Diff of the two buildlogs: -- --- b1/build.log 2025-10-12 20:59:20.387201046 +0000 +++ b2/build.log 2025-10-12 21:04:13.919470293 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Oct 12 08:57:31 -12 2025 -I: pbuilder-time-stamp: 1760302651 +I: Current time: Sun Nov 15 17:22:22 +14 2026 +I: pbuilder-time-stamp: 1794712942 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -30,53 +30,85 @@ dpkg-source: info: applying gcc-14.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/796015/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2649825/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Nov 15 03:22 /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/2649825/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2649825/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + 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=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='854730631dd945d0a63fce1d335cdcc8' - 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='796015' - PS1='# ' - PS2='> ' + INVOCATION_ID=00f29d4fd48940de9786206654a626ee + 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=2649825 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.mujHZlrl/pbuilderrc_Yxrm --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mujHZlrl/b1 --logfile b1/build.log pbseqlib_5.3.5+dfsg-11.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.mujHZlrl/pbuilderrc_PRkJ --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mujHZlrl/b2 --logfile b2/build.log pbseqlib_5.3.5+dfsg-11.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/796015/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2649825/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -301,7 +333,7 @@ Get: 161 http://deb.debian.org/debian forky/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 162 http://deb.debian.org/debian forky/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 163 http://deb.debian.org/debian forky/main arm64 meson all 1.9.1-1 [665 kB] -Fetched 99.2 MB in 0s (277 MB/s) +Fetched 99.2 MB in 1s (154 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 20000 files and directories currently installed.) @@ -835,8 +867,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Oct 12 20:57:58 UTC 2025. -Universal Time is now: Sun Oct 12 20:57:58 UTC 2025. +Local time is now: Sun Nov 15 03:23:08 UTC 2026. +Universal Time is now: Sun Nov 15 03:23:08 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -986,7 +1018,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/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-11_source.changes +I: user script /srv/workspace/pbuilder/2649825/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2649825/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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-11_source.changes dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.5+dfsg-11 dpkg-buildpackage: info: source distribution unstable @@ -1053,8 +1089,7 @@ Found ninja-1.12.1 at /usr/bin/ninja dh_auto_build cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 ninja -j12 -v -[1/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFAttributable.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp -[2/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp +[1/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/BufferedHDF2DArray.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: @@ -1127,8 +1162,9 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[3/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp -[4/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFData.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp +[2/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFAttributable.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp +[3/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFData.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp +[4/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp [5/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_DatasetCollection.cpp.o -MF libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp [6/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: @@ -1144,12 +1180,13 @@ [7/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 [8/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp [9/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFAtom.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp -[10/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, - from ../hdf/HDF2DArray.hpp:4, - from ../hdf/HDFAlnInfoGroup.hpp:8, - from ../hdf/HDFAlnInfoGroup.cpp:1: +[10/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[11/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[12/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +In file included from ../hdf/HDFAtom.hpp:12, + from ../hdf/HDFBaseCallsWriter.hpp:11, + from ../hdf/HDFBaxWriter.hpp:12, + from ../hdf/HDFBaxWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -1157,6 +1194,8 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ +In file included from ../hdf/HDFWriterBase.hpp:11, + from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -1220,11 +1259,32 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[12/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -In file included from ../hdf/HDFAtom.hpp:12, - from ../hdf/HDFBaseCallsWriter.hpp:11, - from ../hdf/HDFBaxWriter.hpp:12, - from ../hdf/HDFBaxWriter.cpp:5: +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +In file included from ../hdf/HDFBaseCallsWriter.hpp:13: +../hdf/HDFZMWMetricsWriter.hpp:57:10: note: by ‘bool HDFZMWMetricsWriter::WriteOneZmw(const SMRTSequence&)’ + 57 | bool WriteOneZmw(const SMRTSequence& read); + | ^~~~~~~~~~~ +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +In file included from ../hdf/HDFBaseCallsWriter.hpp:14: +../hdf/HDFZMWWriter.hpp:53:10: note: by ‘bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord&)’ + 53 | bool WriteOneZmw(const PacBio::BAM::BamRecord& read); + | ^~~~~~~~~~~ +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +../hdf/HDFBaseCallsWriter.hpp:38:10: note: by ‘bool HDFBaseCallsWriter::WriteOneZmw(const SMRTSequence&)’ + 38 | bool WriteOneZmw(const SMRTSequence& read); + | ^~~~~~~~~~~ +[13/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[14/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +In file included from ../hdf/BufferedHDF2DArray.hpp:12, + from ../hdf/HDF2DArray.hpp:4, + from ../hdf/HDFRegionsWriter.hpp:9, + from ../hdf/HDFRegionsWriter.cpp:3: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -1232,8 +1292,6 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ -In file included from ../hdf/HDFWriterBase.hpp:11, - from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -1297,32 +1355,22 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -In file included from ../hdf/HDFBaseCallsWriter.hpp:13: -../hdf/HDFZMWMetricsWriter.hpp:57:10: note: by ‘bool HDFZMWMetricsWriter::WriteOneZmw(const SMRTSequence&)’ - 57 | bool WriteOneZmw(const SMRTSequence& read); - | ^~~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -In file included from ../hdf/HDFBaseCallsWriter.hpp:14: -../hdf/HDFZMWWriter.hpp:53:10: note: by ‘bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord&)’ - 53 | bool WriteOneZmw(const PacBio::BAM::BamRecord& read); - | ^~~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -../hdf/HDFBaseCallsWriter.hpp:38:10: note: by ‘bool HDFBaseCallsWriter::WriteOneZmw(const SMRTSequence&)’ - 38 | bool WriteOneZmw(const SMRTSequence& read); - | ^~~~~~~~~~~ -[13/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[14/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -In file included from ../hdf/BufferedHDF2DArray.hpp:12, - from ../hdf/HDF2DArray.hpp:4, - from ../hdf/HDFRegionsWriter.hpp:9, - from ../hdf/HDFRegionsWriter.cpp:3: +../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: +../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) + | ^~~~~~~~~~~~~~~~ +[15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +In file included from ../hdf/HDFAtom.hpp:12, + from ../hdf/HDFBaseCallsWriter.hpp:11, + from ../hdf/HDFPulseWriter.hpp:12, + from ../hdf/HDFPulseWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -1330,6 +1378,8 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ +In file included from ../hdf/HDFWriterBase.hpp:11, + from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -1393,18 +1443,33 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -../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: -../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) - | ^~~~~~~~~~~~~~~~ -[15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +In file included from ../hdf/HDFBaseCallsWriter.hpp:13: +../hdf/HDFZMWMetricsWriter.hpp:57:10: note: by ‘bool HDFZMWMetricsWriter::WriteOneZmw(const SMRTSequence&)’ + 57 | bool WriteOneZmw(const SMRTSequence& read); + | ^~~~~~~~~~~ +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +In file included from ../hdf/HDFBaseCallsWriter.hpp:14: +../hdf/HDFZMWWriter.hpp:53:10: note: by ‘bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord&)’ + 53 | bool WriteOneZmw(const PacBio::BAM::BamRecord& read); + | ^~~~~~~~~~~ +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +../hdf/HDFBaseCallsWriter.hpp:38:10: note: by ‘bool HDFBaseCallsWriter::WriteOneZmw(const SMRTSequence&)’ + 38 | bool WriteOneZmw(const SMRTSequence& read); + | ^~~~~~~~~~~ +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +In file included from ../hdf/HDFPulseWriter.hpp:13: +../hdf/HDFPulseCallsWriter.hpp:37:10: note: by ‘bool HDFPulseCallsWriter::WriteOneZmw(const SMRTSequence&)’ + 37 | bool WriteOneZmw(const SMRTSequence& read); + | ^~~~~~~~~~~ [16/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/HDFAtom.hpp:12, from ../hdf/HDFScanDataReader.hpp:8, @@ -1483,13 +1548,11 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[19/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -In file included from ../hdf/HDFAtom.hpp:12, - from ../hdf/HDFBaseCallsWriter.hpp:11, - from ../hdf/HDFPulseWriter.hpp:12, - from ../hdf/HDFPulseWriter.cpp:5: +[17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, + from ../hdf/HDF2DArray.hpp:4, + from ../hdf/HDFAlnInfoGroup.hpp:8, + from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -1497,8 +1560,6 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ -In file included from ../hdf/HDFWriterBase.hpp:11, - from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -1562,40 +1623,14 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -In file included from ../hdf/HDFBaseCallsWriter.hpp:13: -../hdf/HDFZMWMetricsWriter.hpp:57:10: note: by ‘bool HDFZMWMetricsWriter::WriteOneZmw(const SMRTSequence&)’ - 57 | bool WriteOneZmw(const SMRTSequence& read); - | ^~~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -In file included from ../hdf/HDFBaseCallsWriter.hpp:14: -../hdf/HDFZMWWriter.hpp:53:10: note: by ‘bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord&)’ - 53 | bool WriteOneZmw(const PacBio::BAM::BamRecord& read); - | ^~~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -../hdf/HDFBaseCallsWriter.hpp:38:10: note: by ‘bool HDFBaseCallsWriter::WriteOneZmw(const SMRTSequence&)’ - 38 | bool WriteOneZmw(const SMRTSequence& read); - | ^~~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -In file included from ../hdf/HDFPulseWriter.hpp:13: -../hdf/HDFPulseCallsWriter.hpp:37:10: note: by ‘bool HDFPulseCallsWriter::WriteOneZmw(const SMRTSequence&)’ - 37 | bool WriteOneZmw(const SMRTSequence& read); - | ^~~~~~~~~~~ -[20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[19/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 [21/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[22/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, - from ../hdf/HDF2DArray.hpp:4, - from ../hdf/HDFRegionTableReader.hpp:9, - from ../hdf/HDFRegionTableReader.cpp:1: +[22/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/HDFAtom.hpp:12, + from ../hdf/HDFBaseCallsWriter.hpp:11, + from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -1603,6 +1638,8 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ +In file included from ../hdf/HDFWriterBase.hpp:11, + from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -1666,10 +1703,32 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[23/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/HDFAtom.hpp:12, - from ../hdf/HDFBaseCallsWriter.hpp:11, - from ../hdf/HDFBaseCallsWriter.cpp:5: +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +In file included from ../hdf/HDFBaseCallsWriter.hpp:13: +../hdf/HDFZMWMetricsWriter.hpp:57:10: note: by ‘bool HDFZMWMetricsWriter::WriteOneZmw(const SMRTSequence&)’ + 57 | bool WriteOneZmw(const SMRTSequence& read); + | ^~~~~~~~~~~ +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +In file included from ../hdf/HDFBaseCallsWriter.hpp:14: +../hdf/HDFZMWWriter.hpp:53:10: note: by ‘bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord&)’ + 53 | bool WriteOneZmw(const PacBio::BAM::BamRecord& read); + | ^~~~~~~~~~~ +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +../hdf/HDFBaseCallsWriter.hpp:38:10: note: by ‘bool HDFBaseCallsWriter::WriteOneZmw(const SMRTSequence&)’ + 38 | bool WriteOneZmw(const SMRTSequence& read); + | ^~~~~~~~~~~ +[23/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[24/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, + from ../hdf/HDF2DArray.hpp:4, + from ../hdf/HDFRegionTableReader.hpp:9, + from ../hdf/HDFRegionTableReader.cpp:1: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -1677,8 +1736,6 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ -In file included from ../hdf/HDFWriterBase.hpp:11, - from ../hdf/HDFBaseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -1742,28 +1799,46 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -In file included from ../hdf/HDFBaseCallsWriter.hpp:13: -../hdf/HDFZMWMetricsWriter.hpp:57:10: note: by ‘bool HDFZMWMetricsWriter::WriteOneZmw(const SMRTSequence&)’ - 57 | bool WriteOneZmw(const SMRTSequence& read); - | ^~~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -In file included from ../hdf/HDFBaseCallsWriter.hpp:14: -../hdf/HDFZMWWriter.hpp:53:10: note: by ‘bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord&)’ - 53 | bool WriteOneZmw(const PacBio::BAM::BamRecord& read); - | ^~~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -../hdf/HDFBaseCallsWriter.hpp:38:10: note: by ‘bool HDFBaseCallsWriter::WriteOneZmw(const SMRTSequence&)’ - 38 | bool WriteOneZmw(const SMRTSequence& read); - | ^~~~~~~~~~~ -[24/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[25/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[25/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/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++/15/bits/alloc_traits.h:674:17: 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]’ + 674 | __a.construct(__p, std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_vector.h:1421:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ + 1421 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1422 | __x); + | ~~~~ +../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here + 112 | alignments.push_back(alignment); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ + 103 | Alignment &operator=(const Alignment &rhs); + | ^~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] + 58 | class Alignment : public AlignmentStats + | ^~~~~~~~~ +In file included from ../alignment/datastructures/alignment/Alignment.hpp:8: +../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ + 19 | AlignmentStats &operator=(const AlignmentStats &rhs); + | ^~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/string:45, + from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4: +/usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/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]’: @@ -1801,7 +1876,8 @@ /usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_ScoreMatrices.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp +[28/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, from ../hdf/HDFWriterBase.hpp:11, from ../hdf/HDFWriterBase.cpp:3: @@ -1875,11 +1951,11 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_ScoreMatrices.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp -[28/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_ExtendAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.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/KBandAlign.hpp:10, + from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, + from ../alignment/algorithms/alignment/ExtendAlign.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++/15/bits/alloc_traits.h:674:17: 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]’ 674 | __a.construct(__p, std::forward<_Args>(__args)...); @@ -1910,12 +1986,53 @@ | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/string:45, - from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:4: + from /usr/include/c++/15/vector:65, + from ../alignment/algorithms/alignment/ExtendAlign.hpp:6: +/usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[30/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[31/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[32/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/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++/15/bits/alloc_traits.h:674:17: 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]’ + 674 | __a.construct(__p, std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_vector.h:1421:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ + 1421 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1422 | __x); + | ~~~~ +../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here + 112 | alignments.push_back(alignment); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ + 103 | Alignment &operator=(const Alignment &rhs); + | ^~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] + 58 | class Alignment : public AlignmentStats + | ^~~~~~~~~ +In file included from ../alignment/datastructures/alignment/Alignment.hpp:8: +../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ + 19 | AlignmentStats &operator=(const AlignmentStats &rhs); + | ^~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/vector:65, + from ../alignment/algorithms/alignment/KBandAlign.hpp:7: /usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[33/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFZMWReader.hpp:8, @@ -1990,54 +2107,9 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[30/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp -[31/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[32/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[33/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/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++/15/bits/alloc_traits.h:674:17: 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]’ - 674 | __a.construct(__p, std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_vector.h:1421:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ - 1421 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1422 | __x); - | ~~~~ -../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here - 112 | alignments.push_back(alignment); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ - 103 | Alignment &operator=(const Alignment &rhs); - | ^~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] - 58 | class Alignment : public AlignmentStats - | ^~~~~~~~~ -In file included from ../alignment/datastructures/alignment/Alignment.hpp:8: -../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ - 19 | AlignmentStats &operator=(const AlignmentStats &rhs); - | ^~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/string:45, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from ../alignment/algorithms/alignment/GuidedAlign.hpp:6: -/usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp +[35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, from ../hdf/HDFZMWMetricsWriter.hpp:6, from ../hdf/HDFZMWMetricsWriter.cpp:3: @@ -2118,50 +2190,11 @@ ../hdf/HDFZMWMetricsWriter.hpp:57:10: note: by ‘bool HDFZMWMetricsWriter::WriteOneZmw(const SMRTSequence&)’ 57 | bool WriteOneZmw(const SMRTSequence& read); | ^~~~~~~~~~~ -[35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_ExtendAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp -In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/KBandAlign.hpp:10, - from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, - from ../alignment/algorithms/alignment/ExtendAlign.