Thu Feb 20 13:19:46 UTC 2025 I: starting to build blasr/trixie/amd64 on jenkins on '2025-02-20 13:19'
Thu Feb 20 13:19:46 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/44713/console.log
Thu Feb 20 13:19:46 UTC 2025 I: Downloading source for trixie/blasr=5.3.5+dfsg-7
--2025-02-20 13:19:46-- 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% 343M=0s
2025-02-20 13:19:46 (343 MB/s) - ‘blasr_5.3.5+dfsg-7.dsc’ saved [2155/2155]
Thu Feb 20 13:19:46 UTC 2025 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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
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:
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Files:
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dcfbbe76317e956aa2cd36bdb4277870 11464 blasr_5.3.5+dfsg-7.debian.tar.xz
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Thu Feb 20 13:19:46 UTC 2025 I: Checking whether the package is not for us
Thu Feb 20 13:19:46 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net.
Thu Feb 20 13:19:46 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net.
Thu Feb 20 13:27:22 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu Feb 20 01:19:48 -12 2025
I: pbuilder-time-stamp: 1740057588
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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
dpkg-source: warning: cannot verify inline signature for ./blasr_5.3.5+dfsg-7.dsc: unsupported subcommand
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/1443687/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=20 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='14d3c4b7fae84d79b4934548fefa0c77'
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='1443687'
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.HwiTDzJn/pbuilderrc_Lx6L --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HwiTDzJn/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://46.16.76.132:3128'
I: uname -a
Linux ionos1-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1443687/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 <pbuilder-maint@lists.alioth.debian.org>
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 ... 19809 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} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgtest-dev{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{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-dev{a} libldap2{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} libp11-kit-dev{a} libp11-kit0{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} libpython3.13-minimal{a} libpython3.13-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{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{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} python3.13{a} python3.13-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, 157 newly installed, 0 to remove and 0 not upgraded.
Need to get 88.5 MB of archives. After unpacking 465 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-6 [257 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B]
Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.5-2 [2267 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 41 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.0+git20250209.89ed161+ds-1 [355 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.5-2 [12.0 MB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 67 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 71 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 googletest all 1.16.0-1 [517 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB]
Get: 75 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B]
Get: 82 http://deb.debian.org/debian trixie/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB]
Get: 83 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get: 86 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get: 87 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get: 88 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.0+git20250209.89ed161+ds-1 [365 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2+b2 [736 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1+b4 [835 kB]
Get: 94 http://deb.debian.org/debian trixie/main amd64 libblasr5.3.5 amd64 5.3.5+dfsg-9+b2 [1121 kB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 libpbcopper-dev amd64 2.3.0+dfsg-2+b2 [1072 kB]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libpbdata-dev amd64 5.3.5+dfsg-9+b2 [41.0 kB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB]
Get: 101 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB]
Get: 102 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB]
Get: 109 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB]
Get: 111 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB]
Get: 115 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 122 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB]
Get: 128 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.12.0+git20250209.89ed161+ds-1 [479 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB]
Get: 137 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 libpbbam-dev amd64 2.4.0+dfsg-1+b4 [88.4 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 libblasr-dev amd64 5.3.5+dfsg-9+b2 [2119 kB]
Get: 140 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB]
Get: 141 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B]
Get: 142 http://deb.debian.org/debian trixie/main amd64 libgtest-dev amd64 1.16.0-1 [259 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 libpbihdf-dev amd64 5.3.5+dfsg-9+b2 [47.5 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 libpbseq-dev amd64 5.3.5+dfsg-9+b2 [5224 B]
Get: 145 http://deb.debian.org/debian trixie/main amd64 ninja-build amd64 1.12.1-1 [142 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 148 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.6.0-1 [720 kB]
Get: 157 http://deb.debian.org/debian trixie/main amd64 meson all 1.7.0-1 [639 kB]
Fetched 88.5 MB in 5s (16.4 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:amd64.
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Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ...
Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ...
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 python3.13-minimal.
Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ...
Unpacking python3.13-minimal (3.13.2-1) ...
Setting up libpython3.13-minimal:amd64 (3.13.2-1) ...
Setting up libexpat1:amd64 (2.6.4-1) ...
Setting up python3.13-minimal (3.13.2-1) ...
Selecting previously unselected package python3-minimal.
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Preparing to unpack .../0-python3-minimal_3.13.1-2_amd64.deb ...
