Diff of the two buildlogs: -- --- b1/build.log 2023-04-26 19:33:38.823563198 +0000 +++ b2/build.log 2023-04-26 19:40:55.048211583 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 26 07:05:12 -12 2023 -I: pbuilder-time-stamp: 1682535912 +I: Current time: Wed May 29 15:56:48 +14 2024 +I: pbuilder-time-stamp: 1716947808 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./pbseqlib_5.3.5+dfsg.orig.tar.xz] I: copying [./pbseqlib_5.3.5+dfsg-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Mar 7 22:52:24 2022 -12 +gpgv: Signature made Wed Mar 9 00:52:24 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,52 +31,84 @@ dpkg-source: info: applying static+shared_lib.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20735/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/16100/tmp/hooks/D01_modify_environment starting +debug: Running on codethink11-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 29 15:56 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/16100/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/16100/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='20735' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=16100 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.T31ICG1u/pbuilderrc_54W2 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.T31ICG1u/b1 --logfile b1/build.log pbseqlib_5.3.5+dfsg-4.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.T31ICG1u/pbuilderrc_r0fB --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.T31ICG1u/b2 --logfile b2/build.log --extrapackages usrmerge pbseqlib_5.3.5+dfsg-4.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink14-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 24 22:27 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/20735/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 29 15:18 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/16100/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -238,7 +270,7 @@ Get: 100 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] -Fetched 60.7 MB in 3s (18.4 MB/s) +Fetched 60.7 MB in 1s (49.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -663,8 +695,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/pbseqlib-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 > ../pbseqlib_5.3.5+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/16100/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/16100/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/pbseqlib-5.3.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pbseqlib_5.3.5+dfsg-4_source.changes dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.5+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -1350,7 +1391,8 @@ [9/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp [10/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp [11/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp -[12/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp +[12/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp +[13/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: @@ -1383,8 +1425,8 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[13/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp -[14/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp +[14/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp +[15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp In file included from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: @@ -1398,23 +1440,25 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp [16/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp -[17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o -c ../hdf/HDFScanDataReader.cpp +[17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, - from ../hdf/HDFScanDataReader.cpp:1: + from ../hdf/HDFPulseDataFile.hpp:10, + from ../hdf/HDFPulseDataFile.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: -../hdf/HDFScanDataReader.cpp:26:33: required from here +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFAtom.hpp:9: + from ../hdf/HDFPulseDataFile.hpp:7: /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: -../hdf/HDFScanDataReader.cpp:29:33: required from here +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1422,31 +1466,29 @@ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFScanDataReader.cpp:33:39: required from here +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp +[18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o -c ../hdf/HDFScanDataReader.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, - from ../hdf/HDFPulseDataFile.hpp:10, - from ../hdf/HDFPulseDataFile.cpp:1: + from ../hdf/HDFScanDataReader.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFScanDataReader.cpp:26:33: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFPulseDataFile.hpp:7: + from ../hdf/HDFAtom.hpp:9: /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFScanDataReader.cpp:29:33: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1454,8 +1496,7 @@ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFScanDataReader.cpp:33:39: required from here ../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] 33 | attribute = object.openAttribute(attributeName.c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1463,7 +1504,20 @@ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ [19/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp -[20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp +[20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp +../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: +../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] + 44 | for (auto annotation : annotations) + | ^~~~~~~~~~~ +In file included from ../pbdata/reads/RegionTable.hpp:17, + from ../pbdata/SMRTSequence.hpp:14, + from ../hdf/HDFWriterBase.hpp:17, + from ../hdf/HDFRegionsWriter.hpp:13, + from ../hdf/HDFRegionsWriter.cpp:3: +../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ + 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) + | ^~~~~~~~~~~~~~~~ +[21/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o -c ../hdf/HDFScanDataWriter.cpp In file included from ../hdf/HDFScanDataWriter.hpp:10, from ../hdf/HDFScanDataWriter.