Wed Dec 11 00:06:43 UTC 2024 I: starting to build blasr/unstable/amd64 on jenkins on '2024-12-11 00:06' Wed Dec 11 00:06:43 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/26049/console.log Wed Dec 11 00:06:43 UTC 2024 I: Downloading source for unstable/blasr=5.3.5+dfsg-7 --2024-12-11 00:06:43-- http://deb.debian.org/debian/pool/main/b/blasr/blasr_5.3.5%2bdfsg-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2155 (2.1K) [text/prs.lines.tag] Saving to: ‘blasr_5.3.5+dfsg-7.dsc’ 0K .. 100% 346M=0s 2024-12-11 00:06:43 (346 MB/s) - ‘blasr_5.3.5+dfsg-7.dsc’ saved [2155/2155] Wed Dec 11 00:06:43 UTC 2024 I: blasr_5.3.5+dfsg-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: blasr Binary: blasr Architecture: any Version: 5.3.5+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/blasr Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/blasr Vcs-Git: https://salsa.debian.org/med-team/blasr.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), python3:any, meson, cmake, pkgconf, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.5+dfsg-9~) Package-List: blasr deb science optional arch=any Checksums-Sha1: 334132438305cfaf3d7ee6208bcb4cc4b493be5d 124460 blasr_5.3.5+dfsg.orig.tar.xz d8ea25c393d4abf10f2b8c1e7ed2ad91f50e4bc9 11464 blasr_5.3.5+dfsg-7.debian.tar.xz Checksums-Sha256: 765ac47ae74f56e3bee17e2a3c81d404faf7419e42eb45bc9f2a71c7a5942205 124460 blasr_5.3.5+dfsg.orig.tar.xz e8548e7e84fb92fd58b5578c48b5a5247b8a27b0dde32f2706fdf5e1f3d7bad4 11464 blasr_5.3.5+dfsg-7.debian.tar.xz Files: 46c888e8f9c606d840b0d9dcc8036b21 124460 blasr_5.3.5+dfsg.orig.tar.xz dcfbbe76317e956aa2cd36bdb4277870 11464 blasr_5.3.5+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdYdkQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFXbQ/8C58FEnXIWrW2/pp4WOmg1uqrYInBjXrv TvAfqj+p6L5S/BTUH32hAPBaDDR1r7QoF4RbORCh+B2jVNL6NsoGo1432KIupZWg rdHEwnUc23kWgCLBfSZc7QHFT3gxTwyO+ZKk4wwxvdKMXSMwiMfKaen5zrc30Ira b+/ALeWq1Qvm0WLGZemFf39ZsyYVfeJ/KTA6Fc9AVn7NV5inl2FwID+4SFZ+Ybt/ h4wod4/nZPqBUPYbyAIcaZL+uCTqNB5ZPPAoElNOmYzzeAOmMDDkn+H4lf6aItJf CyWRIs3BlZHCY/qD03Cb6e9mbvSolaYycSi4+J2S8t+WziRIWOUXa5XTi+TFcj7P 4Q/MCGg7IitTiepxnXFGi4l8FdQfXbDsRtZ4MCLSf6e1yIsKa0IeJgthkXTMelaA cq41ZgrhwkiZ7pxgjxvTvg7J7ATptla9/SzBeUTB6rPxPtvc5U1BOeYeC57x9Qw/ PTP65wIh1Md5XZ8pDqia8pYvTJu9uw8z0KHqYydpy4pLvxHzPRi0rdZ2Px9cvFKy 3IAB85wnSlfIrGMalqyXDIJ3NC/r/139dNXUFK5MEkpM/nlpWUlNS2BGgeqtrtyv qNP7uZrP3LArBBGfVL3Cx6SQMXwD2uzBSd4e1cuxAAvRDslB8GlNt2SPi/STXLjj VbB7uD2tRZw= =AruW -----END PGP SIGNATURE----- Wed Dec 11 00:06:43 UTC 2024 I: Checking whether the package is not for us Wed Dec 11 00:06:43 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Wed Dec 11 00:06:43 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Wed Dec 11 00:08:20 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 12 18:29:45 -12 2026 I: pbuilder-time-stamp: 1768285785 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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_5.3.5+dfsg-7.dsc] I: copying [./blasr_5.3.5+dfsg.orig.tar.xz] I: copying [./blasr_5.3.5+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 10 17:11:32 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./blasr_5.3.5+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting blasr in blasr-5.3.5+dfsg dpkg-source: info: unpacking blasr_5.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking blasr_5.3.5+dfsg-7.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/1817926/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='59a16d3e0b4749d7a2de2e3660e60323' 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='1817926' 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.1UmTJIIH/pbuilderrc_TurK --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1UmTJIIH/b1 --logfile b1/build.log blasr_5.3.5+dfsg-7.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1817926/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:any, meson, cmake, pkgconf, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.5+dfsg-9~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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:any. 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 pkgconf; however: Package pkgconf 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; 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 (>= 5.3.5+dfsg-9~); 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} comerr-dev{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} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libblasr-dev{a} libblasr5.3.5{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgtest-dev{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnsl2{a} libp11-kit-dev{a} libpbbam-dev{a} libpbbam2.4.0{a} libpbcopper-dev{a} libpbcopper2.3.0{a} libpbdata-dev{a} libpbihdf-dev{a} libpbseq-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} meson{a} netbase{a} nettle-dev{a} ninja-build{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 154 newly installed, 0 to remove and 0 not upgraded. Need to get 84.8 MB of archives. After unpacking 455 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.8-1 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.8-1 [2163 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.8-1 [1970 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.8-1 [677 