Thu Jan 5 19:20:58 UTC 2023 I: starting to build blasr/bullseye/amd64 on jenkins on '2023-01-05 19:20' Thu Jan 5 19:20:58 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_31/4427/console.log Thu Jan 5 19:20:58 UTC 2023 I: Downloading source for bullseye/blasr=5.3.3+dfsg-5 --2023-01-05 19:20:58-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/blasr/blasr_5.3.3%2bdfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2141 (2.1K) [text/prs.lines.tag] Saving to: ‘blasr_5.3.3+dfsg-5.dsc’ 0K .. 100% 172M=0s 2023-01-05 19:20:59 (172 MB/s) - ‘blasr_5.3.3+dfsg-5.dsc’ saved [2141/2141] Thu Jan 5 19:20:59 UTC 2023 I: blasr_5.3.3+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: blasr Binary: blasr Architecture: any Version: 5.3.3+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/blasr Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/blasr Vcs-Git: https://salsa.debian.org/med-team/blasr.git Build-Depends: debhelper-compat (= 13), python3, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev (>= 0.18.0~), libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-3~) Package-List: blasr deb science optional arch=any Checksums-Sha1: b6eb48681a0e989963740398298871f305a023ca 123932 blasr_5.3.3+dfsg.orig.tar.xz 808e3fcfca4729466e2616ab75c4157913fd8346 9648 blasr_5.3.3+dfsg-5.debian.tar.xz Checksums-Sha256: e58d4d1765998b0fd6935230d458142f2e3b73d67979c6d2ad6256685b984c81 123932 blasr_5.3.3+dfsg.orig.tar.xz 6f91207b059eabd1de460a11b971f06d713ddd3a8b94b2849bc43dd4d3c11f2c 9648 blasr_5.3.3+dfsg-5.debian.tar.xz Files: 5db2ee053065d0a8e3c0cf1315fae1cd 123932 blasr_5.3.3+dfsg.orig.tar.xz bc0d71bacecbaa5133e42046abeb3bdc 9648 blasr_5.3.3+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+ydpURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFfNw/+PgqNC852pDX5voTDAe9alEEjr25l4l/V Ol+UqkcM/RHeyLWWRGHXGBikCOtP3Rvjva6Xy7S7PSUH4B4GXT8r+uQtKCGihHka wQzNq1Pk2zfaaqhM+uKf+OI5uxSMdlIZW8aynVMS16qBo9yfpQ7TKPayxmvD4K+m xFVZoXO9XtdBIixytWkLSZp70goRmXBJBEeoPciA2GMBJ/w3oPBc0L/4v4dKbMBz G9FAsfOaUMvL055Z66fv3hH8rvyRP2KdMVDVeWFzmXWst4CqTkKYzuCsh76Vo5H0 SoLP3Vot+jcvKwmG/XcdHeo0QW8GthHNkTt7YS9fnK3ND1stx85Aed+lItO43n83 cYmL4uWM1g20zJWtYx750Qlc0OoI0FqgsFF6IMDK6m9gUpI3DbHIG07A7OD5P1Vg M1M9RzWODdzKLpkpaSgAa5x3Dyp/f64AusuM1vSQul+ZTW22d+g1cWJaRA4kHtmw 465qw0UBCfS46H2+OmSTBN9fvO1ilKnSBTi2zP/Zh+MtYoLU3xQo+ujpgijnz3gz S21pJYbV0XeRZ0OkxklMyTIM0bfShph5UZSvdl2MU0AENff110PweFP3IeCOy0T/ 0nrwA5rSTawl+ARypIn7Po7rU1qvHxLFLOPrVSJI9MInj3HASkrfGx08+EnTVugn C5W1P2FMOvg= =QpS1 -----END PGP SIGNATURE----- Thu Jan 5 19:20:59 UTC 2023 I: Checking whether the package is not for us Thu Jan 5 19:20:59 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Thu Jan 5 19:20:59 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Thu Jan 5 19:23:54 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 5 07:21:01 -12 2023 I: pbuilder-time-stamp: 1672946461 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [blasr_5.3.3+dfsg-5.dsc] I: copying [./blasr_5.3.3+dfsg.orig.tar.xz] I: copying [./blasr_5.3.3+dfsg-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.4DsjrquL/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 16 00:54:45 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./blasr_5.3.3+dfsg-5.dsc dpkg-source: info: extracting blasr in blasr-5.3.3+dfsg dpkg-source: info: unpacking blasr_5.3.3+dfsg.orig.tar.xz dpkg-source: info: unpacking blasr_5.3.3+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_pblibs.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3911120/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='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b57e2aaef4b544d190fd2dd2f2c1d5fd' 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='3911120' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/pbuilderrc_lpaX --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/b1 --logfile b1/build.log blasr_5.3.3+dfsg-5.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' I: uname -a Linux ionos11-amd64 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 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 Jan 20 2022 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 Jan 20 2022 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 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 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 Jan 20 2022 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 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 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 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 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 21:25 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 Jan 20 2022 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 