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++/15/bits/alloc_traits.h:674:17: 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]’ - 674 | __a.construct(__p, std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_vector.h:1421:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ - 1421 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1422 | __x); - | ~~~~ -../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here - 112 | alignments.push_back(alignment); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ - 103 | Alignment &operator=(const Alignment &rhs); - | ^~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] - 58 | class Alignment : public AlignmentStats - | ^~~~~~~~~ -In file included from ../alignment/datastructures/alignment/Alignment.hpp:8: -../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ - 19 | AlignmentStats &operator=(const AlignmentStats &rhs); - | ^~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/vector:65, - from ../alignment/algorithms/alignment/ExtendAlign.hpp:6: -/usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[38/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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++/15/bits/alloc_traits.h:674:17: 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]’ 674 | __a.construct(__p, std::forward<_Args>(__args)...); @@ -2192,17 +2225,24 @@ | ^~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/vector:65, - from ../alignment/algorithms/alignment/KBandAlign.hpp:7: + from /usr/include/c++/15/string:45, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from ../alignment/algorithms/alignment/GuidedAlign.hpp:6: /usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[38/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[39/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, - from ../hdf/HDFZMWWriter.hpp:10, - from ../hdf/HDFZMWWriter.cpp:5: +[39/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[42/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp +In file included from ../hdf/HDFAtom.hpp:12, + from ../hdf/HDFPulseCallsWriter.hpp:11, + from ../hdf/HDFPulseCallsWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -2210,6 +2250,8 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ +In file included from ../hdf/HDFWriterBase.hpp:11, + from ../hdf/HDFPulseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -2273,30 +2315,24 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -In file included from ../hdf/HDFZMWWriter.hpp:12: ../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); | ^~~~~~~~~~~ +In file included from ../hdf/HDFPulseCallsWriter.hpp:13: ../hdf/HDFZMWWriter.hpp:53:10: note: by ‘bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord&)’ 53 | bool WriteOneZmw(const PacBio::BAM::BamRecord& read); | ^~~~~~~~~~~ -[40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[42/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[43/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] + 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); + | ^~~~~~~~~~~ +../hdf/HDFPulseCallsWriter.hpp:37:10: note: by ‘bool HDFPulseCallsWriter::WriteOneZmw(const SMRTSequence&)’ + 37 | bool WriteOneZmw(const SMRTSequence& read); + | ^~~~~~~~~~~ [44/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[45/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[46/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_FindMaxInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp -In file included from ../alignment/algorithms/anchoring/FindMaxInterval.hpp:16, - from ../alignment/algorithms/anchoring/FindMaxInterval.cpp:1: -../alignment/statistics/VarianceAccumulator.hpp:14:27: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 14 | VarianceAccumulator(); - | ^ -../alignment/statistics/VarianceAccumulator.hpp:14:27: note: remove the ‘< >’ -[47/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp -In file included from ../hdf/HDFAtom.hpp:12, - from ../hdf/HDFPulseCallsWriter.hpp:11, - from ../hdf/HDFPulseCallsWriter.cpp:5: +[45/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/BufferedHDF2DArray.hpp:12, + from ../hdf/HDFZMWWriter.hpp:10, + from ../hdf/HDFZMWWriter.cpp:5: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -2304,8 +2340,6 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ -In file included from ../hdf/HDFWriterBase.hpp:11, - from ../hdf/HDFPulseCallsWriter.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -2369,20 +2403,25 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ +In file included from ../hdf/HDFZMWWriter.hpp:12: ../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); | ^~~~~~~~~~~ -In file included from ../hdf/HDFPulseCallsWriter.hpp:13: ../hdf/HDFZMWWriter.hpp:53:10: note: by ‘bool HDFZMWWriter::WriteOneZmw(const PacBio::BAM::BamRecord&)’ 53 | bool WriteOneZmw(const PacBio::BAM::BamRecord& read); | ^~~~~~~~~~~ -../hdf/HDFWriterBase.hpp:43:18: warning: ‘virtual bool HDFWriterBase::WriteOneZmw(const SMRTSequence&, const std::vector&)’ was hidden [-Woverloaded-virtual=] - 43 | virtual bool WriteOneZmw(const SMRTSequence& seq, const std::vector& regions); - | ^~~~~~~~~~~ -../hdf/HDFPulseCallsWriter.hpp:37:10: note: by ‘bool HDFPulseCallsWriter::WriteOneZmw(const SMRTSequence&)’ - 37 | bool WriteOneZmw(const SMRTSequence& read); - | ^~~~~~~~~~~ -[48/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[46/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[47/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_FindMaxInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o -c ../alignment/algorithms/anchoring/FindMaxInterval.cpp +In file included from ../alignment/algorithms/anchoring/FindMaxInterval.hpp:16, + from ../alignment/algorithms/anchoring/FindMaxInterval.cpp:1: +../alignment/statistics/VarianceAccumulator.hpp:14:27: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 14 | VarianceAccumulator(); + | ^ +../alignment/statistics/VarianceAccumulator.hpp:14:27: note: remove the ‘< >’ +[48/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[49/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[50/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_AlignmentCandidate.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -c ../alignment/datastructures/alignment/AlignmentCandidate.cpp +[51/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFUtils.hpp:7, @@ -2459,16 +2498,9 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[49/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[50/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[51/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_AlignmentCandidate.