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.2-1 [2267 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.2-1 [11.9 MB] Get: 57 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2~rc1-2 [55.4 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 googletest all 1.15.2-1 [514 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.10.10+repack-5+b1 [23.8 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-5+b1 [1254 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-5+b1 [131 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2+b1 [735 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1+b4 [835 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libblasr5.3.5 amd64 5.3.5+dfsg-9 [1119 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libpbcopper-dev amd64 2.3.0+dfsg-2+b1 [1072 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libpbdata-dev amd64 5.3.5+dfsg-9 [40.7 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-5+b1 [90.1 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-5+b1 [64.2 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-5+b1 [41.1 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-5+b1 [21.7 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.0-1 [472 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.10.10+repack-5+b1 [2656 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libpbbam-dev amd64 2.4.0+dfsg-1+b4 [88.4 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libblasr-dev amd64 5.3.5+dfsg-9 [2113 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 139 http://deb.debian.org/debian unstable/main amd64 libgtest-dev amd64 1.15.2-1 [259 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libpbihdf-dev amd64 5.3.5+dfsg-9 [47.1 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libpbseq-dev amd64 5.3.5+dfsg-9 [4928 B] Get: 142 http://deb.debian.org/debian unstable/main amd64 ninja-build amd64 1.12.1-1 [142 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 149 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 meson all 1.6.0-1 [628 kB] Fetched 84.8 MB in 1s (120 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19965 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_amd64.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:amd64 (3.12.8-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... 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 ... 20285 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-1_amd64.deb ... Unpacking python3.12 (3.12.8-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... 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 ... 21348 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-6_amd64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.2-12_amd64.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../014-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../015-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../018-cmake-data_3.31.2-1_all.deb ... Unpacking cmake-data (3.31.2-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../019-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../020-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../021-libarchive13t64_3.7.4-1.1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../022-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../023-libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../024-libsasl2-2_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../025-libldap-2.5-0_2.5.18+dfsg-3+b1_amd64.deb ... 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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/reproducible-path/blasr-5.3.5+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_5.3.5+dfsg-7_source.changes dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.5+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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/reproducible-path/blasr-5.3.5+dfsg' LDFLAGS="-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-z,relro" CPPFLAGS="-isystem /usr/include/hdf5/serial" dh_auto_configure -- -Dtests=false cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1 -Dtests=false The Meson build system Version: 1.6.0 Source dir: /build/reproducible-path/blasr-5.3.5+dfsg Build dir: /build/reproducible-path/blasr-5.3.5+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: blasr Project version: 5.3.5 C++ compiler for the host machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-8) 14.2.0") C++ linker for the host machine: c++ ld.bfd 2.43.50.20241210 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: YES (/usr/bin/pkg-config) 1.8.1 Run-time dependency Boost found: YES 1.83.0 (/usr/include) Library pbbam found: YES Run-time dependency libblasr found: YES 5.3.5 Run-time dependency zlib found: YES 1.3.1 Run-time dependency htslib found: YES 1.20 Library pbcopper found: YES Configuring BlasrVersion.h using configuration Build targets in project: 5 blasr 5.3.5 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir : /var prefix : /usr python.bytecompile: -1 sysconfdir : /etc tests : false wrap_mode : nodownload Found ninja-1.12.1 at /usr/bin/ninja make[1]: Leaving directory '/build/reproducible-path/blasr-5.3.5+dfsg' dh_auto_build -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j42 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h 