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3911120/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev (>= 0.18.0~), libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-3~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19704 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on meson; however: Package meson is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbseq-dev; however: Package libpbseq-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbbam-dev (>= 0.18.0~); however: Package libpbbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbdata-dev; however: Package libpbdata-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbcopper-dev; however: Package libpbcopper-dev is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on libblasr-dev (>= 5.3.4+dfsg-3~); however: Package libblasr-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libblasr-dev{a} libblasr5.3.4{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgtest-dev{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts-dev{a} libhts3{a} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp24{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpbbam-dev{a} libpbbam1.6.0{a} libpbcopper-dev{a} libpbcopper1.8.0{a} libpbdata-dev{a} libpbihdf-dev{a} libpbseq-dev{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} meson{a} ninja-build{a} pkg-config{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3-pkg-resources{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 64.3 MB of archives. After unpacking 353 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u3 [693 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+deb11u1 [343 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u3 [345 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 googletest all 1.10.0.20201025-1.1 [629 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 hdf5-helpers amd64 1.10.6+repack-4+deb11u1 [40.4 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libaec-dev amd64 1.0.4-1 [18.7 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libhdf5-cpp-103-1 amd64 1.10.6+repack-4+deb11u1 [141 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u3 [342 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libpbcopper1.8.0 amd64 1.8.0+dfsg-2+b1 [452 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libpbbam1.6.0 amd64 1.6.0+dfsg-2 [687 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libblasr5.3.4 amd64 5.3.4+dfsg-3 [1098 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libpbcopper-dev amd64 1.8.0+dfsg-2+b1 [707 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libpbdata-dev amd64 5.3.4+dfsg-3 [41.0 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libblasr-dev amd64 5.3.4+dfsg-3 [2074 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+deb11u3 [433 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libdeflate-dev amd64 1.7-1 [46.9 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libgtest-dev amd64 1.10.0.20201025-1.1 [226 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libhdf5-fortran-102 amd64 1.10.6+repack-4+deb11u1 [105 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-100 amd64 1.10.6+repack-4+deb11u1 [81.8 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-fortran-100 amd64 1.10.6+repack-4+deb11u1 [56.8 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-cpp-100 amd64 1.10.6+repack-4+deb11u1 [37.7 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo-dev amd64 1:2.0.6-4 [278 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libjpeg-dev amd64 1:2.0.6-4 [67.8 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libhdf5-dev amd64 1.10.6+repack-4+deb11u1 [2438 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2.1~deb11u1 [229 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libhts-dev amd64 1.11-4 [3858 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libssl-dev amd64 1.1.1n-0+deb11u3 [1814 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libpbbam-dev amd64 1.6.0+dfsg-2 [87.2 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libpbihdf-dev amd64 5.3.4+dfsg-3 [47.5 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libpbseq-dev amd64 5.3.4+dfsg-3 [5220 B] Get: 100 http://deb.debian.org/debian bullseye/main amd64 ninja-build amd64 1.10.1-1 [112 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 meson all 0.56.2-1 [437 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Fetched 64.3 MB in 26s (2453 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19704 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20571 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20992 