https://launchpad.net/ubuntu/+source/biobambam2/2.0.185+ds-2/+build/28281880 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-077 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 3 May 01:37:23 ntpdate[1846]: adjust time server 10.131.248.1 offset -0.000954 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28281880 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-28281880 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28281880 Starting target for build PACKAGEBUILD-28281880 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28281880 'deb http://ftpmaster.internal/ubuntu oracular main universe' 'deb http://ftpmaster.internal/ubuntu oracular-security main universe' 'deb http://ftpmaster.internal/ubuntu oracular-updates main universe' 'deb http://ftpmaster.internal/ubuntu oracular-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-28281880 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28281880 Updating target for build PACKAGEBUILD-28281880 Get:1 http://ftpmaster.internal/ubuntu oracular InRelease [64.6 kB] Get:2 http://ftpmaster.internal/ubuntu oracular-security InRelease [64.6 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease [64.6 kB] Get:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 Packages [1401 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 Packages [15.3 MB] Get:8 http://ftpmaster.internal/ubuntu oracular/universe Translation-en [5980 kB] Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [99.9 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main Translation-en [34.1 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [242 kB] Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe Translation-en [81.6 kB] Fetched 23.9 MB in 2s (9662 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 177 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 121 MB of archives. After this operation, 78.3 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1build1 [193 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libnsl-dev amd64 1.3.0-3build3 [70.5 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libnsl2 amd64 1.3.0-3build3 [41.4 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1build1 [82.6 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libgssapi-krb5-2 amd64 1.20.1-6ubuntu2 [142 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libkrb5-3 amd64 1.20.1-6ubuntu2 [347 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libk5crypto3 amd64 1.20.1-6ubuntu2 [81.7 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libkrb5support0 amd64 1.20.1-6ubuntu2 [33.5 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libacl1 amd64 2.3.2-1build1 [16.8 kB] Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libapparmor1 amd64 4.0.0-beta3-0ubuntu3 [49.5 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libcap-ng0 amd64 0.8.4-2build2 [15.2 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libaudit1 amd64 1:3.1.2-2.1build1 [46.9 kB] Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libblkid1 amd64 2.39.3-9ubuntu6 [123 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libcap2 amd64 1:2.66-5ubuntu2 [30.0 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libcrypt-dev amd64 1:4.4.36-4build1 [112 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libcrypt1 amd64 1:4.4.36-4build1 [82.3 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpg-error-l10n all 1.47-3build2 [8064 B] Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpg-error0 amd64 1.47-3build2 [70.0 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcrypt20 amd64 1.10.3-2build1 [532 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1 [127 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libzstd1 amd64 1.5.5+dfsg2-2build1 [299 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libkmod2 amd64 31+20240202-2ubuntu7 [51.7 kB] Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 liblz4-1 amd64 1.9.4-1build1 [63.0 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu2 [227 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libselinux1 amd64 3.5-2ubuntu2 [79.6 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libmount1 amd64 2.39.3-9ubuntu6 [134 kB] Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [734 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdbm6t64 amd64 1.23-5.1build1 [34.4 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdbm-compat4t64 amd64 1.23-5.1build1 [6710 B] Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 libperl5.38t64 amd64 5.38.2-3.2build2 [4873 kB] Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 perl amd64 5.38.2-3.2build2 [231 kB] Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 perl-base amd64 5.38.2-3.2build2 [1823 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 liblocale-gettext-perl amd64 1.07-6ubuntu5 [15.8 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 libtext-iconv-perl amd64 1.7-8build3 [13.5 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main amd64 libtext-charwidth-perl amd64 0.04-11build3 [9358 B] Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnss-nisplus amd64 1.3-5build1 [22.4 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnss-nis amd64 3.1-0ubuntu7 [26.5 kB] Get:41 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu8.1 [20.4 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu7 [67.4 kB] Get:43 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu8.1 [2124 kB] Get:44 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-0ubuntu8.1 [3265 kB] Get:45 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-0ubuntu8.1 [682 kB] Get:46 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.0.13-0ubuntu3 [1002 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 libsystemd-shared amd64 255.4-1ubuntu8 [2067 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu4 [266 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.0.13-0ubuntu3 [1936 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd-dev all 255.4-1ubuntu8 [104 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd-sysv amd64 255.4-1ubuntu8 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd amd64 255.4-1ubuntu8 [3471 kB] Get:53 http://ftpmaster.internal/ubuntu oracular/main amd64 libsystemd0 amd64 255.4-1ubuntu8 [429 kB] Get:54 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libapt-pkg6.0t64 amd64 2.9.2 [987 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main amd64 libnettle8t64 amd64 3.9.1-2.2build1 [182 kB] Get:56 http://ftpmaster.internal/ubuntu oracular/main amd64 libhogweed6t64 amd64 3.9.1-2.2build1 [199 kB] Get:57 http://ftpmaster.internal/ubuntu oracular/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu2 [299 kB] Get:58 http://ftpmaster.internal/ubuntu oracular/main amd64 libunistring5 amd64 1.1-2build1 [535 kB] Get:59 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgnutls30t64 amd64 3.8.3-1.1ubuntu3.1 [998 kB] Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 apt amd64 2.9.2 [1403 kB] Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 apt-utils amd64 2.9.2 [223 kB] Get:62 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu1 [51.9 kB] Get:63 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-modules amd64 1.5.3-7ubuntu1 [284 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/main amd64 bzip2 amd64 1.0.8-5.1 [34.5 kB] Get:65 http://ftpmaster.internal/ubuntu oracular/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [34.3 kB] Get:66 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-14-base amd64 14-20240412-0ubuntu1 [47.6 kB] Get:67 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcc-s1 amd64 14-20240412-0ubuntu1 [78.5 kB] Get:68 http://ftpmaster.internal/ubuntu oracular/main amd64 libstdc++6 amd64 14-20240412-0ubuntu1 [795 kB] Get:69 http://ftpmaster.internal/ubuntu oracular/main amd64 libudev1 amd64 255.4-1ubuntu8 [174 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 libxxhash0 amd64 0.8.2-2build1 [24.1 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu2 [62.8 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2ubuntu6 [253 kB] Get:73 http://ftpmaster.internal/ubuntu oracular/main amd64 libffi8 amd64 3.4.6-1build1 [24.7 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 libidn2-0 amd64 2.3.7-2build1 [66.2 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main amd64 libtasn1-6 amd64 4.19.0-3build1 [43.9 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebconfclient0 amd64 0.271ubuntu3 [11.4 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main amd64 base-passwd amd64 3.6.3build1 [51.1 kB] Get:78 http://ftpmaster.internal/ubuntu oracular/main amd64 libassuan0 amd64 2.5.6-1build1 [37.3 kB] Get:79 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libsqlite3-0 amd64 3.45.3-1 [701 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main amd64 gpg amd64 2.4.4-2ubuntu17 [565 kB] Get:81 http://ftpmaster.internal/ubuntu oracular/main amd64 