5.3.5 /build/reproducible-path/blasr-5.3.5+dfsg @BLASR_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [2/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 [3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 [5/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 [6/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 [7/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 [8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 | ^~~~ [9/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 [10/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 [11/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/14/bits/alloc_traits.h:569:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ 569 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1289 | __x); | ~~~~ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here 112 | alignments.push_back(alignment); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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: /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); | ^~~~~~~~ /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++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../extrautils/SWMatcher.cpp:2: /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [12/25] c++ -Isawriter.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 [13/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/14/bits/alloc_traits.h:569:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ 569 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1289 | __x); | ~~~~ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here 112 | alignments.push_back(alignment); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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: /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); | ^~~~~~~~ /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++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../utils/SamToM4.cpp:19: /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [14/25] c++ -ItoAfg.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/ToAfg.cpp:6: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here 132 | void BufferedHDF2DArray::Read(DSLength startX, DSLength endX, DSLength startY, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [15/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/14/bits/alloc_traits.h:569:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ 569 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1289 | __x); | ~~~~ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here 112 | alignments.push_back(alignment); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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: /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); | ^~~~~~~~ /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++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../utils/SDPMatcher.cpp:3: /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [16/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/PulseToFasta.cpp:5: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here 132 | void BufferedHDF2DArray::Read(DSLength startX, DSLength endX, DSLength startY, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [17/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/14/bits/alloc_traits.h:569:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ 569 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1289 | __x); | ~~~~ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here 112 | alignments.push_back(alignment); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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: /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); | ^~~~~~~~ /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++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../utils/SamFilter.cpp:29: /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [18/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFCmpFile.hpp:11, from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:7, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here 132 | void BufferedHDF2DArray::Read(DSLength startX, DSLength endX, DSLength startY, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ 7 | class HDF2DArray : public BufferedHDF2DArray | ^~~~~~~~~~ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here 17 | HDF2DArray fileLog; | ^~~~~~~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ 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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/14/bits/alloc_traits.h:569:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ 569 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1289 | __x); | ~~~~ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here 112 | alignments.push_back(alignment); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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: /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); | ^~~~~~~~ /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++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../utils/SamToCmpH5.cpp:1: /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:79: /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 >]’ 136 | unsigned int