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../01-libncurses6_6.2+20201114-2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../02-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../03-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../04-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../06-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../08-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../09-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../15-cmake-data_3.18.4-2+deb11u1_all.deb ... Unpacking cmake-data (3.18.4-2+deb11u1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../16-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../17-libxml2_2.9.10+dfsg-6.7+deb11u3_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u3) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../18-libarchive13_3.4.3-2+deb11u1_amd64.deb ... Unpacking libarchive13:amd64 (3.4.3-2+deb11u1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../19-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../20-libsasl2-modules-db_2.1.27+dfsg-2.1+deb11u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../21-libsasl2-2_2.1.27+dfsg-2.1+deb11u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../22-libldap-2.4-2_2.4.57+dfsg-3+deb11u1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../23-libnghttp2-14_1.43.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../24-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../25-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../26-libssh2-1_1.9.0-2_amd64.deb ... Unpacking libssh2-1:amd64 (1.9.0-2) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../27-libcurl4_7.74.0-1.3+deb11u3_amd64.deb ... Unpacking libcurl4:amd64 (7.74.0-1.3+deb11u3) ... Selecting previously unselected package libjsoncpp24:amd64. Preparing to unpack .../28-libjsoncpp24_1.9.4-4_amd64.deb ... Unpacking libjsoncpp24:amd64 (1.9.4-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../29-librhash0_1.4.1-2_amd64.deb ... Unpacking librhash0:amd64 (1.4.1-2) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../30-libuv1_1.40.0-2_amd64.deb ... Unpacking libuv1:amd64 (1.40.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../31-cmake_3.18.4-2+deb11u1_amd64.deb ... Unpacking cmake (3.18.4-2+deb11u1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../32-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../33-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../34-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../35-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../36-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. 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Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libhdf5-fortran-102:amd64 (1.10.6+repack-4+deb11u1) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libpbbam1.6.0:amd64 (1.6.0+dfsg-2) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libblasr5.3.4 (5.3.4+dfsg-3) ... Setting up libblasr-dev (5.3.4+dfsg-3) ... Setting up libhdf5-dev (1.10.6+repack-4+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libpbbam-dev (1.6.0+dfsg-2) ... Setting up libpbihdf-dev (5.3.4+dfsg-3) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up libpbseq-dev (5.3.4+dfsg-3) ... Setting up meson (0.56.2-1) ... Processing triggers for libc-bin (2.31-13+deb11u5) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/blasr-5.3.3+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 > ../blasr_5.3.3+dfsg-5_source.changes dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.3+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson dh_auto_clean -O--buildsystem=meson dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary dh binary --buildsystem=meson dh_update_autotools_config -O--buildsystem=meson dh_autoreconf -O--buildsystem=meson debian/rules override_dh_auto_configure make[1]: Entering directory '/build/blasr-5.3.3+dfsg' LDFLAGS="-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5" CPPFLAGS="-isystem /usr/include/hdf5/serial" meson -Dtests=false -Dprefix=/usr build . The Meson build system Version: 0.56.2 Source dir: /build/blasr-5.3.3+dfsg Build dir: /build/blasr-5.3.3+dfsg/build Build type: native build Project name: blasr Project version: 5.3.3 Using 'CXXFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14' Using 'LDFLAGS' from environment with value: '-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5' Using 'CPPFLAGS' from environment with value: '-isystem /usr/include/hdf5/serial' C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Debian 10.2.1-6) 10.2.1 20210110") C++ linker for the host machine: c++ ld.bfd 2.35.2 Using 'CXXFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14' Using 'LDFLAGS' from environment with value: '-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5' Using 'CPPFLAGS' from environment with value: '-isystem /usr/include/hdf5/serial' Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency Boost found: YES 1.74.0 (/usr/include) Library pbbam found: YES Run-time dependency libblasr found: YES 5.3.4 Run-time dependency zlib found: YES 1.2.11 Library pbcopper found: YES Configuring BlasrVersion.h using configuration Build targets in project: 5 Found ninja-1.10.1 at /usr/bin/ninja make[1]: Leaving directory '/build/blasr-5.3.3+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/blasr-5.3.3+dfsg' ln -s build obj-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j15 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /build/blasr-5.3.3+dfsg @BLASR_GIT_SHA1@ '(.