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = short unsigned int; std::string = std::__cxx11::basic_string]’: @@ -1513,19 +1567,6 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[21/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp -../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: -../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] - 44 | for (auto annotation : annotations) - | ^~~~~~~~~~~ -In file included from ../pbdata/reads/RegionTable.hpp:17, - from ../pbdata/SMRTSequence.hpp:14, - from ../hdf/HDFWriterBase.hpp:17, - from ../hdf/HDFRegionsWriter.hpp:13, - from ../hdf/HDFRegionsWriter.cpp:3: -../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ - 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) - | ^~~~~~~~~~~~~~~~ [22/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp [23/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, @@ -1574,9 +1615,10 @@ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ [25/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp -[26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp +[26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: + from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, + from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: ../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++/12/bits/alloc_traits.h:516:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/12/bits/stl_vector.h:1281:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ @@ -1600,14 +1642,37 @@ In file included from /usr/include/aarch64-linux-gnu/c++/12/bits/c++allocator.h:33, from /usr/include/c++/12/bits/allocator.h:46, from /usr/include/c++/12/string:41, - from ../alignment/algorithms/alignment/AlignmentUtils.hpp:4: + from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4: /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp +[27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp +In file included from ../hdf/HDFWriterBase.hpp:13, + from ../hdf/HDFWriterBase.cpp:3: +../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFWriterBase.cpp:49:29: required from here +../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/BufferedHDF2DArray.hpp:8, + from ../hdf/HDFWriterBase.hpp:11: +/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 32 | Attribute(const Attribute &original); + | ^~~~~~~~~ +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 32 | Attribute(const Attribute &original); + | ^~~~~~~~~ +[28/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp +[29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, - from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: + from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../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++/12/bits/alloc_traits.h:516:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/12/bits/stl_vector.h:1281:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ @@ -1631,34 +1696,10 @@ In file included from /usr/include/aarch64-linux-gnu/c++/12/bits/c++allocator.h:33, from /usr/include/c++/12/bits/allocator.h:46, from /usr/include/c++/12/string:41, - from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4: + from ../alignment/algorithms/alignment/AlignmentUtils.hpp:4: /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[28/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp -In file included from ../hdf/HDFWriterBase.hpp:13, - from ../hdf/HDFWriterBase.cpp:3: -../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFWriterBase.cpp:49:29: required from here -../hdf/HDFAtom.hpp:103:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 103 | attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/BufferedHDF2DArray.hpp:8, - from ../hdf/HDFWriterBase.hpp:11: -/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 32 | Attribute(const Attribute &original); - | ^~~~~~~~~ -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 32 | Attribute(const Attribute &original); - | ^~~~~~~~~ -[29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp [30/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWMetricsWriter.hpp:8, @@ -1709,7 +1750,25 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp +[34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp +In file included from ../hdf/HDFWriterBase.hpp:13, + from ../hdf/HDFZMWWriter.hpp:12, + from ../hdf/HDFZMWWriter.cpp:5: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/BufferedHDF2DArray.hpp:8, + from ../hdf/HDFZMWWriter.hpp:10: +/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 32 | Attribute(const Attribute &original); + | ^~~~~~~~~ +[35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp +[36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp +[37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp In file included from /usr/include/c++/12/cassert:44, from ../pbdata/reads/RegionTypeMap.hpp:7, from ../pbdata/reads/RegionAnnotation.hpp:17, @@ -1767,31 +1826,13 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp -[36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp -In file included from ../hdf/HDFWriterBase.hpp:13, - from ../hdf/HDFZMWWriter.hpp:12, - from ../hdf/HDFZMWWriter.cpp:5: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/BufferedHDF2DArray.hpp:8, - from ../hdf/HDFZMWWriter.hpp:10: -/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 32 | Attribute(const Attribute &original); - | ^~~~~~~~~ -[37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp [38/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp [39/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp -[40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp -[41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp +[40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp +[41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/KBandAlign.hpp:10, - from ../alignment/algorithms/alignment/KBandAlign.cpp:1: + from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, + from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: ../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++/12/bits/alloc_traits.h:516:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/12/bits/stl_vector.h:1281:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ @@ -1814,16 +1855,21 @@ | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/12/bits/c++allocator.h:33, from /usr/include/c++/12/bits/allocator.h:46, - from /usr/include/c++/12/vector:61, - from ../alignment/algorithms/alignment/KBandAlign.hpp:7: + from /usr/include/c++/12/string:41, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from ../alignment/algorithms/alignment/GuidedAlign.hpp:6: /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[42/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp -[43/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp +[42/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp +[43/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp +[44/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, - from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: + from ../alignment/algorithms/alignment/KBandAlign.hpp:10, + from ../alignment/algorithms/alignment/KBandAlign.cpp:1: ../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++/12/bits/alloc_traits.h:516:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/12/bits/stl_vector.h:1281:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ @@ -1846,20 +1892,15 @@ | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/12/bits/c++allocator.h:33, from /usr/include/c++/12/bits/allocator.h:46, - from /usr/include/c++/12/string:41, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from ../alignment/algorithms/alignment/GuidedAlign.hpp:6: + from /usr/include/c++/12/vector:61, + from ../alignment/algorithms/alignment/KBandAlign.hpp:7: /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[44/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp [45/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -c ../alignment/datastructures/alignment/AlignmentStats.cpp [46/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -c ../alignment/datastructures/alignment/AlignmentMap.cpp -[47/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o -c ../alignment/datastructures/alignment/CmpFile.cpp -[48/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp +[47/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o -c ../alignment/algorithms/anchoring/BWTSearch.cpp +[48/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor 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../alignment/algorithms/anchoring/FindMaxInterval.cpp [50/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o -c ../alignment/algorithms/sorting/MultikeyQuicksort.cpp [51/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp @@ -1883,9 +1924,7 @@ [60/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -c ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp [61/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -c ../alignment/datastructures/anchoring/MatchPos.cpp [62/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -c ../alignment/datastructures/anchoring/WeightedInterval.cpp -[63/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -c ../alignment/files/CCSIterator.cpp -[64/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp -[65/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -c ../alignment/format/CompareSequencesPrinter.cpp +[63/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -c ../alignment/format/CompareSequencesPrinter.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: @@ -1921,6 +1960,8 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[64/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -c ../alignment/files/CCSIterator.cpp +[65/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp [66/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -c ../alignment/format/IntervalPrinter.cpp [67/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o -c ../alignment/format/SAMPrinter.cpp [68/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o -c ../alignment/format/SummaryPrinter.cpp @@ -1937,8 +1978,8 @@ | ~~~~~~~~~~~^~~~ [70/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o -MF libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o.d -o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o -c ../alignment/qvs/QualityValueProfile.cpp [71/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o -c ../alignment/statistics/cdfs.cpp -[72/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o -c ../alignment/simulator/ContextSample.cpp -[73/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o -MF libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o.d -o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o -c ../alignment/query/SequentialZmwGroupQuery.cpp +[72/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o -MF libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o.d -o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o -c ../alignment/query/SequentialZmwGroupQuery.cpp +[73/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o -c ../alignment/simulator/ContextSample.cpp [74/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o -c ../alignment/statistics/pdfs.cpp [75/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o -c ../alignment/tuples/BaseTuple.cpp [76/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o -c ../alignment/statistics/StatUtils.cpp @@ -1987,13 +2028,18 @@ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ [86/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o -c ../alignment/simulator/QualitySample.cpp -[87/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -c ../alignment/MappingMetrics.cpp -[88/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -c ../alignment/tuples/DNATuple.cpp -[89/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -MF libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -c ../pbdata/alignment/CmpAlignment.cpp -[90/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -c ../pbdata/loadpulses/MovieAlnIndexLookupTable.cpp +[87/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o -c ../alignment/tuples/DNATuple.cpp +[88/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o -c ../alignment/MappingMetrics.cpp +[89/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o -c ../pbdata/loadpulses/MovieAlnIndexLookupTable.cpp +[90/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -MF libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o -c ../pbdata/alignment/CmpAlignment.cpp [91/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o -MF libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o -c ../pbdata/loadpulses/MetricField.cpp [92/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o -c ../pbdata/reads/AcqParams.cpp -[93/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp +[93/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o -MF libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o -c ../pbdata/qvs/QualityTransform.cpp +[94/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o -c ../pbdata/reads/HoleXY.cpp +[95/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o -MF libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o -c ../pbdata/qvs/BlasrQualityValue.cpp +[96/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o -c ../pbdata/metagenome/TitleTable.cpp +[97/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o -c ../pbdata/reads/ReadType.cpp +[98/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: @@ -2031,17 +2077,12 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[94/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o -c ../pbdata/reads/HoleXY.cpp -[95/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o -MF libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o -c ../pbdata/qvs/BlasrQualityValue.cpp -[96/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o -MF libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o -c ../pbdata/qvs/QualityTransform.cpp -[97/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o -c ../pbdata/metagenome/TitleTable.cpp -[98/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o -c ../pbdata/reads/ReadType.cpp -[99/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o -c ../pbdata/reads/PulseBaseCommon.cpp -[100/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o -c ../alignment/utils/FileOfFileNames.cpp +[99/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o -c ../alignment/utils/FileOfFileNames.cpp +[100/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o -c ../pbdata/reads/PulseBaseCommon.cpp [101/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o -c ../pbdata/reads/RegionAnnotation.cpp [102/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o -c ../alignment/utils/RegionUtils.cpp [103/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o -c ../pbdata/reads/ZMWGroupEntry.cpp -[104/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -MF libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -c ../pbdata/amos/AfgBasWriter.cpp +[104/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -c ../pbdata/reads/RegionTypeMap.cpp [105/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o -c ../pbdata/saf/AlnGroup.cpp [106/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -c ../pbdata/reads/RegionAnnotations.cpp ../pbdata/reads/RegionAnnotations.cpp: In constructor ‘RegionAnnotations::RegionAnnotations(UInt, const std::vector&, const std::vector&)’: @@ -2088,16 +2129,16 @@ ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ -[107/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -c ../pbdata/reads/RegionTypeMap.cpp -[108/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o -c ../pbdata/saf/RefGroup.cpp -[109/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -c ../pbdata/saf/MovieInfo.cpp -[110/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -c ../pbdata/saf/RefInfo.cpp -[111/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o -c ../pbdata/reads/RegionTable.cpp -[112/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp -[113/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o -c ../pbdata/utils/BitUtils.cpp +[107/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -c ../pbdata/saf/MovieInfo.cpp +[108/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -MF libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o -c ../pbdata/amos/AfgBasWriter.cpp +[109/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o -c ../pbdata/reads/RegionTable.cpp +[110/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o -c ../pbdata/saf/RefGroup.cpp +[111/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp +[112/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -c ../pbdata/saf/RefInfo.cpp +[113/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -c ../pbdata/sam/SAMHeader.cpp [114/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o -c ../pbdata/sam/ReadGroup.cpp [115/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o -c ../pbdata/sam/ReferenceSequence.cpp -[116/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -c ../pbdata/sam/SAMHeader.cpp +[116/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o -c ../pbdata/utils/BitUtils.cpp [117/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o -c ../pbdata/reads/BaseFile.cpp [118/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o -c ../pbdata/sam/SAMKeywordValuePair.cpp [119/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o -c ../pbdata/sam/SAMAlignment.cpp @@ -2136,11 +2177,11 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[130/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp -[131/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat 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-I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o -c ../pbdata/MD5Utils.cpp +[131/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp +[132/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp [133/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o -MF libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o -c ../pbdata/ReverseCompressIndex.cpp -[134/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp +[134/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp [135/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -c ../pbdata/StringUtils.cpp [136/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o -c ../pbdata/FASTQSequence.cpp [137/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp @@ -2161,9 +2202,9 @@ [139/187] c++ -o libblasr.so.5.3.5 libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -I/usr/include/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libblasr.so.5.3.5 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-rpath-link,/usr/lib/aarch64-linux-gnu/hdf5/serial /usr/lib/aarch64-linux-gnu/libpbbam.so /usr/lib/aarch64-linux-gnu/libpbcopper.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so -lrt /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so -Wl,--end-group [140/187] /usr/bin/meson --internal symbolextractor /build/pbseqlib-5.3.5+dfsg/obj-aarch64-linux-gnu libblasr.so.5.3.5 libblasr.so.5.3.5 libblasr.so.5.3.5.p/libblasr.so.5.3.5.symbols [141/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -[142/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp +[142/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, - from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: + from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here @@ -2175,9 +2216,9 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp +[143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, - from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: + from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here @@ -2189,7 +2230,8 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp +[144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMPrinter_gtest.cpp +[145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: @@ -2203,14 +2245,14 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp -[146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMPrinter_gtest.cpp +[146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp [147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp -[148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -c ../unittest/alignment/utils/FileUtils_gtest.cpp -[149/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -c ../unittest/alignment/utils/RangeUtils_gtest.cpp -[150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp -[151/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp -[152/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -c ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp +[148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -c ../unittest/alignment/utils/RangeUtils_gtest.cpp +[149/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -c ../unittest/alignment/utils/FileUtils_gtest.cpp +[150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp +[151/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp +[152/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp +[153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -c ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: @@ -2245,7 +2287,6 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp [154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp [155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -c ../unittest/alignment/utils/RegionUtils_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, @@ -2262,9 +2303,7 @@ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ [156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -c ../unittest/hdf/HDFZMWReader_gtest.cpp -[157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -c ../unittest/hdf/HDF2DArray_gtest.cpp -[158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -c ../unittest/pbdata/metagenome/TitleTable_gtest.cpp -[159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -c ../unittest/hdf/HDFScanDataReader_gtest.cpp +[157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -c ../unittest/hdf/HDFScanDataReader_gtest.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: @@ -2296,6 +2335,8 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ +[158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -c ../unittest/hdf/HDF2DArray_gtest.cpp +[159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -c ../unittest/pbdata/metagenome/TitleTable_gtest.cpp [160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -c ../unittest/hdf/HDFUtils_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, @@ -2314,8 +2355,8 @@ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ [161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -c ../unittest/pbdata/saf/RefInfo_gtest.cpp -[162/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -c ../unittest/pbdata/saf/AlnGroup_gtest.cpp -[163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp +[162/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp +[163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -c ../unittest/pbdata/saf/AlnGroup_gtest.cpp [164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -c ../unittest/pbdata/utils/SMRTTitle_gtest.cpp [165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -c ../unittest/hdf/HDFPlsReader_gtest.cpp In file included from ../hdf/HDFPlsReader.hpp:11, @@ -2393,7 +2434,8 @@ | ^~~~~~~~~ [168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -c ../unittest/pbdata/reads/ReadType_gtest.cpp [169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -c ../unittest/pbdata/reads/RegionTypeMap_gtest.cpp -[170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp +[170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -c ../unittest/pbdata/ScanData_gtest.cpp +[171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: @@ -2430,10 +2472,9 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -c ../unittest/pbdata/ScanData_gtest.cpp -[172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -c ../unittest/pbdata/VectorUtils_gtest.cpp +[172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -c ../unittest/pbdata/defs_gtest.cpp [173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp -[174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -c ../unittest/pbdata/defs_gtest.cpp +[174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -c ../unittest/pbdata/VectorUtils_gtest.cpp [175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -c ../unittest/pbdata/StringUtils_gtest.cpp [176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp [177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -c ../unittest/pbdata/ChangeListID_gtest.cpp @@ -2510,8 +2551,8 @@ 673 | vector(initializer_list __l, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ [182/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp -[183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp -[184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -c ../unittest/pbdata/CCSSequence_gtest.cpp +[183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -c ../unittest/pbdata/CCSSequence_gtest.cpp +[184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp [185/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp [186/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o -c ../unittest/pbdata/DNASequence_gtest.cpp [187/187] c++ -o unittest/libblasr_unittest unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_DNASequence_gtest.cpp.o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -I/usr/include/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 '-Wl,-rpath,$ORIGIN/..:/usr/lib/aarch64-linux-gnu/hdf5/serial' -Wl,-rpath-link,/build/pbseqlib-5.3.5+dfsg/obj-aarch64-linux-gnu/ -Wl,-rpath-link,/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,--start-group libblasr.so.5.3.5 /usr/lib/aarch64-linux-gnu/libpbbam.so /usr/lib/aarch64-linux-gnu/libpbcopper.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so -lrt /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/aarch64-linux-gnu/libgtest_main.a /usr/lib/aarch64-linux-gnu/libgtest.a -lpthread -Wl,--end-group @@ -2890,13 +2931,13 @@ dpkg-gencontrol: warning: package libblasr-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libblasr5.3.5' in '../libblasr5.3.5_5.3.5+dfsg-4_arm64.deb'. -dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.5+dfsg-4_arm64.deb'. -dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-4_arm64.deb'. dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.5+dfsg-4_arm64.deb'. +dpkg-deb: building package 'libblasr5.3.5-dbgsym' in '../libblasr5.3.5-dbgsym_5.3.5+dfsg-4_arm64.deb'. +dpkg-deb: building package 'libblasr5.3.5' in '../libblasr5.3.5_5.3.5+dfsg-4_arm64.deb'. dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.5+dfsg-4_arm64.deb'. +dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-4_arm64.deb'. +dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.5+dfsg-4_arm64.deb'. dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.5+dfsg-4_arm64.deb'. -dpkg-deb: building package 'libblasr5.3.5-dbgsym' in '../libblasr5.3.5-dbgsym_5.3.5+dfsg-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../pbseqlib_5.3.5+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../pbseqlib_5.3.5+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2904,12 +2945,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/16100/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/16100/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/20735 and its subdirectories -I: Current time: Wed Apr 26 07:33:37 -12 2023 -I: pbuilder-time-stamp: 1682537617 +I: removing directory /srv/workspace/pbuilder/16100 and its subdirectories +I: Current time: Wed May 29 16:03:54 +14 2024 +I: pbuilder-time-stamp: 1716948234