Unpacking python3-minimal (3.13.1-2) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../2-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../3-tzdata_2024b-6_all.deb ...
Unpacking tzdata (2024b-6) ...
Selecting previously unselected package libffi8:amd64.
Preparing to unpack .../4-libffi8_3.4.7-1_amd64.deb ...
Unpacking libffi8:amd64 (3.4.7-1) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../5-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:amd64.
Preparing to unpack .../6-libreadline8t64_8.2-6_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 (8.2-6) ...
Selecting previously unselected package libpython3.13-stdlib:amd64.
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Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ...
Selecting previously unselected package python3.13.
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Unpacking python3.13 (3.13.2-1) ...
Selecting previously unselected package libpython3-stdlib:amd64.
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Unpacking libpython3-stdlib:amd64 (3.13.1-2) ...
Setting up python3-minimal (3.13.1-2) ...
Selecting previously unselected package python3.
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Preparing to unpack .../000-python3_3.13.1-2_amd64.deb ...
Unpacking python3 (3.13.1-2) ...
Selecting previously unselected package libproc2-0:amd64.
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Unpacking libproc2-0:amd64 (2:4.0.4-7) ...
Selecting previously unselected package procps.
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Unpacking procps (2:4.0.4-7) ...
Selecting previously unselected package sensible-utils.
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Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
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Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:amd64.
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Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
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Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
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Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:amd64.
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Unpacking libuchardet0:amd64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
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Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../010-bsdextrautils_2.40.4-3_amd64.deb ...
Unpacking bsdextrautils (2.40.4-3) ...
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.
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Unpacking man-db (2.13.0-1) ...
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Unpacking m4 (1.4.19-5) ...
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Unpacking autoconf (2.72-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Unpacking automake (1:1.17-3) ...
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Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package cmake-data.
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Unpacking cmake-data (3.31.5-2) ...
Selecting previously unselected package libicu72:amd64.
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Unpacking libicu72:amd64 (72.1-6) ...
Selecting previously unselected package libxml2:amd64.
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Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package libarchive13t64:amd64.
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Unpacking libarchive13t64:amd64 (3.7.4-1.1) ...
Selecting previously unselected package libbrotli1:amd64.
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Unpacking libbrotli1:amd64 (1.1.0-2+b6) ...
Selecting previously unselected package libkrb5support0:amd64.
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Unpacking libkrb5support0:amd64 (1.21.3-4) ...
Selecting previously unselected package libcom-err2:amd64.
Preparing to unpack .../024-libcom-err2_1.47.2-1_amd64.deb ...
Unpacking libcom-err2:amd64 (1.47.2-1) ...
Selecting previously unselected package libk5crypto3:amd64.
Preparing to unpack .../025-libk5crypto3_1.21.3-4_amd64.deb ...
Unpacking libk5crypto3:amd64 (1.21.3-4) ...
Selecting previously unselected package libkeyutils1:amd64.
Preparing to unpack .../026-libkeyutils1_1.6.3-4_amd64.deb ...
Unpacking libkeyutils1:amd64 (1.6.3-4) ...
Selecting previously unselected package libkrb5-3:amd64.
Preparing to unpack .../027-libkrb5-3_1.21.3-4_amd64.deb ...
Unpacking libkrb5-3:amd64 (1.21.3-4) ...
Selecting previously unselected package libgssapi-krb5-2:amd64.
Preparing to unpack .../028-libgssapi-krb5-2_1.21.3-4_amd64.deb ...
Unpacking libgssapi-krb5-2:amd64 (1.21.3-4) ...
Selecting previously unselected package libunistring5:amd64.