*)' /build/blasr-5.3.3+dfsg/git describe --always '--dirty=*' [2/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp [3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SAModify.cpp.o -MF libblasr_impl.a.p/extrautils_SAModify.cpp.o.d -o libblasr_impl.a.p/extrautils_SAModify.cpp.o -c ../extrautils/SAModify.cpp [4/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -MF libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o.d -o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -c ../extrautils/BuildSequenceDB.cpp [5/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -MF libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o.d -o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -c ../extrautils/SimpleShredder.cpp [6/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -MF libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o.d -o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -c ../extrautils/ExciseRepeats.cpp [7/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c ../extrautils/SuffixArrayToBWT.cpp In file included from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’: /usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 192 | charCount[0]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here 193 | case 0: //A | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 194 | charCount[1]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here 195 | case 1: //C | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 196 | charCount[2]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here 197 | case 2: //G | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 198 | charCount[3]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here 199 | case 3: //T | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 200 | charCount[4]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here 201 | case 4: //N | ^~~~ [8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -MF libblasr_impl.a.p/extrautils_SWMatcher.cpp.o.d -o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -c ../extrautils/SWMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/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/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from ../extrautils/SWMatcher.cpp:2: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [9/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -MF libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o.d -o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -c ../extrautils/BwtToSuffixArray.cpp [10/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -MF libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o.d -o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -c ../extrautils/PrintTupleCountTable.cpp [11/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_Evolve.cpp.o -MF libblasr_impl.a.p/extrautils_Evolve.cpp.o.d -o libblasr_impl.a.p/extrautils_Evolve.cpp.o -c ../extrautils/Evolve.cpp [12/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToM4.cpp.o -MF libblasr_impl.a.p/utils_SamToM4.cpp.o.d -o libblasr_impl.a.p/utils_SamToM4.cpp.o -c ../utils/SamToM4.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/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/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from ../utils/SamToM4.cpp:19: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [13/25] c++ -Isawriter.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ sawriter.p/utils_SAWriter.cpp.o -MF sawriter.p/utils_SAWriter.cpp.o.d -o sawriter.p/utils_SAWriter.cpp.o -c ../utils/SAWriter.cpp [14/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SDPMatcher.cpp.o -MF libblasr_impl.a.p/utils_SDPMatcher.cpp.o.d -o libblasr_impl.a.p/utils_SDPMatcher.cpp.o -c ../utils/SDPMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/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/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from ../utils/SDPMatcher.cpp:3: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [15/25] c++ -ItoAfg.