libreadline8t64 amd64 8.2-4build1 [153 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main amd64 readline-common all 8.2-4build1 [56.5 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu2 [148 kB] Get:84 http://ftpmaster.internal/ubuntu oracular/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu2 [108 kB] Get:85 http://ftpmaster.internal/ubuntu oracular/main amd64 gpg-agent amd64 2.4.4-2ubuntu17 [227 kB] Get:86 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgconf amd64 2.4.4-2ubuntu17 [103 kB] Get:87 http://ftpmaster.internal/ubuntu oracular/main amd64 pinentry-curses amd64 1.2.1-3ubuntu5 [35.2 kB] Get:88 http://ftpmaster.internal/ubuntu oracular/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main amd64 libnpth0t64 amd64 1.6-3.1build1 [8378 B] Get:90 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgv amd64 2.4.4-2ubuntu17 [157 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:92 http://ftpmaster.internal/ubuntu oracular/main amd64 libseccomp2 amd64 2.5.5-1ubuntu3 [50.3 kB] Get:93 http://ftpmaster.internal/ubuntu oracular/main amd64 debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:94 http://ftpmaster.internal/ubuntu oracular/main amd64 debconf all 1.5.86ubuntu1 [124 kB] Get:95 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam0g amd64 1.5.3-7ubuntu1 [67.8 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/main amd64 libargon2-1 amd64 0~20190702+dfsg-4build1 [20.8 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu3 [139 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main amd64 libjson-c5 amd64 0.17-1build1 [35.3 kB] Get:99 http://ftpmaster.internal/ubuntu oracular/main amd64 libuuid1 amd64 2.39.3-9ubuntu6 [35.2 kB] Get:100 http://ftpmaster.internal/ubuntu oracular/main amd64 libfdisk1 amd64 2.39.3-9ubuntu6 [146 kB] Get:101 http://ftpmaster.internal/ubuntu oracular/main amd64 mount amd64 2.39.3-9ubuntu6 [118 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/main amd64 libcom-err2 amd64 1.47.0-2.4~exp1ubuntu4 [22.8 kB] Get:103 http://ftpmaster.internal/ubuntu oracular/main amd64 libkeyutils1 amd64 1.6.3-3build1 [9490 B] Get:104 http://ftpmaster.internal/ubuntu oracular/main amd64 linux-libc-dev amd64 6.8.0-31.31 [1598 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/main amd64 base-files amd64 13.1ubuntu1 [73.8 kB] Get:106 http://ftpmaster.internal/ubuntu oracular/main amd64 debianutils amd64 5.17build1 [89.9 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main amd64 bash amd64 5.2.21-2ubuntu4 [794 kB] Get:108 http://ftpmaster.internal/ubuntu oracular/main amd64 bsdutils amd64 1:2.39.3-9ubuntu6 [95.0 kB] Get:109 http://ftpmaster.internal/ubuntu oracular/main amd64 coreutils amd64 9.4-3ubuntu6 [1412 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/main amd64 tar amd64 1.35+dfsg-3build1 [253 kB] Get:111 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 dpkg amd64 1.22.6ubuntu10 [1283 kB] Get:112 http://ftpmaster.internal/ubuntu oracular/main amd64 dash amd64 0.5.12-6ubuntu5 [89.8 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/main amd64 diffutils amd64 1:3.10-1build1 [177 kB] Get:114 http://ftpmaster.internal/ubuntu oracular/main amd64 findutils amd64 4.9.0-5build1 [298 kB] Get:115 http://ftpmaster.internal/ubuntu oracular/main amd64 grep amd64 3.11-4build1 [162 kB] Get:116 http://ftpmaster.internal/ubuntu oracular/main amd64 gzip amd64 1.12-1ubuntu3 [98.8 kB] Get:117 http://ftpmaster.internal/ubuntu oracular/main amd64 hostname amd64 3.23+nmu2ubuntu2 [11.1 kB] Get:118 http://ftpmaster.internal/ubuntu oracular/main amd64 login amd64 1:4.13+dfsg1-4ubuntu3 [202 kB] Get:119 http://ftpmaster.internal/ubuntu oracular/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu2 [188 kB] Get:120 http://ftpmaster.internal/ubuntu oracular/main amd64 sed amd64 4.9-2build1 [193 kB] Get:121 http://ftpmaster.internal/ubuntu oracular/main amd64 util-linux amd64 2.39.3-9ubuntu6 [1127 kB] Get:122 http://ftpmaster.internal/ubuntu oracular/main amd64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu oracular/main amd64 sysvinit-utils amd64 3.08-6ubuntu3 [34.2 kB] Get:124 http://ftpmaster.internal/ubuntu oracular/main amd64 logsave amd64 1.47.0-2.4~exp1ubuntu4 [22.5 kB] Get:125 http://ftpmaster.internal/ubuntu oracular/main amd64 libext2fs2t64 amd64 1.47.0-2.4~exp1ubuntu4 [222 kB] Get:126 http://ftpmaster.internal/ubuntu oracular/main amd64 e2fsprogs amd64 1.47.0-2.4~exp1ubuntu4 [601 