refGroupId = StoreRefGroup(alignment.tName, cmpFile); | ^~~~~~~~~~~~~ /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 >]’ 246 | StoreAlignmentCandidate(alignments[a], a, cmpFile, moleculeNumber, copyQVs); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../utils/SamToCmpH5.cpp:199:56: required from here 199 | alignmentSetAdapter.StoreAlignmentCandidateList(convertedAlignments, cmpFile, -1, copyQVs); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:64:86: warning: implicitly-declared ‘RefGroupNameId& RefGroupNameId::operator=(const RefGroupNameId&)’ is deprecated [-Wdeprecated-copy] 64 | refNameToRefGroupNameandId[refName] = RefGroupNameId(refGroupName, refGroupId); | ^ /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) | ^~~~~~~~~~~~~~ [19/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here 132 | void BufferedHDF2DArray::Read(DSLength startX, DSLength endX, DSLength startY, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ 7 | class HDF2DArray : public BufferedHDF2DArray | ^~~~~~~~~~ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here 17 | HDF2DArray fileLog; | ^~~~~~~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ 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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/14/bits/alloc_traits.h:569:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ 569 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1289 | __x); | ~~~~ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here 112 | alignments.push_back(alignment); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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: /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); | ^~~~~~~~ /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++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /usr/include/pbseq/alignment/datastructures/alignment/CmpFile.hpp:4, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:1: /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [20/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here 132 | void BufferedHDF2DArray::Read(DSLength startX, DSLength endX, DSLength startY, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ 7 | class HDF2DArray : public BufferedHDF2DArray | ^~~~~~~~~~ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here 17 | HDF2DArray fileLog; | ^~~~~~~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ 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 std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/14/bits/alloc_traits.h:569:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ 569 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1289 | __x); | ~~~~ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here 112 | alignments.push_back(alignment); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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: /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); | ^~~~~~~~ /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++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/stl_tree.h:64, from /usr/include/c++/14/map:62, from ../utils/LoadPulses.cpp:6: /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [21/25] rm -f libblasr_impl.a && gcc-ar csrDT 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 toAfg toAfg.p/utils_ToAfg.cpp.o -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial 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 /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group [23/25] c++ -o sawriter sawriter.p/utils_SAWriter.cpp.o -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial 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 /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group [24/25] c++ -Iblasr.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -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 /usr/include/pbseq/alignment/algorithms/anchoring/FindMaxInterval.hpp:16, from ../iblasr/BlasrHeaders.h:44, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/statistics/VarianceAccumulator.hpp:14:27: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 14 | VarianceAccumulator(); | ^ /usr/include/pbseq/alignment/statistics/VarianceAccumulator.hpp:14:27: note: remove the ‘< >’ In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../iblasr/BlasrHeaders.h:59: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here 132 | void BufferedHDF2DArray::Read(DSLength startX, DSLength endX, DSLength startY, \ | ^~ /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../iblasr/BlasrMiscs.hpp:56, from ../iblasr/BlasrAlign.hpp:5: ../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: /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/MappingIPC.h:5, from ../iblasr/BlasrHeaders.h:99: ../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: /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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60: /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:170:25: 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]’ 170 | AlignmentToBamRecord(alignment, read, subread, bamRecord, context, qvList, clipping, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 171 | cigarUseSeqMatch, allowAdjacentIndels); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../iblasr/BlasrUtilsImpl.hpp:951:38: required from here 951 | BAMOutput::PrintAlignment(alignment, fullRead, subread, *bamWriterPtr, alignmentContext, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 952 | params.samQVList, params.clipping, params.cigarUseSeqMatch, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 953 | params.allowAdjacentIndels); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:30:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress] 30 | if (dynamic_cast(&read) == NULL) { | ^ /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:19:72: note: ‘read’ declared here 19 | void AlignmentToBamRecord(T_AlignmentCandidate &alignment, T_Sequence &read, T_Sequence &subread, | ~~~~~~~~~~~~^~~~ 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: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/14/bits/alloc_traits.h:569:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ 569 | __a.construct(__p, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1289 | __x); | ~~~~ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here 112 | alignments.push_back(alignment); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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: /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); | ^~~~~~~~ /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++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../iblasr/BlasrHeaders.h:10: /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/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: /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]’ 526 | return GuidedAlign(origQSeq, origTSeq, guideAlignment, scoreFn, bandSize, alignment, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 527 | buffers.scoreMat, buffers.pathMat, buffers.probMat, buffers.optPathProbMat, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 528 | buffers.lnSubPValueMat, buffers.lnInsPValueMat, buffers.lnDelPValueMat, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 529 | buffers.lnMatchPValueMat, alignType, computeProb); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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]’ 512 | return GuidedAlign(origQSeq, origTSeq, sdpAlignment, scoreFn, bandSize, buffers, alignment, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | // fill in optional parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | alignType, computeProb); | ~~~~~~~~~~~~~~~~~~~~~~~ ../iblasr/BlasrAlignImpl.hpp:1449:20: required from here 1449 | GuidedAlign(alignedRead, alignedRefSequence, idsScoreFn, 12, params.sdpIns, params.sdpDel, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1450 | params.indelRate, mappingBuffers, exploded, Local, computeProbIsFalse, 6); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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++/14/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: /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]’ 30 | return KBandAlign(pqSeq, ptSeq, matchMat, ins, del, k, scoreMat, pathMat, alignment, alignType, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | scoreFn, samplePaths); | ~~~~~~~~~~~~~~~~~~~~~ ../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]’ 639 | KBandAlign(subread, alignmentCandidate.tAlignedSeq, SMRTDistanceMatrix, params.insertion, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 640 | params.deletion, drift, mappingBuffers.scoreMat, mappingBuffers.pathMat, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 641 | refinedAlignment, idsScoreFn, Global); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here 1555 | RefineAlignment(vquery, alignedRefSequence, exploded, params, mappingBuffers); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/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]’ 526 | return GuidedAlign(origQSeq, origTSeq, guideAlignment, scoreFn, bandSize, alignment, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 527 | buffers.scoreMat, buffers.pathMat, buffers.probMat, buffers.optPathProbMat, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 528 | buffers.lnSubPValueMat, buffers.lnInsPValueMat, buffers.lnDelPValueMat, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 529 | buffers.lnMatchPValueMat, alignType, computeProb); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../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]’ 689 | GuidedAlign(qSeq, tSeq, alignmentCandidate, idsScoreFn, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 690 | params.guidedAlignBandSize, mappingBuffers, refinedAlignment, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 691 | Global, false); | ~~~~~~~~~~~~~~ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here 1555 | RefineAlignment(vquery, alignedRefSequence, exploded, params, mappingBuffers); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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]’ 526 | return GuidedAlign(origQSeq, origTSeq, guideAlignment, scoreFn, bandSize, alignment, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 527 | buffers.scoreMat, buffers.pathMat, buffers.probMat, buffers.optPathProbMat, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 528 | buffers.lnSubPValueMat, buffers.lnInsPValueMat, buffers.lnDelPValueMat, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 