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ toAfg.p/utils_ToAfg.cpp.o -MF toAfg.p/utils_ToAfg.cpp.o.d -o toAfg.p/utils_ToAfg.cpp.o -c ../utils/ToAfg.cpp In file included from ../utils/ToAfg.cpp:9: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ [16/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -MF libblasr_impl.a.p/utils_SamToCmpH5.cpp.o.d -o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -c ../utils/SamToCmpH5.cpp In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp:6, from /usr/include/pbseq/hdf/HDFCmpFile.hpp:12, from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:7, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:20: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/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/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from ../utils/SamToCmpH5.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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:79, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp: In instantiation of ‘unsigned int AlignmentSetToCmpH5Adapter::StoreRefGroup(std::string, T_CmpFile&) [with T_CmpFile = HDFCmpFile >; std::string = std::__cxx11::basic_string]’: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:136:31: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidate(AlignmentCandidate<>&, int, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:246:32: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidateList(std::vector >&, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ ../utils/SamToCmpH5.cpp:199:98: required from here /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:64:45: warning: implicitly-declared ‘RefGroupNameId& RefGroupNameId::operator=(const RefGroupNameId&)’ is deprecated [-Wdeprecated-copy] 64 | refNameToRefGroupNameandId[refName] = RefGroupNameId(refGroupName, refGroupId); In file included from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:28:5: note: because ‘RefGroupNameId’ has user-provided ‘RefGroupNameId::RefGroupNameId(const RefGroupNameId&)’ 28 | RefGroupNameId(const RefGroupNameId &rhs) | ^~~~~~~~~~~~~~ [17/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_PulseToFasta.cpp.o -MF libblasr_impl.a.p/utils_PulseToFasta.cpp.o.d -o libblasr_impl.a.p/utils_PulseToFasta.cpp.o -c ../utils/PulseToFasta.cpp In file included from ../utils/PulseToFasta.cpp:8: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ In file included from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/PulseToFasta.cpp:5: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: ../utils/PulseToFasta.cpp:157:41: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’ ../utils/PulseToFasta.cpp:157:41: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ [18/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamFilter.cpp.o -MF libblasr_impl.a.p/utils_SamFilter.cpp.o.d -o libblasr_impl.a.p/utils_SamFilter.cpp.o -c ../utils/SamFilter.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/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/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from ../utils/SamFilter.cpp:29: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [19/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -MF libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d -o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -c ../extrautils/StoreQualityByContextFromCmpH5.cpp In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:20: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/CmpFile.hpp:4, from ../extrautils/StoreQualityByContextFromCmpH5.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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [20/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_LoadPulses.cpp.o -MF libblasr_impl.a.p/utils_LoadPulses.cpp.o.d -o libblasr_impl.a.p/utils_LoadPulses.cpp.o -c ../utils/LoadPulses.cpp In file included from ../utils/LoadPulses.cpp:19: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:20: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:20: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:135:23: required from ‘DNALength T_HDFBasReader::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:680:59: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^ In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:20: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = unsigned char; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1525:62: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:20: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = char; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1537:64: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:20: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = short unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1547:76: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/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/bits/stl_tree.h:64, from /usr/include/c++/10/map:60, from ../utils/LoadPulses.cpp:6: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’ /usr/include/pbseq/hdf/HDFBasReader.hpp:135:23: required from ‘DNALength T_HDFBasReader::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:680:59: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^ [21/25] rm -f libblasr_impl.a && gcc-ar csrD libblasr_impl.a libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o libblasr_impl.a.p/extrautils_SAModify.cpp.o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o libblasr_impl.a.p/extrautils_SALS.cpp.o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o libblasr_impl.a.p/extrautils_Evolve.cpp.o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o libblasr_impl.a.p/utils_SamToM4.cpp.o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o libblasr_impl.a.p/utils_SDPMatcher.cpp.o libblasr_impl.a.p/utils_LoadPulses.cpp.o libblasr_impl.a.p/utils_PulseToFasta.cpp.o libblasr_impl.a.p/utils_SamFilter.cpp.o [22/25] c++ -o sawriter sawriter.p/utils_SAWriter.cpp.o -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so -lpbbam -lpbcopper -Wl,--end-group [23/25] c++ -o toAfg toAfg.p/utils_ToAfg.cpp.o -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so -lpbbam -lpbcopper -Wl,--end-group [24/25] c++ -Iblasr.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ blasr.p/Blasr.cpp.o -MF blasr.p/Blasr.cpp.o.d -o blasr.p/Blasr.cpp.o -c ../Blasr.cpp In file included from ../iblasr/BlasrMiscs.hpp:56, from ../iblasr/BlasrAlign.hpp:5, from ../Blasr.cpp:3: ../iblasr/BlasrMiscsImpl.hpp: In function ‘void MakeSubreadIntervals(std::vector&, std::vector&)’: ../iblasr/BlasrMiscsImpl.hpp:136:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 136 | for (auto subread : subreads) { | ^~~~~~~~ In file included from /usr/include/pbseq/pbdata/CCSSequence.hpp:5, from /usr/include/pbseq/alignment/files/CCSIterator.hpp:4, from ../iblasr/BlasrHeaders.h:57, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from ../iblasr/BlasrUtils.hpp:138, from ../iblasr/BlasrAlignImpl.hpp:4, from ../iblasr/BlasrAlign.hpp:67, from ../Blasr.cpp:3: ../iblasr/BlasrUtilsImpl.hpp: In function ‘void PrintAlignment(T_AlignmentCandidate&, SMRTSequence&, MappingParameters&, AlignmentContext&, std::ostream&, SMRTSequence&, PacBio::BAM::IRecordWriter*)’: ../iblasr/BlasrUtilsImpl.hpp:976:36: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=] 976 | } catch (std::ostream::failure f) { | ^ In file included from ../iblasr/MappingIPC.h:5, from ../iblasr/BlasrHeaders.h:99, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: ../iblasr/MappingParameters.h: In copy constructor ‘MappingParameters::MappingParameters(const MappingParameters&)’: ../iblasr/MappingParameters.h:19:7: warning: implicitly-declared ‘constexpr AnchorParameters::AnchorParameters(const AnchorParameters&)’ is deprecated [-Wdeprecated-copy] 19 | class MappingParameters | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:7, from ../iblasr/BlasrHeaders.h:42, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/anchoring/AnchorParameters.hpp:33:23: note: because ‘AnchorParameters’ has user-provided ‘AnchorParameters& AnchorParameters::operator=(const AnchorParameters&)’ 33 | AnchorParameters &operator=(const AnchorParameters &rhs); | ^~~~~~~~ ../Blasr.cpp: In function ‘void MapReadsNonCCS(MappingData >, FASTASequence, DNATuple>*, MappingBuffers&, SMRTSequence&, SMRTSequence&, std::vector&, MappingParameters&, const int&, ReadAlignments&, std::ofstream&)’: ../Blasr.cpp:382:49: note: synthesized method ‘MappingParameters::MappingParameters(const MappingParameters&)’ first required here 382 | MappingParameters sensitiveParams = params; | ^~~~~~ ../Blasr.cpp: In function ‘int main(int, char**)’: ../Blasr.cpp:1407:32: warning: cast between incompatible function types from ‘void (*)(MappingData >, FASTASequence, DNATuple>*)’ to ‘void* (*)(void*)’ [-Wcast-function-type] 1407 | (void *(*)(void *))MapReads, &mapdb[procIndex]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Blasr.cpp:1462:37: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 1462 | } catch (std::exception e) { | ^ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:167:25: required from ‘void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:953:65: required from here /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress] 27 | if (dynamic_cast(&read) == NULL) { | ^ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/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]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/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 | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/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); | ^~~~~~~~ /usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/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 /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/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/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from ../iblasr/BlasrHeaders.h:10, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /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)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/cassert:44, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:18, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlign.hpp:44, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:512:23: required from ‘int GuidedAlign(QSequence&, TSequence&, T_ScoreFn&, int, int, int, float, T_BufferCache&, blasr::Alignment&, AlignmentType, bool, int) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrAlignImpl.hpp:1450:93: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 97 | assert(matrixNElem >= 0); | ~~~~~~~~~~~~^~~~ In file included from /usr/include/c++/10/cassert:44, from /usr/include/pbseq/alignment/statistics/StatUtils.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:12, from /usr/include/pbseq/alignment/algorithms/alignment/AffineKBandAlign.hpp:9, from ../iblasr/BlasrHeaders.h:31, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrUtilsImpl.hpp:639:19: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:93: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ In file included from /usr/include/c++/10/cassert:44, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:18, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlign.hpp:44, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrUtilsImpl.hpp:689:32: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:93: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 97 | assert(matrixNElem >= 0); | ~~~~~~~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrUtilsImpl.hpp:698:32: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:93: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] In file included from /usr/include/c++/10/cassert:44, from /usr/include/pbseq/alignment/statistics/StatUtils.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:12, from /usr/include/pbseq/alignment/algorithms/alignment/AffineKBandAlign.hpp:9, from ../iblasr/BlasrHeaders.h:31, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/OneGapAlignment.hpp: In instantiation of ‘int OneGapAlign(T_QuerySequence&, T_RefSequence&, T_ScoreFunction&, T_BufferList&, blasr::Alignment&) [with T_QuerySequence = FASTQSequence; T_RefSequence = DNASequence; T_ScoreFunction = DistanceMatrixScoreFunction; T_BufferList = MappingBuffers]’: ../iblasr/BlasrAlignImpl.hpp:918:40: required from ‘void AlignIntervals(T_TargetSequence&, T_QuerySequence&, T_QuerySequence&, WeightedIntervalSet&, int (*)[5], int, int, int, int, SequenceIndexDatabase&, std::vector*>&, MappingParameters&, MappingBuffers&, int) [with T_TargetSequence = FASTASequence; T_QuerySequence = SMRTSequence; TDBSequence = FASTQSequence]’ ../iblasr/BlasrAlignImpl.hpp:280:23: required from ‘void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr&, T_TupleCountTable&, SequenceIndexDatabase&, MappingParameters&, MappingMetrics&, std::vector*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray >; T_TupleCountTable = TupleCountTable; BWT = Bwt; MappingIPC = MappingData >, FASTASequence, DNATuple>]’ ../Blasr.cpp:371:27: required from here /usr/include/pbseq/alignment/algorithms/alignment/OneGapAlignment.hpp:337:40: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 337 | assert(distanceBetweenLeftAndRight >= 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrAlignImpl.hpp:1301:38: required from ‘void PairwiseLocalAlign(T_Sequence&, T_RefSequence&, int, MappingParameters&, T_AlignmentCandidate&, MappingBuffers&, AlignmentType) [with T_RefSequence = DNASequence; T_Sequence = FASTQSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:873:27: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:93: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = QualityValueScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = QualityValueScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrAlignImpl.hpp:1310:38: required from ‘void PairwiseLocalAlign(T_Sequence&, T_RefSequence&, int, MappingParameters&, T_AlignmentCandidate&, MappingBuffers&, AlignmentType) [with T_RefSequence = DNASequence; T_Sequence = FASTQSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:873:27: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:93: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:5: warning: ‘nonnull’ argument ‘read’ compared to NULL [-Wnonnull-compare] 27 | if (dynamic_cast(&read) == NULL) { | ^~ [25/25] c++ -o blasr blasr.p/Blasr.cpp.o -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so -lpbbam -lpbcopper -Wl,--end-group make[1]: Leaving directory '/build/blasr-5.3.