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-> 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 <nilesh@debian.org>
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: 1.7.0
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 14.2.0-16) 14.2.0")
C++ linker for the host machine: c++ ld.bfd 2.44
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 1.21
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 -j20 -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_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp
[3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/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
[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_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
[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_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
[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_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
[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_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<T_BWT_Sequence, T_DNASequence>::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’:
/usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
192 | charCount[0]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here
193 | case 0: //A
| ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
194 | charCount[1]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here
195 | case 1: //C
| ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
196 | charCount[2]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here
197 | case 2: //G
| ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
198 | charCount[3]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here
199 | case 3: //T
| ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
200 | charCount[4]++;
| ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here
201 | case 4: //N
| ^~~~
[8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/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
[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++ -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
[12/25] 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:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __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<blasr::CompSeqAlignment>; 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)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __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<blasr::CompSeqAlignment>; 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<int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; 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<unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; 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<unsigned char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; 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<short unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; 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<short int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; 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<float>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; 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<char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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_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<int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; 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<unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; 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<unsigned char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; 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<short unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; 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<short int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; 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<float>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; 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<char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0,
| ^~~~~~~~~~
[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_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:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __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<blasr::CompSeqAlignment>; 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)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __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<blasr::CompSeqAlignment>; 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<int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; 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<unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; 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<unsigned char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; 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<short unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; 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<short int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; 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<float>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; 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<char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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<std::__cxx11::basic_string<char> >’:
/usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray<std::__cxx11::basic_string<char> >’
7 | class HDF2DArray : public BufferedHDF2DArray<T>
| ^~~~~~~~~~
/usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here
17 | HDF2DArray<std::string> 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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
70 | int BufferedHDF2DArray<T>::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:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __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<blasr::CompSeqAlignment>; 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<T_CmpFile>::StoreRefGroup(std::string, T_CmpFile&) [with T_CmpFile = HDFCmpFile<AlignmentCandidate<> >; std::string = std::__cxx11::basic_string<char>]’:
/usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:136:31: required from ‘void AlignmentSetToCmpH5Adapter<T_CmpFile>::StoreAlignmentCandidate(AlignmentCandidate<>&, int, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile<AlignmentCandidate<> >]’
136 | unsigned int refGroupId = StoreRefGroup(alignment.tName, cmpFile);
| ^~~~~~~~~~~~~
/usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:246:32: required from ‘void AlignmentSetToCmpH5Adapter<T_CmpFile>::StoreAlignmentCandidateList(std::vector<AlignmentCandidate<> >&, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile<AlignmentCandidate<> >]’
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<int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; 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<unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; 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<unsigned char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; 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<short unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; 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<short int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; 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<float>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; 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<char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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<std::__cxx11::basic_string<char> >’:
/usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray<std::__cxx11::basic_string<char> >’
7 | class HDF2DArray : public BufferedHDF2DArray<T>
| ^~~~~~~~~~
/usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here
17 | HDF2DArray<std::string> 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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
70 | int BufferedHDF2DArray<T>::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:575:17: required from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __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<blasr::CompSeqAlignment>; 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<int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; 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<unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; 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<unsigned char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; 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<short unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; 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<short int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; 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<float>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; 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<char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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<std::__cxx11::basic_string<char> >’:
/usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray<std::__cxx11::basic_string<char> >’
7 | class HDF2DArray : public BufferedHDF2DArray<T>
| ^~~~~~~~~~
/usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here
17 | HDF2DArray<std::string> 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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string<char>; std::string = std::__cxx11::basic_string<char>; DSLength = long unsigned int]’
70 | int BufferedHDF2DArray<T>::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:575:17: required from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __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<blasr::CompSeqAlignment>; 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<T>();
| ^
/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<int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string<char>; 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<unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string<char>; 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<unsigned char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string<char>; 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<short unsigned int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string<char>; 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<short int>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string<char>; 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<float>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here
120 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string<char>; 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<char>’:
/usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here
132 | void BufferedHDF2DArray<T>::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<T>::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string<char>; 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<SMRTSequence>&, std::vector<ReadInterval>&)’:
../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<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>*, MappingBuffers&, SMRTSequence&, SMRTSequence&, std::vector<SMRTSequence>&, 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<SuffixArray<unsigned char, std::vector<int> >, 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<DNASequence, FASTQSequence>]’:
/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<DNASequence, FASTQSequence>]’
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<SMRTSequence *>(&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:575:17: required from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator<blasr::CompSeqAlignment>]’
575 | __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<blasr::CompSeqAlignment>; 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<int>&, std::vector<Arrow>&, std::vector<double>&, std::vector<double>&, std::vector<float>&, std::vector<float>&, std::vector<float>&, std::vector<float>&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>]’:
/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<DNASequence, FASTQSequence>; 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<DNASequence, FASTQSequence>; 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<int>&, std::vector<Arrow>&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate<DNASequence, FASTQSequence>; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>; 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<int>&, std::vector<Arrow>&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate<DNASequence, FASTQSequence>; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>; 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_Sequence*>&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]’
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<int>&, std::vector<Arrow>&, std::vector<double>&, std::vector<double>&, std::vector<float>&, std::vector<float>&, std::vector<float>&, std::vector<float>&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>]’:
/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<DNASequence, FASTQSequence>; 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_Sequence*>&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]’
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<int>&, std::vector<Arrow>&, std::vector<double>&, std::vector<double>&, std::vector<float>&, std::vector<float>&, std::vector<float>&, std::vector<float>&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>]’:
/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<DNASequence, FASTQSequence>; 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_Sequence*>&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]’
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<DNASequence, FASTQSequence>; 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<TDBSequence>&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, 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<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, 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<int>&, std::vector<Arrow>&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate<DNASequence, FASTQSequence>; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>; 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<int>&, std::vector<Arrow>&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate<DNASequence, FASTQSequence>; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>; 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<DNASequence, FASTQSequence>]’
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_Sequence*>&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]’
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<int>&, std::vector<Arrow>&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate<DNASequence, FASTQSequence>; T_ScoreFn = QualityValueScoreFunction<DNASequence, FASTQSequence>; 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<int>&, std::vector<Arrow>&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate<DNASequence, FASTQSequence>; T_ScoreFn = QualityValueScoreFunction<DNASequence, FASTQSequence>; 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<DNASequence, FASTQSequence>]’
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_Sequence*>&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]’
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<SMRTSequence *>(&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/1443687 and its subdirectories
I: Current time: Thu Feb 20 01:27:21 -12 2025
I: pbuilder-time-stamp: 1740058041
Thu Feb 20 13:27:22 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net.
Thu Feb 20 13:27:22 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net.
Thu Feb 20 13:30:01 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
Thu Feb 20 13:30:02 UTC 2025 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 <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
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:
6c88a81f1351fd126596adb5dae56f4d2a8247d4 3204096 blasr-dbgsym_5.3.5+dfsg-7_amd64.deb
4a9cb775c6533a237020c6ba644828e85db71dfa 9084 blasr_5.3.5+dfsg-7_amd64.buildinfo
1c9f2dcdb8b8bf1e8c28a6d742dcb0e5ef4ec7ac 238176 blasr_5.3.5+dfsg-7_amd64.deb
Checksums-Sha256:
38bbb0f410bc33330e7c80d5e034239ae2a6e228c73af863b88263f603f74280 3204096 blasr-dbgsym_5.3.5+dfsg-7_amd64.deb
068b046355dcc4313e00259fe49a587d45d2aa91bc79ffa29c6b366e8c399f30 9084 blasr_5.3.5+dfsg-7_amd64.buildinfo
5bb67cd35fc038e8c26b0b522eb0f342104277498de1ab5b2aa46ad1a37c7f65 238176 blasr_5.3.5+dfsg-7_amd64.deb
Files:
8a4a264fd9e6b328d931612d569e7f77 3204096 debug optional blasr-dbgsym_5.3.5+dfsg-7_amd64.deb
bdd32e29827a437b4a5a01c82dfa812c 9084 science optional blasr_5.3.5+dfsg-7_amd64.buildinfo
4c93477d4e8ce047d361570e83922e31 238176 science optional blasr_5.3.5+dfsg-7_amd64.deb
Thu Feb 20 13:30:04 UTC 2025 I: diffoscope 288 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_11-44713.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.HwiTDzJn/blasr_5.3.5+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.HwiTDzJn/blasr_5.3.5+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.HwiTDzJn/blasr_5.3.5+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.HwiTDzJn/b1/blasr_5.3.5+dfsg-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.HwiTDzJn/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 diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 268ms
CPU time consumed: 270ms
Thu Feb 20 13:30:16 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists.
Thu Feb 20 13:30:16 UTC 2025 I: blasr from trixie built successfully and reproducibly on amd64.
Thu Feb 20 13:30:17 UTC 2025 I: Submitting .buildinfo files to external archives:
Thu Feb 20 13:30:17 UTC 2025 I: Submitting 12K b1/blasr_5.3.5+dfsg-7_amd64.buildinfo.asc
Thu Feb 20 13:30:19 UTC 2025 I: Submitting 12K b2/blasr_5.3.5+dfsg-7_amd64.buildinfo.asc
Thu Feb 20 13:30:21 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Feb 20 13:30:21 UTC 2025 I: Done submitting .buildinfo files.
Thu Feb 20 13:30:21 UTC 2025 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'