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -c ../alignment/datastructures/alignment/AlignmentCandidate.cpp -[52/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_BaseSequenceIO.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o -c ../alignment/files/BaseSequenceIO.cpp -[53/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[54/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_AnchorParameters.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -c ../alignment/datastructures/anchoring/AnchorParameters.cpp -[55/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_ClusterList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -c ../alignment/datastructures/anchoring/ClusterList.cpp -[56/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_alignmentset_SAMSupplementalQVList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -c ../alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp -[57/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB 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libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp +[53/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_BaseSequenceIO.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o -c ../alignment/files/BaseSequenceIO.cpp +[54/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_Alignment.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o -c ../alignment/datastructures/alignment/Alignment.cpp ../alignment/datastructures/alignment/Alignment.cpp: In member function ‘void blasr::Alignment::CopyStats(blasr::Alignment&)’: ../alignment/datastructures/alignment/Alignment.cpp:35:47: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 35 | AlignmentStats::CopyStats((AlignmentStats)rhs); @@ -2478,10 +2510,26 @@ ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ -[59/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[63/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[64/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +In file included from ../alignment/files/FragmentCCSIterator.hpp:6, + from ../alignment/files/FragmentCCSIterator.cpp:1: +../alignment/files/CCSIterator.hpp:13:18: warning: ‘virtual void CCSIterator::Initialize(CCSSequence*)’ was hidden [-Woverloaded-virtual=] + 13 | virtual void Initialize(CCSSequence *_seqPtr); + | ^~~~~~~~~~ +../alignment/files/FragmentCCSIterator.hpp:17:18: note: by ‘virtual void FragmentCCSIterator::Initialize(CCSSequence*, RegionTable*)’ + 17 | virtual void Initialize(CCSSequence *_seqPtr, RegionTable *_regionTablePtr); + | ^~~~~~~~~~ +[65/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[66/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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: @@ -2525,22 +2573,9 @@ /usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[63/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_FilterCriteria.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -c ../alignment/datastructures/alignment/FilterCriteria.cpp -[64/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[65/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -In file included from ../alignment/files/FragmentCCSIterator.hpp:6, - from ../alignment/files/FragmentCCSIterator.cpp:1: -../alignment/files/CCSIterator.hpp:13:18: warning: ‘virtual void CCSIterator::Initialize(CCSSequence*)’ was hidden [-Woverloaded-virtual=] - 13 | virtual void Initialize(CCSSequence *_seqPtr); - | ^~~~~~~~~~ -../alignment/files/FragmentCCSIterator.hpp:17:18: note: by ‘virtual void FragmentCCSIterator::Initialize(CCSSequence*, RegionTable*)’ - 17 | virtual void Initialize(CCSSequence *_seqPtr, RegionTable *_regionTablePtr); - | ^~~~~~~~~~ -[66/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 [68/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[69/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[70/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_LengthHistogram.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp +[69/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_LengthHistogram.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp In file included from /usr/include/c++/15/cassert:46, from ../alignment/statistics/StatUtils.hpp:5, from ../alignment/simulator/CDFMap.hpp:8, @@ -2553,46 +2588,42 @@ ../alignment/simulator/CDFMap.hpp:37:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 37 | assert(cdf.size() >= 0); | ~~~~~~~~~~~^~~~ +[70/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 [71/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[72/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[72/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 [73/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_TupleMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o -c ../alignment/tuples/TupleMetrics.cpp -[74/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall 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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 -[100/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[101/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always 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-O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC 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-ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[104/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC 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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&)’: ../pbdata/reads/RegionAnnotations.cpp:14:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 14 | for (auto annotation : annotations) { @@ -2637,8 +2668,22 @@ ../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) | ^~~~~~~~~~~~~~~~ -[111/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[112/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp +[106/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[107/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[108/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[109/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[111/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[112/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[113/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[114/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[115/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[116/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_TimeUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o -c ../pbdata/utils/TimeUtils.cpp +[117/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_SMRTTitle.