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/blasr-5.3.3+dfsg' echo Tests require data not available in the source distribution Tests require data not available in the source distribution make[1]: Leaving directory '/build/blasr-5.3.3+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson dh_prep -O--buildsystem=meson dh_auto_install -O--buildsystem=meson cd obj-x86_64-linux-gnu && DESTDIR=/build/blasr-5.3.3\+dfsg/debian/blasr LC_ALL=C.UTF-8 ninja install [1/4] Generating BlasrGitHash.h with a custom command [1/2] Installing files. Installing blasr to /build/blasr-5.3.3+dfsg/debian/blasr/usr/bin Installing sawriter to /build/blasr-5.3.3+dfsg/debian/blasr/usr/bin dh_install -O--buildsystem=meson dh_installdocs -O--buildsystem=meson dh_installchangelogs -O--buildsystem=meson dh_installman -O--buildsystem=meson dh_installsystemduser -O--buildsystem=meson dh_lintian -O--buildsystem=meson dh_perl -O--buildsystem=meson dh_link -O--buildsystem=meson dh_strip_nondeterminism -O--buildsystem=meson dh_compress -O--buildsystem=meson dh_fixperms -O--buildsystem=meson dh_missing -O--buildsystem=meson dh_dwz -a -O--buildsystem=meson dh_strip -a -O--buildsystem=meson dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -a -O--buildsystem=meson dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson dpkg-deb: building package 'blasr' in '../blasr_5.3.3+dfsg-5_amd64.deb'. dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3.3+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../blasr_5.3.3+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3911120 and its subdirectories I: Current time: Thu Jan 5 07:23:53 -12 2023 I: pbuilder-time-stamp: 1672946633 Thu Jan 5 19:23:54 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Jan 5 19:23:54 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Jan 5 19:26:42 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Thu Jan 5 19:26:42 UTC 2023 I: blasr_5.3.3+dfsg-5_amd64.changes: Format: 1.8 Date: Mon, 16 Nov 2020 13:51:01 +0100 Source: blasr Binary: blasr blasr-dbgsym Architecture: amd64 Version: 5.3.3+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: blasr - mapping single-molecule sequencing reads Changes: blasr (5.3.3+dfsg-5) unstable; urgency=medium . * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Repository, Repository-Browse. * Versioned Build-Depends: libblasr-dev (>= 5.3.4+dfsg-3~) since other Debian releases put header file on wrong location Checksums-Sha1: ec1dd539e12e74809824a82a96c089aa6d4114d1 3196888 blasr-dbgsym_5.3.3+dfsg-5_amd64.deb 3c6bcbbd81cdc20ba9d6624675ad0769d3acd349 7832 blasr_5.3.3+dfsg-5_amd64.buildinfo 2f2a89537a33aabf989d27bdca2141f5955c839e 222352 blasr_5.3.3+dfsg-5_amd64.deb Checksums-Sha256: 2336a5205e993ec56eb2fda10ac73a5df02f4a8e88892523d1f557e90af0f16a 3196888 blasr-dbgsym_5.3.3+dfsg-5_amd64.deb 1b7b3289cc57104a31445016063c6b5fffc7995d863161e10de2d7657c4f4a67 7832 blasr_5.3.3+dfsg-5_amd64.buildinfo be06da1f7950ae70a58da99a38129437af987ff164e08634adbff9ca2bd25716 222352 blasr_5.3.3+dfsg-5_amd64.deb Files: 891e40e65b80350390f42fd770dd64b5 3196888 debug optional blasr-dbgsym_5.3.3+dfsg-5_amd64.deb 927d1131ce9bebbf95b194760261e85a 7832 science optional blasr_5.3.3+dfsg-5_amd64.buildinfo f254986d1507c3526423f04fe4f08f43 222352 science optional blasr_5.3.3+dfsg-5_amd64.deb Thu Jan 5 19:26:43 UTC 2023 I: diffoscope 228 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/blasr_5.3.3+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/blasr_5.3.3+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/blasr_5.3.3+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/b1/blasr_5.3.3+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/b2/blasr_5.3.3+dfsg-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.250s) 0.250s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.046s) 0.045s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Thu Jan 5 19:26:44 UTC 2023 I: diffoscope 228 found no differences in the changes files, and a .buildinfo file also exists. Thu Jan 5 19:26:44 UTC 2023 I: blasr from bullseye built successfully and reproducibly on amd64. Thu Jan 5 19:26:46 UTC 2023 I: Submitting .buildinfo files to external archives: Thu Jan 5 19:26:46 UTC 2023 I: Submitting 12K b1/blasr_5.3.3+dfsg-5_amd64.buildinfo.asc Thu Jan 5 19:26:48 UTC 2023 I: Submitting 12K b2/blasr_5.3.3+dfsg-5_amd64.buildinfo.asc Thu Jan 5 19:26:49 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jan 5 19:26:49 UTC 2023 I: Done submitting .buildinfo files. Thu Jan 5 19:26:49 UTC 2023 I: Removing signed blasr_5.3.3+dfsg-5_amd64.buildinfo.asc files: removed './b1/blasr_5.3.3+dfsg-5_amd64.buildinfo.asc' removed './b2/blasr_5.3.3+dfsg-5_amd64.buildinfo.asc'