../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: +../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ +../hdf/HDFAlnGroupGroup.cpp:16:29: required from here +../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] + 146 | } catch (H5::DataSetIException e) { + | ^ +../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: +../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ +../hdf/HDFAlnGroupGroup.cpp:18:25: required from here +../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] +[13/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp ../hdf/BufferedHDFArray.cpp: In member function ‘void BufferedHDFArray::TypedCreate(H5::DataSpace&, H5::DSetCreatPropList&) [with T = int]’: ../hdf/BufferedHDFArray.cpp:64:88: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 64 | dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \ @@ -1978,25 +2029,70 @@ /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ -[12/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp -[13/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp -[14/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp -In file included from ../hdf/BufferedHDFArray.hpp:217, - from ../hdf/HDFArray.hpp:9, - from ../hdf/HDFAlnGroupGroup.hpp:6, - from ../hdf/HDFAlnGroupGroup.cpp:1: -../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: -../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ -../hdf/HDFAlnGroupGroup.cpp:16:29: required from here -../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] - 146 | } catch (H5::DataSetIException e) { - | ^ -../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: -../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ -../hdf/HDFAlnGroupGroup.cpp:18:25: required from here -../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] +[14/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp [15/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp -[16/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp +[16/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp +In file included from ../hdf/HDFScanDataReader.hpp:8, + from ../hdf/HDFPulseDataFile.hpp:10, + from ../hdf/HDFPulseDataFile.cpp:1: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/HDFPulseDataFile.hpp:7, + from ../hdf/HDFPulseDataFile.cpp:1: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +In file included from ../hdf/HDFScanDataReader.hpp:8, + from ../hdf/HDFPulseDataFile.hpp:10, + from ../hdf/HDFPulseDataFile.cpp:1: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/HDFPulseDataFile.hpp:7, + from ../hdf/HDFPulseDataFile.cpp:1: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +In file included from ../hdf/HDFScanDataReader.hpp:8, + from ../hdf/HDFPulseDataFile.hpp:10, + from ../hdf/HDFPulseDataFile.cpp:1: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/HDFPulseDataFile.hpp:7, + from ../hdf/HDFPulseDataFile.cpp:1: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +[17/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp +[18/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp +[19/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp +../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: +../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] + 44 | for (auto annotation : annotations) + | ^~~~~~~~~~~ +In file included from ../pbdata/reads/RegionTable.hpp:17, + from ../pbdata/SMRTSequence.hpp:14, + from ../hdf/HDFWriterBase.hpp:17, + from ../hdf/HDFRegionsWriter.hpp:13, + from ../hdf/HDFRegionsWriter.cpp:3: +../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ + 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) + | ^~~~~~~~~~~~~~~~ +[20/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: @@ -2072,7 +2168,22 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[17/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp +[21/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp +In file included from ../hdf/HDFRegionTableReader.hpp:11, + from ../hdf/HDFRegionTableReader.cpp:1: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:45:26: required from ‘int HDFAtom::Initialize(HDFData&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ +../hdf/HDFRegionTableReader.cpp:31:54: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/HDFRegionTableReader.hpp:7, + from ../hdf/HDFRegionTableReader.cpp:1: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +[22/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: @@ -2120,83 +2231,8 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[18/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp -[19/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp -../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: -../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] - 44 | for (auto annotation : annotations) - | ^~~~~~~~~~~ -In file included from ../pbdata/reads/RegionTable.hpp:17, - from ../pbdata/SMRTSequence.hpp:14, - from ../hdf/HDFWriterBase.hpp:17, - from ../hdf/HDFRegionsWriter.hpp:13, - from ../hdf/HDFRegionsWriter.cpp:3: -../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ - 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) - | ^~~~~~~~~~~~~~~~ -[20/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp -In file included from ../hdf/HDFScanDataReader.hpp:8, - from ../hdf/HDFPulseDataFile.hpp:10, - from ../hdf/HDFPulseDataFile.cpp:1: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFPulseDataFile.hpp:7, - from ../hdf/HDFPulseDataFile.cpp:1: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ -In file included from ../hdf/HDFScanDataReader.hpp:8, - from ../hdf/HDFPulseDataFile.hpp:10, - from ../hdf/HDFPulseDataFile.cpp:1: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFPulseDataFile.hpp:7, - from ../hdf/HDFPulseDataFile.cpp:1: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ -In file included from ../hdf/HDFScanDataReader.hpp:8, - from ../hdf/HDFPulseDataFile.hpp:10, - from ../hdf/HDFPulseDataFile.cpp:1: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFPulseDataFile.hpp:7, - from ../hdf/HDFPulseDataFile.cpp:1: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ -[21/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp -In file included from ../hdf/HDFRegionTableReader.hpp:11, - from ../hdf/HDFRegionTableReader.cpp:1: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:45:26: required from ‘int HDFAtom::Initialize(HDFData&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ -../hdf/HDFRegionTableReader.cpp:31:54: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFRegionTableReader.hpp:7, - from ../hdf/HDFRegionTableReader.cpp:1: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ -[22/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp -[23/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp +[23/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp +[24/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFArray.hpp:9, from ../hdf/HDFCmpExperimentGroup.hpp:10, @@ -2211,7 +2247,6 @@ ../hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = char]’ ../hdf/HDFCmpExperimentGroup.cpp:199:72: required from here ../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] -[24/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp [25/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp ../hdf/HDFBaseCallsWriter.cpp: In member function ‘virtual void HDFBaseCallsWriter::Close()’: ../hdf/HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] @@ -2244,40 +2279,10 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[26/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp -In file included from ../hdf/HDFWriterBase.hpp:13, - from ../hdf/HDFWriterBase.cpp:3: -../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFWriterBase.cpp:49:88: required from here -../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/BufferedHDF2DArray.hpp:8, - from ../hdf/HDFWriterBase.hpp:11, - from ../hdf/HDFWriterBase.cpp:3: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ -In file included from ../hdf/HDFWriterBase.hpp:13, - from ../hdf/HDFWriterBase.cpp:3: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/BufferedHDF2DArray.hpp:8, - from ../hdf/HDFWriterBase.hpp:11, - from ../hdf/HDFWriterBase.cpp:3: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ -[27/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp +[26/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp +[27/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp [28/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp -[29/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp -[30/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp +[29/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: @@ -2312,7 +2317,7 @@ /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[31/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp +[30/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: @@ -2350,8 +2355,38 @@ /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[32/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp -[33/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp +[31/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp +[32/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp +In file included from ../hdf/HDFWriterBase.hpp:13, + from ../hdf/HDFWriterBase.cpp:3: +../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFWriterBase.cpp:49:88: required from here +../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/BufferedHDF2DArray.hpp:8, + from ../hdf/HDFWriterBase.hpp:11, + from ../hdf/HDFWriterBase.cpp:3: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +In file included from ../hdf/HDFWriterBase.hpp:13, + from ../hdf/HDFWriterBase.cpp:3: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/BufferedHDF2DArray.hpp:8, + from ../hdf/HDFWriterBase.hpp:11, + from ../hdf/HDFWriterBase.cpp:3: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +[33/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp [34/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp [35/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, @@ -2394,50 +2429,7 @@ /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[36/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp -[37/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp -In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/KBandAlign.hpp:10, - from ../alignment/algorithms/alignment/KBandAlign.cpp:1: -../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: -/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ -/usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ -../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here -../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ - 103 | Alignment &operator=(const Alignment &rhs); - | ^~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] - 58 | class Alignment : public AlignmentStats - | ^~~~~~~~~ -In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, - from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/KBandAlign.hpp:10, - from ../alignment/algorithms/alignment/KBandAlign.cpp:1: -../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ - 19 | AlignmentStats &operator=(const AlignmentStats &rhs); - | ^~~~~~~~ -In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/KBandAlign.hpp:10, - from ../alignment/algorithms/alignment/KBandAlign.cpp:1: -../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, - from /usr/include/c++/10/bits/allocator.h:46, - from /usr/include/c++/10/vector:64, - from ../alignment/algorithms/alignment/KBandAlign.hpp:7, - from ../alignment/algorithms/alignment/KBandAlign.cpp:1: -/usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here - 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[38/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -c ../alignment/datastructures/alignment/AlignmentStats.cpp -[39/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp -[40/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp -[41/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -c ../alignment/datastructures/alignment/AlignmentMap.cpp -[42/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp +[36/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp In file included from ../hdf/BufferedHDFArray.hpp:217, from ../hdf/HDFZMWMetricsWriter.hpp:7, from ../hdf/HDFZMWMetricsWriter.cpp:3: @@ -2465,7 +2457,11 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[43/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp +[37/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -c ../alignment/datastructures/alignment/AlignmentStats.cpp +[38/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp +[39/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp +[40/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -c ../alignment/datastructures/alignment/AlignmentMap.cpp +[41/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: @@ -2507,8 +2503,48 @@ /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[44/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o -c ../alignment/datastructures/alignment/CmpFile.cpp -[45/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp +[42/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o -c ../alignment/datastructures/alignment/CmpFile.cpp +[43/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp +In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../alignment/algorithms/alignment/KBandAlign.hpp:10, + from ../alignment/algorithms/alignment/KBandAlign.cpp:1: +../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: +/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ +/usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ +../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here +../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ + 103 | Alignment &operator=(const Alignment &rhs); + | ^~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] + 58 | class Alignment : public AlignmentStats + | ^~~~~~~~~ +In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, + from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../alignment/algorithms/alignment/KBandAlign.hpp:10, + from ../alignment/algorithms/alignment/KBandAlign.cpp:1: +../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ + 19 | AlignmentStats &operator=(const AlignmentStats &rhs); + | ^~~~~~~~ +In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../alignment/algorithms/alignment/KBandAlign.hpp:10, + from ../alignment/algorithms/alignment/KBandAlign.cpp:1: +../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, + from /usr/include/c++/10/bits/allocator.h:46, + from /usr/include/c++/10/vector:64, + from ../alignment/algorithms/alignment/KBandAlign.hpp:7, + from ../alignment/algorithms/alignment/KBandAlign.cpp:1: +/usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here + 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[44/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp +[45/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp +[46/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp ../hdf/HDFPulseCallsWriter.cpp: In member function ‘virtual void HDFPulseCallsWriter::Close()’: ../hdf/HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type ‘class H5::Exception’ by value [-Wcatch-value=] 513 | } catch (H5::Exception e) { @@ -2573,56 +2609,11 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[46/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp -[47/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp -[48/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -c ../alignment/algorithms/sorting/MultikeyQuicksort.cpp -[49/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o -c ../alignment/files/BaseSequenceIO.cpp -[50/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp -In file included from ../hdf/BufferedHDFArray.hpp:217, - from ../hdf/HDFZMWWriter.hpp:11, - from ../hdf/HDFZMWWriter.cpp:5: -../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: -../hdf/HDFZMWWriter.cpp:149:26: required from here -../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] - 146 | } catch (H5::DataSetIException e) { - | ^ -../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: -../hdf/HDFZMWWriter.cpp:151:28: required from here -../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] -In file included from ../hdf/HDFWriterBase.hpp:13, - from ../hdf/HDFZMWWriter.hpp:12, - from ../hdf/HDFZMWWriter.cpp:5: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/BufferedHDF2DArray.hpp:8, - from ../hdf/HDFZMWWriter.hpp:10, - from ../hdf/HDFZMWWriter.cpp:5: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ -[51/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -c ../alignment/datastructures/alignment/AlignmentCandidate.cpp -[52/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -c ../alignment/datastructures/alignmentset/SAMQVConversion.cpp -[53/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp -[54/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -c ../alignment/datastructures/anchoring/AnchorParameters.cpp -[55/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o -c ../alignment/datastructures/anchoring/ClusterList.cpp -[56/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -c ../alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp -[57/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o -c ../alignment/datastructures/anchoring/MatchPos.cpp -[58/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o -c ../alignment/datastructures/alignment/Alignment.cpp -../alignment/datastructures/alignment/Alignment.cpp: In member function ‘void blasr::Alignment::CopyStats(blasr::Alignment&)’: -../alignment/datastructures/alignment/Alignment.cpp:35:47: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] - 35 | AlignmentStats::CopyStats((AlignmentStats)rhs); - | ^~~ -In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, - from ../alignment/datastructures/alignment/Alignment.cpp:2: -../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ - 19 | AlignmentStats &operator=(const AlignmentStats &rhs); - | ^~~~~~~~ -[59/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp +[47/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -c ../alignment/datastructures/alignment/AlignmentCandidate.cpp +[48/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o -c ../alignment/files/BaseSequenceIO.cpp +[49/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp +[50/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -c ../alignment/algorithms/sorting/MultikeyQuicksort.cpp +[51/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp In file included from /usr/include/c++/10/cassert:44, from ../pbdata/reads/RegionTypeMap.hpp:7, from ../pbdata/reads/RegionAnnotation.hpp:17, @@ -2711,13 +2702,55 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[60/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -c ../alignment/datastructures/anchoring/WeightedInterval.cpp +[52/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp +[53/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -c ../alignment/datastructures/alignmentset/SAMQVConversion.cpp +[54/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp +In file included from ../hdf/BufferedHDFArray.hpp:217, + from ../hdf/HDFZMWWriter.hpp:11, + from ../hdf/HDFZMWWriter.cpp:5: +../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: +../hdf/HDFZMWWriter.cpp:149:26: required from here +../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] + 146 | } catch (H5::DataSetIException e) { + | ^ +../hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: +../hdf/HDFZMWWriter.cpp:151:28: required from here +../hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] +In file included from ../hdf/HDFWriterBase.hpp:13, + from ../hdf/HDFZMWWriter.hpp:12, + from ../hdf/HDFZMWWriter.cpp:5: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/BufferedHDF2DArray.hpp:8, + from ../hdf/HDFZMWWriter.hpp:10, + from ../hdf/HDFZMWWriter.cpp:5: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +[55/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -c ../alignment/datastructures/anchoring/AnchorParameters.cpp +[56/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o -c ../alignment/datastructures/anchoring/ClusterList.cpp +[57/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o -c ../alignment/datastructures/alignment/Alignment.cpp +../alignment/datastructures/alignment/Alignment.cpp: In member function ‘void blasr::Alignment::CopyStats(blasr::Alignment&)’: +../alignment/datastructures/alignment/Alignment.cpp:35:47: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] + 35 | AlignmentStats::CopyStats((AlignmentStats)rhs); + | ^~~ +In file included from ../alignment/datastructures/alignment/Alignment.hpp:8, + from ../alignment/datastructures/alignment/Alignment.cpp:2: +../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ + 19 | AlignmentStats &operator=(const AlignmentStats &rhs); + | ^~~~~~~~ +[58/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -c ../alignment/datastructures/anchoring/WeightedInterval.cpp +[59/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -c ../alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp +[60/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o -c ../alignment/datastructures/anchoring/MatchPos.cpp [61/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp -[62/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -c ../alignment/datastructures/alignment/FilterCriteria.cpp -[63/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -MF libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -c ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -[64/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o -c ../alignment/format/SummaryPrinter.cpp -[65/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o -c ../alignment/files/CCSIterator.cpp -[66/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ 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-Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp +[64/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o -c ../alignment/format/CompareSequencesPrinter.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: @@ -2760,15 +2793,10 @@ /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[67/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp -[68/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o -MF libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o.d -o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o -c ../alignment/statistics/cdfs.cpp -[69/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ 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-Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o -MF libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o.d -o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o -c ../alignment/statistics/pdfs.cpp -[73/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o -c ../alignment/statistics/StatUtils.cpp -[74/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o -c ../alignment/utils/LogUtils.cpp -[75/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o -MF libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp +[65/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor 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libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -c ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp +[67/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o -c ../alignment/format/IntervalPrinter.cpp +[68/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o -MF libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp In file included from /usr/include/c++/10/cassert:44, from ../alignment/statistics/StatUtils.hpp:5, from ../alignment/simulator/CDFMap.hpp:8, @@ -2779,39 +2807,48 @@ ../alignment/simulator/CDFMap.hpp:37:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 37 | assert(cdf.size() >= 0); | ~~~~~~~~~~~^~~~ 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../pbdata/sam/ReadGroup.cpp +[106/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o -c ../pbdata/sam/SAMHeader.cpp +[107/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp +[108/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o -c ../pbdata/reads/RegionTypeMap.cpp +[109/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o -MF libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o -c ../pbdata/amos/AfgBasWriter.cpp +[110/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o -c ../pbdata/reads/RegionAnnotations.cpp ../pbdata/reads/RegionAnnotations.cpp: In constructor ‘RegionAnnotations::RegionAnnotations(UInt, const std::vector&, const std::vector&)’: ../pbdata/reads/RegionAnnotations.cpp:14:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 14 | for (auto annotation : annotations) { @@ -2881,30 +2918,61 @@ ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ -[109/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o -c ../pbdata/sam/ReferenceSequence.cpp -[110/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o -c ../pbdata/sam/SAMHeader.cpp -[111/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp -[112/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o -c ../pbdata/utils/BitUtils.cpp -[113/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o -MF libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o -c ../pbdata/reads/RegionTable.cpp -[114/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o -MF libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o.d -o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o -c ../alignment/utils/RegionUtils.cpp -[115/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ 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libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -c ../pbdata/StringUtils.cpp -[128/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp -[129/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o -MF libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o -c ../pbdata/CommandLineParser.cpp -[130/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp -[131/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp -[132/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp +[128/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp +[129/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp +[130/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp +[131/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o -MF libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o -c ../pbdata/CommandLineParser.cpp +[132/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp +[133/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -c ../unittest/pbdata/metagenome/TitleTable_gtest.cpp +[134/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp +In file