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o -c ../pbdata/utils/SMRTTitle.cpp +[118/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[120/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_PulseFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o -c ../pbdata/reads/PulseFile.cpp +[121/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp In file included from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, @@ -2716,27 +2761,71 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[113/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB 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c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[117/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 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libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o -c ../pbdata/GFFFile.cpp +[125/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[126/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp +[127/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[128/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp +[129/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[130/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_CommandLineParser.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o -c ../pbdata/CommandLineParser.cpp +[131/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[132/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[133/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 +[135/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp +In file included from ../pbdata/FASTAReader.hpp:7, + from ../pbdata/BlasrFASTAReader.cpp:2: +../pbdata/FASTASequence.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = FASTASequence; _Args = {FASTASequence}; _Tp = FASTASequence]’: +/usr/include/c++/15/bits/alloc_traits.h:674:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = FASTASequence; _Args = {FASTASequence}; _Tp = FASTASequence; allocator_type = std::allocator]’ + 674 | __a.construct(__p, std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_uninitialized.h:1288:26: required from ‘void std::__relocate_object_a(_Tp*, _Up*, _Allocator&) [with _Tp = FASTASequence; _Up = FASTASequence; _Allocator = allocator]’ + 1288 | __traits::construct(__alloc, __dest, std::move(*__orig)); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_uninitialized.h:1317:26: required from ‘_ForwardIterator std::__relocate_a_1(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = allocator]’ + 1317 | std::__relocate_object_a(std::__addressof(*__cur), + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ + 1318 | std::__addressof(*__first), __alloc); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_uninitialized.h:1359:33: required from ‘_ForwardIterator std::__relocate_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = allocator]’ + 1359 | return std::__relocate_a_1(std::__niter_base(__first), + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1360 | std::__niter_base(__last), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1361 | std::__niter_base(__result), __alloc); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_vector.h:539:26: required from ‘static std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_S_relocate(pointer, pointer, pointer, _Tp_alloc_type&) [with _Tp = FASTASequence; _Alloc = std::allocator; pointer = FASTASequence*; _Tp_alloc_type = std::vector::_Tp_alloc_type]’ + 539 | return std::__relocate_a(__first, __last, __result, __alloc); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/vector.tcc:799:18: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; size_type = long unsigned int]’ + 799 | _S_relocate(__old_start, __old_finish, + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | __new_start, _M_get_Tp_allocator()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_vector.h:1146:4: required from ‘void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; size_type = long unsigned int]’ + 1146 | _M_default_append(__new_size - size()); + | ^~~~~~~~~~~~~~~~~ +../pbdata/BlasrFASTAReader.cpp:441:21: required from here + 441 | sequences.resize(nSeq); + | ~~~~~~~~~~~~~~~~^~~~~~ +../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared ‘constexpr DNASequence::DNASequence(const DNASequence&)’ is deprecated [-Wdeprecated-copy] + 19 | class FASTASequence : public DNASequence + | ^~~~~~~~~~~~~ +In file included from ../pbdata/FASTASequence.hpp:13: +../pbdata/DNASequence.hpp:51:18: note: because ‘DNASequence’ has user-provided ‘DNASequence& DNASequence::operator=(const DNASequence&)’ + 51 | DNASequence &operator=(const DNASequence &rhs); + | ^~~~~~~~ +In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, + from /usr/include/c++/15/bits/allocator.h:46, + from /usr/include/c++/15/string:45, + from ../pbdata/FASTAReader.hpp:5: +/usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[136/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, @@ -2813,59 +2902,6 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[134/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[135/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 -[136/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp -In file included from ../pbdata/FASTAReader.hpp:7, - from ../pbdata/BlasrFASTAReader.cpp:2: -../pbdata/FASTASequence.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = FASTASequence; _Args = {FASTASequence}; _Tp = FASTASequence]’: -/usr/include/c++/15/bits/alloc_traits.h:674:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = FASTASequence; _Args = {FASTASequence}; _Tp = FASTASequence; allocator_type = std::allocator]’ - 674 | __a.construct(__p, std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_uninitialized.h:1288:26: required from ‘void std::__relocate_object_a(_Tp*, _Up*, _Allocator&) [with _Tp = FASTASequence; _Up = FASTASequence; _Allocator = allocator]’ - 1288 | __traits::construct(__alloc, __dest, std::move(*__orig)); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_uninitialized.h:1317:26: required from ‘_ForwardIterator std::__relocate_a_1(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = allocator]’ - 1317 | std::__relocate_object_a(std::__addressof(*__cur), - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ - 1318 | std::__addressof(*__first), __alloc); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_uninitialized.h:1359:33: required from ‘_ForwardIterator std::__relocate_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = FASTASequence*; _ForwardIterator = FASTASequence*; _Allocator = allocator]’ - 1359 | return std::__relocate_a_1(std::__niter_base(__first), - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1360 | std::__niter_base(__last), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1361 | std::__niter_base(__result), __alloc); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_vector.h:539:26: required from ‘static std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_S_relocate(pointer, pointer, pointer, _Tp_alloc_type&) [with _Tp = FASTASequence; _Alloc = std::allocator; pointer = FASTASequence*; _Tp_alloc_type = std::vector::_Tp_alloc_type]’ - 539 | return std::__relocate_a(__first, __last, __result, __alloc); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/vector.tcc:799:18: required from ‘void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; size_type = long unsigned int]’ - 799 | _S_relocate(__old_start, __old_finish, - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | __new_start, _M_get_Tp_allocator()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_vector.h:1146:4: required from ‘void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = FASTASequence; _Alloc = std::allocator; size_type = long unsigned int]’ - 1146 | _M_default_append(__new_size - size()); - | ^~~~~~~~~~~~~~~~~ -../pbdata/BlasrFASTAReader.cpp:441:21: required from here - 441 | sequences.resize(nSeq); - | ~~~~~~~~~~~~~~~~^~~~~~ -../pbdata/FASTASequence.hpp:19:7: warning: implicitly-declared ‘constexpr DNASequence::DNASequence(const DNASequence&)’ is deprecated [-Wdeprecated-copy] - 19 | class FASTASequence : public DNASequence - | ^~~~~~~~~~~~~ -In file included from ../pbdata/FASTASequence.hpp:13: -../pbdata/DNASequence.hpp:51:18: note: because ‘DNASequence’ has user-provided ‘DNASequence& DNASequence::operator=(const DNASequence&)’ - 51 | DNASequence &operator=(const DNASequence &rhs); - | ^~~~~~~~ -In file included from /usr/include/aarch64-linux-gnu/c++/15/bits/c++allocator.h:33, - from /usr/include/c++/15/bits/allocator.h:46, - from /usr/include/c++/15/string:45, - from ../pbdata/FASTAReader.hpp:5: -/usr/include/c++/15/bits/new_allocator.h:191:11: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[137/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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 [138/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [139/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -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_SMRTSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o -c ../pbdata/SMRTSequence.cpp ../pbdata/SMRTSequence.cpp: In member function ‘void SMRTSequence::MadeFromSubreadsAsPolymerase(const std::vector&)’: @@ -2881,7 +2917,20 @@ ../pbdata/SMRTSequence.cpp:210:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 210 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ -[140/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[140/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[141/187] 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,-soname,libblasr.so.5.3.5 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,--start-group /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 +/usr/lib/aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libhts.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_cpp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +[142/187] /usr/bin/meson --internal symbolextractor /build/reproducible-path/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 +[143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../alignment/files/FragmentCCSIterator.hpp:6, from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:26: ../alignment/files/CCSIterator.hpp:13:18: warning: ‘virtual void CCSIterator::Initialize(CCSSequence*)’ was hidden [-Woverloaded-virtual=] @@ -2964,19 +3013,11 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[141/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:27: -../alignment/files/CCSIterator.hpp:13:18: warning: ‘virtual void CCSIterator::Initialize(CCSSequence*)’ was hidden [-Woverloaded-virtual=] - 13 | virtual void Initialize(CCSSequence *_seqPtr); - | ^~~~~~~~~~ -In file included from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:28: -../alignment/files/FragmentCCSIterator.hpp:17:18: note: by ‘virtual void FragmentCCSIterator::Initialize(CCSSequence*, RegionTable*)’ - 17 | virtual void Initialize(CCSSequence *_seqPtr, RegionTable *_regionTablePtr); - | ^~~~~~~~~~ +[145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionTableReader.hpp:9, - from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: + from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -3047,24 +3088,19 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[142/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[144/187] 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,-soname,libblasr.so.5.3.5 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,--start-group /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 -/usr/lib/aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libhts.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5_cpp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -[145/187] /usr/bin/meson --internal symbolextractor /build/reproducible-path/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 -[146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:27: +../alignment/files/CCSIterator.hpp:13:18: warning: ‘virtual void CCSIterator::Initialize(CCSSequence*)’ was hidden [-Woverloaded-virtual=] + 13 | virtual void Initialize(CCSSequence *_seqPtr); + | ^~~~~~~~~~ +In file included from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:28: +../alignment/files/FragmentCCSIterator.hpp:17:18: note: by ‘virtual void FragmentCCSIterator::Initialize(CCSSequence*, RegionTable*)’ + 17 | virtual void Initialize(CCSSequence *_seqPtr, RegionTable *_regionTablePtr); + | ^~~~~~~~~~ In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionTableReader.hpp:9, - from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: + from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -3135,16 +3171,16 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[148/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [149/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[151/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../alignment/files/ReaderAgglomerate.hpp:8, - from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: + from ../alignment/format/SAMHeaderPrinter.hpp:14, + from ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp:28: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -3217,12 +3253,14 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, - from ../alignment/files/ReaderAgglomerate.hpp:8, - from ../alignment/format/SAMHeaderPrinter.hpp:14, - from ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp:28: + from ../hdf/HDFUtils.hpp:7, + from ../unittest/hdf/HDFUtils_gtest.cpp:22: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -3295,8 +3333,7 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, from ../hdf/HDFRegionTableReader.hpp:9, @@ -3371,11 +3408,11 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/DatasetCollection.hpp:9, - from ../hdf/HDFBasReader.hpp:11, - from ../hdf/HDFUtils.hpp:7, - from ../unittest/hdf/HDFUtils_gtest.cpp:22: +[157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +In file included from ../hdf/BufferedHDF2DArray.hpp:12, + from ../hdf/HDF2DArray.hpp:4, + from ../hdf/HDFZMWReader.hpp:8, + from ../unittest/hdf/HDFZMWReader_gtest.cpp:22: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -3383,8 +3420,6 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ -In file included from ../hdf/HDF2DArray.hpp:4, - from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -3448,12 +3483,11 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -In file included from ../hdf/BufferedHDF2DArray.hpp:12, - from ../hdf/HDF2DArray.hpp:4, - from ../unittest/hdf/HDF2DArray_gtest.cpp:24: +[158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/DatasetCollection.hpp:9, + from ../hdf/HDFBasReader.hpp:11, + from ../alignment/files/ReaderAgglomerate.hpp:8, + from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -3461,6 +3495,8 @@ ../hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ +In file included from ../hdf/HDF2DArray.hpp:4, + from ../hdf/HDFBasReader.hpp:12: ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ @@ -3524,11 +3560,12 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../hdf/BufferedHDF2DArray.hpp:12, from ../hdf/HDF2DArray.hpp:4, - from ../hdf/HDFZMWReader.hpp:8, - from ../unittest/hdf/HDFZMWReader_gtest.cpp:22: + from ../unittest/hdf/HDF2DArray_gtest.cpp:24: ../hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: ../hdf/BufferedHDF2DArray.hpp:123:1: required from here 120 | void BufferedHDF2DArray::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \ @@ -3599,15 +3636,13 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_qvs_QualityValueVector_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -c ../unittest/pbdata/qvs/QualityValueVector_gtest.cpp +[164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_qvs_QualityValueVector_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -c ../unittest/pbdata/qvs/QualityValueVector_gtest.cpp +[165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [166/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [167/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/DatasetCollection.hpp:9, from ../hdf/HDFPlsReader.hpp:8, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: @@ -3683,8 +3718,9 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ +[169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp -[171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, @@ -3761,9 +3797,11 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -c ../unittest/hdf/HDFCCSReader_gtest.cpp +[173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp +[175/187] 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 +[176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -c ../unittest/hdf/HDFCCSReader_gtest.cpp In file included from ../hdf/DatasetCollection.hpp:9, from ../hdf/HDFBasReader.hpp:11, from ../hdf/HDFCCSReader.hpp:4, @@ -3840,12 +3878,12 @@ ../hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[177/187] 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 [178/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -c ../unittest/pbdata/utils_gtest.cpp -[179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -c ../unittest/pbdata/FASTQReader_gtest.cpp -[180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -c ../unittest/pbdata/SeqUtils_gtest.cpp -[181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -c ../unittest/pbdata/SMRTSequence_gtest.cpp +[179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -c ../unittest/pbdata/SeqUtils_gtest.cpp +[180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -c ../unittest/pbdata/FASTQReader_gtest.cpp +[181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[182/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -c ../unittest/pbdata/SMRTSequence_gtest.cpp ../unittest/pbdata/SMRTSequence_gtest.cpp: In function ‘SMRTSequence _make_a_smrt_read_(const std::string&, const UInt&, DNALength, DNALength, const std::string&, bool, bool, bool, int, int, char, int, char)’: ../unittest/pbdata/SMRTSequence_gtest.cpp:66:12: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 66 | return smrt; @@ -3914,9 +3952,7 @@ /usr/include/c++/15/bits/stl_vector.h:708:43: note: initializing argument 1 of ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = SMRTSequence; _Alloc = std::allocator; allocator_type = std::allocator]’ 708 | 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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp -[184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [185/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp [186/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 '-Wl,-rpath,$ORIGIN/..:/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 -Wl,--end-group @@ -4298,13 +4334,13 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.5+dfsg-11_arm64.deb'. -dpkg-deb: building package 'libblasr5.3.5-dbgsym' in '../libblasr5.3.5-dbgsym_5.3.5+dfsg-11_arm64.deb'. dpkg-deb: building package 'libblasr5.3.5' in '../libblasr5.3.5_5.3.5+dfsg-11_arm64.deb'. +dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.5+dfsg-11_arm64.deb'. dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.5+dfsg-11_arm64.deb'. +dpkg-deb: building package 'libblasr5.3.5-dbgsym' in '../libblasr5.3.5-dbgsym_5.3.5+dfsg-11_arm64.deb'. +dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-11_arm64.deb'. dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.5+dfsg-11_arm64.deb'. dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.5+dfsg-11_arm64.deb'. -dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-11_arm64.deb'. dpkg-genbuildinfo --build=binary -O../pbseqlib_5.3.5+dfsg-11_arm64.buildinfo dpkg-genchanges --build=binary -O../pbseqlib_5.3.5+dfsg-11_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4312,12 +4348,14 @@ 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/2649825/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2649825/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/796015 and its subdirectories -I: Current time: Sun Oct 12 08:59:19 -12 2025 -I: pbuilder-time-stamp: 1760302759 +I: removing directory /srv/workspace/pbuilder/2649825 and its subdirectories +I: Current time: Sun Nov 15 17:27:11 +14 2026 +I: pbuilder-time-stamp: 1794713231