529 | buffers.lnMatchPValueMat, alignType, computeProb); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../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]’ 698 | GuidedAlign(qSeq, tSeq, alignmentCandidate, distScoreFn, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 699 | params.guidedAlignBandSize, mappingBuffers, refinedAlignment, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 700 | Global, false); | ~~~~~~~~~~~~~~ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here 1555 | RefineAlignment(vquery, alignedRefSequence, exploded, params, mappingBuffers); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/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]’ 918 | OneGapAlign(qSubSeq, tSubSeq, distScoreFn, mappingBuffers, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 919 | alignmentInGap); | ~~~~~~~~~~~~~~~ ../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>]’ 280 | AlignIntervals(genome, read, readRC, topIntervals, SMRTDistanceMatrix, params.indel, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | params.indel, params.sdpTupleSize, params.useSeqDB, seqdb, alignmentPtrs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 282 | params, mappingBuffers, params.startRead); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Blasr.cpp:347:16: required from here 347 | MapRead(subreadSequence, subreadSequenceRC, | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 348 | genome, // possibly multi fasta file read into one sequence | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 349 | sarray, *bwtPtr, // The suffix array, and the bwt-fm index structures | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 350 | seqBoundary, // Boundaries of contigs in the | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 | // genome, alignments do not span | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 | // the ends of boundaries. | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | ct, // Count table to use word frequencies in the genome to weight matches. | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 | seqdb, // Information about the names of | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 | // chromosomes in the genome, and | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 | // where their sequences are in the genome. | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 | params, // A huge list of parameters for | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 358 | // mapping, only compile/command | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 359 | // line values set. | ~~~~~~~~~~~~~~~~~~~ 360 | mapData->metrics, // Keep track of time/ hit counts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 361 | // etc.. Not fully developed, but | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 362 | // should be. | ~~~~~~~~~~~~~ 363 | alignmentPtrs, // Where the results are stored. | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 364 | mappingBuffers, // A class of buffers for structurs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 | // like dyanmic programming | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 366 | // matrices, match lists, etc., that are not | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 | // reallocated between calls to | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 | // MapRead. They are cleared though. | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 369 | mapData, // Some values that are shared | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 370 | // across threads. | ~~~~~~~~~~~~~~~~~~ 371 | semaphores); | ~~~~~~~~~~~ /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]’ 30 | return KBandAlign(pqSeq, ptSeq, matchMat, ins, del, k, scoreMat, pathMat, alignment, alignType, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | scoreFn, samplePaths); | ~~~~~~~~~~~~~~~~~~~~~ ../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]’ 1301 | qvAwareScore = KBandAlign(qSeq, tSeq, SMRTDistanceMatrix, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1302 | params.indel + 2, // ins | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1303 | params.indel + 2, // del | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1304 | k, mappingBuffers.scoreMat, mappingBuffers.pathMat, alignment, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1305 | idsScoreFn, alignType); | ~~~~~~~~~~~~~~~~~~~~~~ ../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]’ 873 | PairwiseLocalAlign(qSeq, tSeq, k, params, alignmentCandidate, mappingBuffers, Fit); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here 1555 | RefineAlignment(vquery, alignedRefSequence, exploded, params, mappingBuffers); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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]’ 30 | return KBandAlign(pqSeq, ptSeq, matchMat, ins, del, k, scoreMat, pathMat, alignment, alignType, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | scoreFn, samplePaths); | ~~~~~~~~~~~~~~~~~~~~~ ../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]’ 1310 | qvAwareScore = KBandAlign(qSeq, tSeq, SMRTDistanceMatrix, | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1311 | params.indel + 2, // ins | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1312 | params.indel + 2, // del | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1313 | k, mappingBuffers.scoreMat, mappingBuffers.pathMat, alignment, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1314 | scoreFn, alignType); | ~~~~~~~~~~~~~~~~~~~ ../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]’ 873 | PairwiseLocalAlign(qSeq, tSeq, k, params, alignmentCandidate, mappingBuffers, Fit); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here 1555 | RefineAlignment(vquery, alignedRefSequence, exploded, params, mappingBuffers); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/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:30:5: warning: ‘nonnull’ argument ‘read’ compared to NULL [-Wnonnull-compare] 30 | if (dynamic_cast(&read) == NULL) { | ^~ [25/25] c++ -o blasr blasr.p/Blasr.cpp.o -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial 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 /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/blasr-5.3.5+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/reproducible-path/blasr-5.3.5+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson dh_prep -O--buildsystem=meson dh_auto_install --destdir=debian/blasr/ -O--buildsystem=meson cd obj-x86_64-linux-gnu && DESTDIR=/build/reproducible-path/blasr-5.3.5\+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/reproducible-path/blasr-5.3.5+dfsg/debian/blasr/usr/bin Installing sawriter to /build/reproducible-path/blasr-5.3.5+dfsg/debian/blasr/usr/bin dh_install -O--buildsystem=meson dh_installdocs -O--buildsystem=meson dh_installchangelogs -O--buildsystem=meson dh_installexamples -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-dbgsym' in '../blasr-dbgsym_5.3.5+dfsg-7_amd64.deb'. dpkg-deb: building package 'blasr' in '../blasr_5.3.5+dfsg-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../blasr_5.3.5+dfsg-7_amd64.buildinfo dpkg-genchanges --build=binary -O../blasr_5.3.5+dfsg-7_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/1817926 and its subdirectories I: Current time: Mon Jan 12 18:31:20 -12 2026 I: pbuilder-time-stamp: 1768285880 Wed Dec 11 00:08:21 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Wed Dec 11 00:08:21 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Wed Dec 11 00:20:43 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Wed Dec 11 00:20:44 UTC 2024 I: blasr_5.3.5+dfsg-7_amd64.changes: Format: 1.8 Date: Tue, 10 Dec 2024 12:21:50 +0100 Source: blasr Binary: blasr blasr-dbgsym Architecture: amd64 Version: 5.3.5+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: blasr - mapping single-molecule sequencing reads Closes: 1067374 Changes: blasr (5.3.5+dfsg-7) unstable; urgency=medium . [ Nilesh Patra ] * Team upload. * Bump Standards-Version to 4.7.0 (no changes needed) * Build with updated pbseqlib Closes: #1067374 . [ Andreas Tille ] * d/copyright: Fixes by lrc * Build-Depends: s/pkg-config/pkgconf/ Checksums-Sha1: 46e8c846cfeef72cbe424be1569b5d57c2e188be 3199204 blasr-dbgsym_5.3.5+dfsg-7_amd64.deb 9684249df6de10302628184fe52cf613ff8ce74b 9321 blasr_5.3.5+dfsg-7_amd64.buildinfo 142f6be376a0e3953242f4bdf5cf82b17b0279e7 238196 blasr_5.3.5+dfsg-7_amd64.deb Checksums-Sha256: 0059bdc7a0ca89beae9684e96941df9ea72b10a3baab22898f7a5dffe4b11e49 3199204 blasr-dbgsym_5.3.5+dfsg-7_amd64.deb 4a003db1f2377b35c9d543bee34e81fcf5d827dcf1f319843b02f64fb22424c2 9321 blasr_5.3.5+dfsg-7_amd64.buildinfo f6c7288cf2651e597ca07b678c51725eb10593d5a47f2a0a2299af70371cae80 238196 blasr_5.3.5+dfsg-7_amd64.deb Files: 10bf432c0970a6bf80ce3ff79d14c3ff 3199204 debug optional blasr-dbgsym_5.3.5+dfsg-7_amd64.deb 6b398b23573f36ea34e33ea8ae52e502 9321 science optional blasr_5.3.5+dfsg-7_amd64.buildinfo 44b3c6c4faae3d644534fe652d5dc5f4 238196 science optional blasr_5.3.5+dfsg-7_amd64.deb Wed Dec 11 00:20:45 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_26-26049.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.1UmTJIIH/blasr_5.3.5+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.1UmTJIIH/blasr_5.3.5+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.1UmTJIIH/blasr_5.3.5+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.1UmTJIIH/b1/blasr_5.3.5+dfsg-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.1UmTJIIH/b2/blasr_5.3.5+dfsg-7_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: 0.388s) 0.388s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.056s) 0.056s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 682ms CPU time consumed: 683ms Wed Dec 11 00:20:46 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Wed Dec 11 00:20:46 UTC 2024 I: blasr from unstable built successfully and reproducibly on amd64. Wed Dec 11 00:20:48 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Dec 11 00:20:48 UTC 2024 I: Submitting 12K b1/blasr_5.3.5+dfsg-7_amd64.buildinfo.asc Wed Dec 11 00:20:49 UTC 2024 I: Submitting 12K b2/blasr_5.3.5+dfsg-7_amd64.buildinfo.asc Wed Dec 11 00:20:50 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Dec 11 00:20:50 UTC 2024 I: Done submitting .buildinfo files. Wed Dec 11 00:20:50 UTC 2024 I: Removing signed blasr_5.3.5+dfsg-7_amd64.buildinfo.asc files: removed './b1/blasr_5.3.5+dfsg-7_amd64.buildinfo.asc' removed './b2/blasr_5.3.5+dfsg-7_amd64.buildinfo.asc'