included from ../pbdata/FASTAReader.hpp:7, + from ../pbdata/BlasrFASTAReader.cpp:2: +../pbdata/FASTASequence.hpp: In instantiation of ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = FASTASequence; _Args = {FASTASequence}]’: +/usr/include/c++/10/bits/stl_uninitialized.h:91:18: required from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; bool _TrivialValueTypes = false]’ +/usr/include/c++/10/bits/stl_uninitialized.h:150:15: required from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*]’ +/usr/include/c++/10/bits/stl_uninitialized.h:325:37: required from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; _Tp = FASTASequence]’ +/usr/include/c++/10/bits/stl_uninitialized.h:347:2: required from ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = std::allocator]’ +/usr/include/c++/10/bits/vector.tcc:659:48: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ +/usr/include/c++/10/bits/stl_vector.h:940:4: required from ‘void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ +../pbdata/BlasrFASTAReader.cpp:441:26: required from here +../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared ‘constexpr DNASequence::DNASequence(const DNASequence&)’ is deprecated [-Wdeprecated-copy] + 19 | class FASTASequence : public DNASequence + | ^~~~~~~~~~~~~ +In file included from ../pbdata/FASTASequence.hpp:13, + from ../pbdata/FASTAReader.hpp:7, + from ../pbdata/BlasrFASTAReader.cpp:2: +../pbdata/DNASequence.hpp:51:18: note: because ‘DNASequence’ has user-provided ‘DNASequence& DNASequence::operator=(const DNASequence&)’ + 51 | DNASequence &operator=(const DNASequence &rhs); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/alloc_traits.h:33, + from /usr/include/c++/10/ext/alloc_traits.h:34, + from /usr/include/c++/10/bits/basic_string.h:40, + from /usr/include/c++/10/string:55, + from ../pbdata/FASTAReader.hpp:5, + from ../pbdata/BlasrFASTAReader.cpp:2: +/usr/include/c++/10/bits/stl_construct.h:109:7: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here + 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[135/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp +[136/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp +[137/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, @@ -2965,41 +3033,9 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[133/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp -In file included from ../pbdata/FASTAReader.hpp:7, - from ../pbdata/BlasrFASTAReader.cpp:2: -../pbdata/FASTASequence.hpp: In instantiation of ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = FASTASequence; _Args = {FASTASequence}]’: -/usr/include/c++/10/bits/stl_uninitialized.h:91:18: required from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; bool _TrivialValueTypes = false]’ -/usr/include/c++/10/bits/stl_uninitialized.h:150:15: required from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*]’ -/usr/include/c++/10/bits/stl_uninitialized.h:325:37: required from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = FASTASequence*; _Tp = FASTASequence]’ -/usr/include/c++/10/bits/stl_uninitialized.h:347:2: required from ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = std::allocator]’ -/usr/include/c++/10/bits/vector.tcc:659:48: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ -/usr/include/c++/10/bits/stl_vector.h:940:4: required from ‘void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’ -../pbdata/BlasrFASTAReader.cpp:441:26: required from here -../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared ‘constexpr DNASequence::DNASequence(const DNASequence&)’ is deprecated [-Wdeprecated-copy] - 19 | class FASTASequence : public DNASequence - | ^~~~~~~~~~~~~ -In file included from ../pbdata/FASTASequence.hpp:13, - from ../pbdata/FASTAReader.hpp:7, - from ../pbdata/BlasrFASTAReader.cpp:2: -../pbdata/DNASequence.hpp:51:18: note: because ‘DNASequence’ has user-provided ‘DNASequence& DNASequence::operator=(const DNASequence&)’ - 51 | DNASequence &operator=(const DNASequence &rhs); - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/alloc_traits.h:33, - from /usr/include/c++/10/ext/alloc_traits.h:34, - from /usr/include/c++/10/bits/basic_string.h:40, - from /usr/include/c++/10/string:55, - from ../pbdata/FASTAReader.hpp:5, - from ../pbdata/BlasrFASTAReader.cpp:2: -/usr/include/c++/10/bits/stl_construct.h:109:7: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here - 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[134/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp -[135/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -c ../unittest/pbdata/metagenome/TitleTable_gtest.cpp -[136/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -c ../unittest/pbdata/saf/RefInfo_gtest.cpp -[137/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o -c ../pbdata/FASTQSequence.cpp -[138/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp -[139/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -c ../unittest/hdf/HDFScanDataReader_gtest.cpp +[138/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o -c ../pbdata/FASTQSequence.cpp +[139/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -c ../unittest/pbdata/saf/RefInfo_gtest.cpp +[140/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -c ../unittest/hdf/HDFScanDataReader_gtest.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: @@ -3045,7 +3081,6 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[140/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp [141/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o -MF libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o.d -o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o -c ../pbdata/SMRTSequence.cpp In file included from ../pbdata/SMRTSequence.cpp:3: ../pbdata/SMRTSequence.cpp: In member function ‘float SMRTSequence::HQRegionSnr(char) const’: @@ -3073,7 +3108,39 @@ | ^~~~~~~~~~~~ [142/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp [143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -c ../unittest/alignment/utils/RangeUtils_gtest.cpp -[144/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp +[144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -c ../unittest/alignment/utils/FileUtils_gtest.cpp +[145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp +In file included from ../hdf/HDFRegionTableReader.hpp:11, + from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/HDFRegionTableReader.hpp:7, + from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +[146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp +[147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp +In file included from ../hdf/HDFRegionTableReader.hpp:11, + from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/HDFRegionTableReader.hpp:7, + from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: +/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 33 | Attribute(const Attribute& original); + | ^~~~~~~~~ +[148/187] c++ -Ilibblasr.so.5.3.4.p -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp ../alignment/files/ReaderAgglomerate.cpp: In member function ‘int ReaderAgglomerate::Initialize(bool, bool)’: ../alignment/files/ReaderAgglomerate.cpp:267:37: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 267 | } catch (std::exception e) { @@ -3178,43 +3245,11 @@ ../alignment/files/ReaderAgglomerate.cpp:671:9: note: here 671 | case FileType::Fourbit: | ^~~~ -[145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -c ../unittest/alignment/utils/FileUtils_gtest.cpp -[146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp -[147/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -[148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp -[149/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp -In file included from ../hdf/HDFRegionTableReader.hpp:11, - from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFRegionTableReader.hpp:7, - from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ -[150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp -In file included from ../hdf/HDFRegionTableReader.hpp:11, - from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFRegionTableReader.hpp:7, - from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: -/usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 33 | Attribute(const Attribute& original); - | ^~~~~~~~~ +[149/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp +[150/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o [151/187] c++ -o libblasr.so.5.3.4 libblasr.so.5.3.4.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.4.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.4.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.4.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.4.p/hdf_HDFData.cpp.o libblasr.so.5.3.4.p/hdf_HDFFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.4.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.4.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.4.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.4.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.4.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.4.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.4.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.4.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.4.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.4.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.4.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.4.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.4.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.4.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.4.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.4.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.4.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.4.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.4.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.4.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.4.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.4.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.4.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.4.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.4.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.4.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.4.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.4.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.4.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.4.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.4.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.4.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.4.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.4.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.4.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.4.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.4.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.4.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.4.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.4.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.4.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.4.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.4.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.4.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.4.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.4.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.4.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.4.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.4.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.4.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.4.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.4.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.4.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.4.p/pbdata_StringUtils.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libblasr.so.5.3.4 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lrt /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -Wl,--end-group [152/187] /usr/bin/meson --internal symbolextractor /build/pbseqlib-5.3.4+dfsg/obj-x86_64-linux-gnu libblasr.so.5.3.4 libblasr.so.5.3.4 libblasr.so.5.3.4.p/libblasr.so.5.3.4.symbols -[153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMPrinter_gtest.cpp +[153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp [154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: @@ -3230,9 +3265,11 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp +[155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMPrinter_gtest.cpp [156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -c ../unittest/pbdata/saf/AlnGroup_gtest.cpp -[157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -c ../unittest/alignment/utils/RegionUtils_gtest.cpp +[157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -c ../unittest/pbdata/utils/SMRTTitle_gtest.cpp +[158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp +[159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -c ../unittest/alignment/utils/RegionUtils_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: @@ -3247,13 +3284,10 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -c ../unittest/pbdata/utils/SMRTTitle_gtest.cpp -[159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp -[160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp -[161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -c ../unittest/hdf/HDFZMWReader_gtest.cpp +[160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -c ../unittest/hdf/HDFZMWReader_gtest.cpp +[161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable 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unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -c ../unittest/pbdata/qvs/QualityValueVector_gtest.cpp -[163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -c ../unittest/pbdata/reads/ReadType_gtest.cpp -[164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -c ../unittest/hdf/HDFUtils_gtest.cpp +[163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -c ../unittest/hdf/HDFUtils_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: @@ -3272,13 +3306,17 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch 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-fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp -[171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 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-MF unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -c ../unittest/hdf/HDF2DArray_gtest.cpp +[165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -c ../unittest/pbdata/ScanData_gtest.cpp +[166/187] c++ -Iunittest/libblasr_unittest.p -Iunittest 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unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp +[170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -c ../unittest/pbdata/ChangeListID_gtest.cpp +[171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -c ../unittest/pbdata/defs_gtest.cpp +[172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -c ../unittest/pbdata/utils_gtest.cpp +[173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp +[174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -c ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: @@ -3333,10 +3371,7 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -c ../unittest/pbdata/defs_gtest.cpp -[173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -c ../unittest/pbdata/StringUtils_gtest.cpp -[174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp -[175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -c ../unittest/pbdata/utils_gtest.cpp +[175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -c ../unittest/pbdata/StringUtils_gtest.cpp [176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -c ../unittest/hdf/HDFPlsReader_gtest.cpp In file included from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: @@ -3391,38 +3426,28 @@ /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -c ../unittest/hdf/HDFCCSReader_gtest.cpp -In file included from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: -../hdf/HDFCCSReader.hpp: In instantiation of ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’: -../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here -../hdf/HDFCCSReader.hpp:270:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] - 270 | } catch (H5::DataSetIException e) { - | ^ -In file included from ../hdf/HDFCCSReader.hpp:4, - from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: +[177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -c ../unittest/pbdata/FASTQReader_gtest.cpp +[178/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp +In file included from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’: -../hdf/HDFCCSReader.hpp:217:51: required from ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’ -../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here +../unittest/hdf/HDFBasReader_gtest.cpp:47:27: required from here ../hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]’: ../hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’ -../hdf/HDFCCSReader.hpp:217:51: required from ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’ -../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here +../unittest/hdf/HDFBasReader_gtest.cpp:47:27: required from here ../hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFBasReader.hpp:14, - from ../hdf/HDFCCSReader.hpp:4, - from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: + from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = CCSSequence]’ -../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = CCSSequence]’ -../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = CCSSequence]’ -../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ -../hdf/HDFCCSReader.hpp:93:57: required from ‘int HDFCCSReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ -../unittest/hdf/HDFCCSReader_gtest.cpp:39:5: required from here +../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’ +../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = SMRTSequence]’ +../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = SMRTSequence]’ +../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string]’ +../unittest/hdf/HDFBasReader_gtest.cpp:33:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3430,14 +3455,12 @@ from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, - from ../hdf/HDFCCSReader.hpp:4, - from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: + from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, - from ../hdf/HDFCCSReader.hpp:4, - from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: + from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here @@ -3448,14 +3471,12 @@ from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, - from ../hdf/HDFCCSReader.hpp:4, - from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: + from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, - from ../hdf/HDFCCSReader.hpp:4, - from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: + from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here @@ -3466,34 +3487,42 @@ from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, - from ../hdf/HDFCCSReader.hpp:4, - from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: + from ../unittest/hdf/HDFBasReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[178/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -c ../unittest/pbdata/SeqUtils_gtest.cpp -[179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -c ../unittest/pbdata/FASTQReader_gtest.cpp -[180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp -In file included from ../unittest/hdf/HDFBasReader_gtest.cpp:22: +[179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -c ../unittest/hdf/HDFCCSReader_gtest.cpp +In file included from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: +../hdf/HDFCCSReader.hpp: In instantiation of ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’: +../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here +../hdf/HDFCCSReader.hpp:270:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] + 270 | } catch (H5::DataSetIException e) { + | ^ +In file included from ../hdf/HDFCCSReader.hpp:4, + from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’: -../unittest/hdf/HDFBasReader_gtest.cpp:47:27: required from here +../hdf/HDFCCSReader.hpp:217:51: required from ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’ +../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here ../hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ ../hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]’: ../hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]’ -../unittest/hdf/HDFBasReader_gtest.cpp:47:27: required from here +../hdf/HDFCCSReader.hpp:217:51: required from ‘int HDFCCSReader::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]’ +../unittest/hdf/HDFCCSReader_gtest.cpp:45:27: required from here ../hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ In file included from ../hdf/HDFBasReader.hpp:14, - from ../unittest/hdf/HDFBasReader_gtest.cpp:22: + from ../hdf/HDFCCSReader.hpp:4, + from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = SMRTSequence]’ -../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = SMRTSequence]’ -../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = SMRTSequence]’ -../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = SMRTSequence; std::string = std::__cxx11::basic_string]’ -../unittest/hdf/HDFBasReader_gtest.cpp:33:9: required from here +../hdf/HDFBasReader.hpp:273:40: required from ‘int T_HDFBasReader::InitializeForReadingBases() [with T_Sequence = CCSSequence]’ +../hdf/HDFBasReader.hpp:323:13: required from ‘int T_HDFBasReader::InitializeCommon() [with T_Sequence = CCSSequence]’ +../hdf/HDFBasReader.hpp:518:13: required from ‘int T_HDFBasReader::Initialize() [with T_Sequence = CCSSequence]’ +../hdf/HDFBasReader.hpp:581:26: required from ‘int T_HDFBasReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ +../hdf/HDFCCSReader.hpp:93:57: required from ‘int HDFCCSReader::Initialize(std::string, const H5::FileAccPropList&) [with T_Sequence = CCSSequence; std::string = std::__cxx11::basic_string]’ +../unittest/hdf/HDFCCSReader_gtest.cpp:39:5: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3501,12 +3530,14 @@ from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, - from ../unittest/hdf/HDFBasReader_gtest.cpp:22: + from ../hdf/HDFCCSReader.hpp:4, + from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, - from ../unittest/hdf/HDFBasReader_gtest.cpp:22: + from ../hdf/HDFCCSReader.hpp:4, + from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = float; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here @@ -3517,12 +3548,14 @@ from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, - from ../unittest/hdf/HDFBasReader_gtest.cpp:22: + from ../hdf/HDFCCSReader.hpp:4, + from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ In file included from ../hdf/HDFBasReader.hpp:14, - from ../unittest/hdf/HDFBasReader_gtest.cpp:22: + from ../hdf/HDFCCSReader.hpp:4, + from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here @@ -3533,15 +3566,16 @@ from ../hdf/HDFData.hpp:6, from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, - from ../unittest/hdf/HDFBasReader_gtest.cpp:22: + from ../hdf/HDFCCSReader.hpp:4, + from ../unittest/hdf/HDFCCSReader_gtest.cpp:22: /usr/include/hdf5/serial/H5Attribute.h:33:9: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 33 | Attribute(const Attribute& original); | ^~~~~~~~~ -[181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp +[180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -c ../unittest/pbdata/SeqUtils_gtest.cpp +[181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp [182/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -c ../unittest/pbdata/CCSSequence_gtest.cpp -[183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp -[184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp -[185/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -c ../unittest/pbdata/SMRTSequence_gtest.cpp +[183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp +[184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -c ../unittest/pbdata/SMRTSequence_gtest.cpp ../unittest/pbdata/SMRTSequence_gtest.cpp: In function ‘SMRTSequence _make_a_smrt_read_(const string&, const UInt&, DNALength, DNALength, const string&, bool, bool, bool, int, int, char, int, char)’: ../unittest/pbdata/SMRTSequence_gtest.cpp:66:12: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 66 | return smrt; @@ -3631,6 +3665,7 @@ /usr/include/c++/10/bits/stl_vector.h:625:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::allocator_type = std::allocator]’ 625 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +[185/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp [186/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -c ../unittest/pbdata/DNASequence_gtest.cpp [187/187] c++ -o unittest/libblasr_unittest unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -Wl,-z,relro -Wl,-z,now -Wl,--start-group libblasr.so.5.3.4 /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lrt /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libgtest_main.a -lpthread /usr/lib/x86_64-linux-gnu/libgtest.a -Wl,--end-group '-Wl,-rpath,$ORIGIN/..' -Wl,-rpath-link,/build/pbseqlib-5.3.4+dfsg/obj-x86_64-linux-gnu/ debian/rules override_dh_auto_test @@ -4008,12 +4043,12 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.4+dfsg-3_amd64.deb'. -dpkg-deb: building package 'libblasr5.3.4-dbgsym' in '../libblasr5.3.4-dbgsym_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libblasr5.3.4' in '../libblasr5.3.4_5.3.4+dfsg-3_amd64.deb'. +dpkg-deb: building package 'libblasr5.3.4-dbgsym' in '../libblasr5.3.4-dbgsym_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.4+dfsg-3_amd64.deb'. -dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.4+dfsg-3_amd64.deb'. dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.4+dfsg-3_amd64.deb'. +dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.4+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pbseqlib_5.3.4+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4021,12 +4056,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/826658/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/826658/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1697420 and its subdirectories -I: Current time: Thu Dec 30 09:19:35 -12 2021 -I: pbuilder-time-stamp: 1640899175 +I: removing directory /srv/workspace/pbuilder/826658 and its subdirectories +I: Current time: Thu Feb 2 17:45:13 +14 2023 +I: pbuilder-time-stamp: 1675309513