kB] Get:127 http://ftpmaster.internal/ubuntu oracular/main amd64 optipng amd64 0.7.8+ds-1build2 [110 kB] Get:128 http://ftpmaster.internal/ubuntu oracular/main amd64 libpng16-16t64 amd64 1.6.43-5build1 [187 kB] Get:129 http://ftpmaster.internal/ubuntu oracular/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:130 http://ftpmaster.internal/ubuntu oracular/main amd64 libsmartcols1 amd64 2.39.3-9ubuntu6 [64.8 kB] Get:131 http://ftpmaster.internal/ubuntu oracular/main amd64 uuid-runtime amd64 2.39.3-9ubuntu6 [33.1 kB] Get:132 http://ftpmaster.internal/ubuntu oracular/main amd64 libattr1 amd64 1:2.5.2-1build1 [11.3 kB] Get:133 http://ftpmaster.internal/ubuntu oracular/main amd64 libmd0 amd64 1.1.0-2build1 [27.0 kB] Get:134 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu oracular/main amd64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu oracular/main amd64 libsepol2 amd64 3.5-2build1 [303 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main amd64 libsemanage2 amd64 3.5-1build5 [93.2 kB] Get:138 http://ftpmaster.internal/ubuntu oracular/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu3 [845 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu3 [59.1 kB] Get:140 http://ftpmaster.internal/ubuntu oracular/main amd64 libss2 amd64 1.47.0-2.4~exp1ubuntu4 [17.0 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/main amd64 mawk amd64 1.3.4.20240123-1build1 [127 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/main amd64 procps amd64 2:4.0.4-4ubuntu3 [708 kB] Get:143 http://ftpmaster.internal/ubuntu oracular/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main amd64 ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu oracular/main amd64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 tzdata all 2024a-4ubuntu1 [274 kB] Get:147 http://ftpmaster.internal/ubuntu oracular/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/main amd64 bsdextrautils amd64 2.39.3-9ubuntu6 [73.8 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpm2 amd64 1.20.7-11 [14.1 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/main amd64 libip4tc2 amd64 1.8.10-3ubuntu2 [23.3 kB] Get:151 http://ftpmaster.internal/ubuntu oracular/main amd64 libjansson4 amd64 2.14-2build2 [32.8 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main amd64 psmisc amd64 23.7-1build1 [179 kB] Get:153 http://ftpmaster.internal/ubuntu oracular/main amd64 xz-utils amd64 5.6.1+really5.4.5-1 [267 kB] Get:154 http://ftpmaster.internal/ubuntu oracular/main amd64 advancecomp amd64 2.5-1build1 [182 kB] Get:155 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42-4ubuntu2 [851 kB] Get:156 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42-4ubuntu2 [94.5 kB] Get:157 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42-4ubuntu2 [97.1 kB] Get:158 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42-4ubuntu2 [2469 kB] Get:159 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42-4ubuntu2 [572 kB] Get:160 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42-4ubuntu2 [18.0 kB] Get:161 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42-4ubuntu2 [239 kB] Get:162 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42-4ubuntu2 [14.8 kB] Get:163 http://ftpmaster.internal/ubuntu oracular/main amd64 libubsan1 amd64 14-20240412-0ubuntu1 [1175 kB] Get:164 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-13 amd64 13.2.0-23ubuntu4 [14.5 kB] Get:165 http://ftpmaster.internal/ubuntu oracular/main amd64 libstdc++-13-dev amd64 13.2.0-23ubuntu4 [2399 kB] Get:166 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14-20240412-0ubuntu1 [147 kB] Get:167 http://ftpmaster.internal/ubuntu oracular/main amd64 libitm1 amd64 14-20240412-0ubuntu1 [28.9 kB] Get:168 http://ftpmaster.internal/ubuntu oracular/main amd64 libatomic1 amd64 14-20240412-0ubuntu1 [10.4 kB] Get:169 http://ftpmaster.internal/ubuntu oracular/main amd64 libasan8 amd64 14-20240412-0ubuntu1 [3024 kB] Get:170 http://ftpmaster.internal/ubuntu oracular/main amd64 liblsan0 amd64 14-20240412-0ubuntu1 [1313 kB] Get:171 http://ftpmaster.internal/ubuntu oracular/main amd64 libhwasan0 amd64 14-20240412-0ubuntu1 [1632 kB] Get:172 http://ftpmaster.internal/ubuntu oracular/main amd64 libquadmath0 amd64 14-20240412-0ubuntu1 [153 kB] Get:173 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13 amd64 13.2.0-23ubuntu4 [482 kB] Get:174 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcc-13-dev amd64 13.2.0-23ubuntu4 [2688 kB] Get:175 http://ftpmaster.internal/ubuntu oracular/main amd64 libtsan2 amd64 14-20240412-0ubuntu1 [2736 kB] Get:176 http://ftpmaster.internal/ubuntu oracular/main amd64 libcc1-0 amd64 14-20240412-0ubuntu1 [47.7 kB] Get:177 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-13 amd64 13.2.0-23ubuntu4 [1032 B] Get:178 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13-base amd64 13.2.0-23ubuntu4 [49.0 kB] Get:179 http://ftpmaster.internal/ubuntu oracular/main amd64 libisl23 amd64 0.26-3build1 [680 kB] Get:180 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpfr6 amd64 4.2.1-1build1 [355 kB] Get:181 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpc3 amd64 1.3.1-1build1 [54.5 kB] Get:182 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [21.9 MB] Get:183 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [12.5 MB] Get:184 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [11.2 MB] Get:185 http://ftpmaster.internal/ubuntu oracular/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:186 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:187 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:188 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:189 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:190 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:191 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 dpkg-dev all 1.22.6ubuntu10 [1074 kB] Get:192 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libdpkg-perl all 1.22.6ubuntu10 [269 kB] Get:193 http://ftpmaster.internal/ubuntu oracular/main amd64 patch amd64 2.7.6-7build3 [104 kB] Get:194 http://ftpmaster.internal/ubuntu oracular/main amd64 make amd64 4.3-4.1build2 [180 kB] Get:195 http://ftpmaster.internal/ubuntu oracular/main amd64 lto-disabled-list all 47 [12.4 kB] Get:196 http://ftpmaster.internal/ubuntu oracular/main amd64 libfakeroot amd64 1.34-1 [32.4 kB] Get:197 http://ftpmaster.internal/ubuntu oracular/main amd64 fakeroot amd64 1.34-1 [67.2 kB] Get:198 http://ftpmaster.internal/ubuntu oracular/main amd64 liblockfile-bin amd64 1.17-1build3 [11.2 kB] Get:199 http://ftpmaster.internal/ubuntu oracular/main amd64 liblockfile1 amd64 1.17-1build3 [6840 B] Get:200 http://ftpmaster.internal/ubuntu oracular/main amd64 lockfile-progs amd64 0.1.19build2 [8522 B] Preconfiguring packages ... 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Setting up libctf0:amd64 (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up cpp-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build2) ... Setting up libgprofng0:amd64 (2.42-4ubuntu2) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19build2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu10) ... Setting up libreadline8t64:amd64 (8.2-4build1) ... Setting up libgcc-13-dev:amd64 (13.2.0-23ubuntu4) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:amd64 (2.39-0ubuntu8.1) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:amd64 (13.2.0-23ubuntu4) ... Setting up binutils-x86-64-linux-gnu (2.42-4ubuntu2) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-23ubuntu4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.1build1) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up binutils (2.42-4ubuntu2) ... Setting up dpkg-dev (1.22.6ubuntu10) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu4) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:amd64 (1.3.0-3build3) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:amd64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:amd64 (3.1-0ubuntu7) ... Setting up libnsl-dev:amd64 (1.3.0-3build3) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu4) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15825 files and directories currently installed.) Purging configuration files for libssl3:amd64 (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28281880 amd64 oracular-proposed -c chroot:build-PACKAGEBUILD-28281880 --arch=amd64 --dist=oracular-proposed --nolog -A biobambam2_2.0.185+ds-2.dsc Initiating build PACKAGEBUILD-28281880 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-077.buildd +==============================================================================+ | biobambam2 2.0.185+ds-2 (amd64) Fri, 03 May 2024 01:37:52 +0000 | +==============================================================================+ Package: biobambam2 Version: 2.0.185+ds-2 Source Version: 2.0.185+ds-2 Distribution: oracular-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28281880/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/biobambam2-PT97ga/resolver-iXAa19' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- biobambam2_2.0.185+ds-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/biobambam2-PT97ga/biobambam2-2.0.185+ds' with '<>' I: NOTICE: Log filtering will replace 'build/biobambam2-PT97ga' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), pkgconf, libmaus2-dev (>= 2.0.800), libxerces-c-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), pkgconf, libmaus2-dev (>= 2.0.800), libxerces-c-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [405 B] Get:5 copy:/<>/apt_archive ./ Packages [486 B] Fetched 1848 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libbrotli1 libcurl3t64-gnutls libdebhelper-perl libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libgpgme11t64 libicu-dev libicu74 libldap2 libmagic-mgc libmagic1t64 libmaus2-2 libmaus2-dev libnghttp2-14 libpipeline1 libpkgconf3 libpsl5t64 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxerces-c-dev libxerces-c3.2t64 libxml2 m4 man-db pkgconf pkgconf-bin po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff icu-doc secrecy libtool-doc gfortran | fortran95-compiler gcj-jdk libxerces-c-doc m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl dirmngr gpg-wks-client gpgsm libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libbrotli1 libcurl3t64-gnutls libdebhelper-perl libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libgpgme11t64 libicu-dev libicu74 libldap2 libmagic-mgc libmagic1t64 libmaus2-2 libmaus2-dev libnghttp2-14 libpipeline1 libpkgconf3 libpsl5t64 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxerces-c-dev libxerces-c3.2t64 libxml2 m4 man-db pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 42.3 MB of archives. After this operation, 224 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [700 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libelf1t64 amd64 0.190-1.1build4 [57.6 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libicu74 amd64 74.2-1ubuntu3 [10.9 MB] Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu3 [762 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libmagic-mgc amd64 1:5.45-3build1 [307 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libmagic1t64 amd64 1:5.45-3build1 [87.2 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 file amd64 1:5.45-3build1 [22.0 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 gettext-base amd64 0.21-14ubuntu2 [38.4 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libuchardet0 amd64 0.0.8-1build1 [75.3 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 groff-base amd64 1.23.0-3build2 [1020 kB] Get:11 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http://ftpmaster.internal/ubuntu oracular/main amd64 libtool all 2.4.7-7build1 [166 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libdw1t64 amd64 0.190-1.1build4 [261 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 debugedit amd64 1:5.0-5build2 [46.1 kB] Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 dwz amd64 0.15-1build6 [115 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 gettext amd64 0.21-14ubuntu2 [864 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 debhelper all 13.14.1ubuntu5 [869 kB] Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 icu-devtools amd64 74.2-1ubuntu3 [212 kB] Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 libbrotli1 amd64 1.1.0-2build2 [331 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-5ubuntu3 [20.3 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-5ubuntu3 [53.2 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main amd64 libldap2 amd64 2.6.7+dfsg-1~exp1ubuntu8 [195 kB] Get:39 http://ftpmaster.internal/ubuntu oracular/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build7 [56.3 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 libssh-4 amd64 0.10.6-2build2 [188 kB] Get:41 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libcurl3t64-gnutls amd64 8.5.0-2ubuntu10.1 [333 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpgme11t64 amd64 1.18.0-4.1ubuntu4 [136 kB] Get:43 http://ftpmaster.internal/ubuntu oracular/main amd64 libicu-dev amd64 74.2-1ubuntu3 [11.9 MB] Get:44 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaus2-2 amd64 2.0.813+ds-1build1 [1563 kB] Get:45 http://ftpmaster.internal/ubuntu oracular/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1ubuntu2 [894 kB] Get:46 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaus2-dev amd64 2.0.813+ds-1build1 [4616 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 libpkgconf3 amd64 1.8.1-2build1 [30.7 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxerces-c3.2t64 amd64 3.2.4+debian-1.2ubuntu2 [919 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxerces-c-dev amd64 3.2.4+debian-1.2ubuntu2 [1815 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/main amd64 pkgconf-bin amd64 1.8.1-2build1 [20.7 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/main amd64 pkgconf amd64 1.8.1-2build1 [16.8 kB] Preconfiguring packages ... Fetched 42.3 MB in 0s (127 MB/s) Selecting previously unselected package libelf1t64:amd64. (Reading database ... 15825 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.190-1.1build4_amd64.deb ... Unpacking libelf1t64:amd64 (0.190-1.1build4) ... Selecting previously unselected package libicu74:amd64. Preparing to unpack .../01-libicu74_74.2-1ubuntu3_amd64.deb ... Unpacking libicu74:amd64 (74.2-1ubuntu3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3ubuntu3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3build1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3build1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3build1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3build1) ... 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Setting up autopoint (0.21-14ubuntu2) ... Setting up pkgconf-bin (1.8.1-2build1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-5ubuntu3) ... Setting up libssh-4:amd64 (0.10.6-2build2) ... Setting up autoconf (2.71-3) ... Setting up libicu74:amd64 (74.2-1ubuntu3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build6) ... Setting up libuchardet0:amd64 (0.0.8-1build1) ... Setting up debugedit (1:5.0-5build2) ... Setting up libsub-override-perl (0.10-1) ... Setting up libgpgme11t64:amd64 (1.18.0-4.1ubuntu4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu8) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14ubuntu2) ... Setting up libtool (2.4.7-7build1) ... Setting up libmaus2-2:amd64 (2.0.813+ds-1build1) ... Setting up libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu10.1) ... Setting up libxerces-c3.2t64:amd64 (3.2.4+debian-1.2ubuntu2) ... Setting up pkgconf:amd64 (1.8.1-2build1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up icu-devtools (74.2-1ubuntu3) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build2) ... Setting up libicu-dev:amd64 (74.2-1ubuntu3) ... Setting up libmaus2-dev (2.0.813+ds-1build1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-4build2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up libxerces-c-dev:amd64 (3.2.4+debian-1.2ubuntu2) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu10 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8.1 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.9.2 apt-utils_2.9.2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13.1ubuntu1 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-x86-64-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu4 cpp-13-x86-64-linux-gnu_13.2.0-23ubuntu4 cpp-x86-64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu10 dpkg-dev_1.22.6ubuntu10 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.34-1 file_1:5.45-3build1 findutils_4.9.0-5build1 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu4 g++-13-x86-64-linux-gnu_13.2.0-23ubuntu4 g++-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu4 gcc-13-base_13.2.0-23ubuntu4 gcc-13-x86-64-linux-gnu_13.2.0-23ubuntu4 gcc-14-base_14-20240412-0ubuntu1 gcc-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu2 gettext-base_0.21-14ubuntu2 gpg_2.4.4-2ubuntu17 gpg-agent_2.4.4-2ubuntu17 gpgconf_2.4.4-2ubuntu17 gpgv_2.4.4-2ubuntu17 grep_3.11-4build1 groff-base_1.23.0-3build2 gzip_1.12-1ubuntu3 hostname_3.23+nmu2ubuntu2 icu-devtools_74.2-1ubuntu3 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-1build1 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.9.2 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4build1 libasan8_14-20240412-0ubuntu1 libassuan0_2.5.6-1build1 libatomic1_14-20240412-0ubuntu1 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libbinutils_2.42-4ubuntu2 libblkid1_2.39.3-9ubuntu6 libbrotli1_1.1.0-2build2 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8.1 libc-dev-bin_2.39-0ubuntu8.1 libc6_2.39-0ubuntu8.1 libc6-dev_2.39-0ubuntu8.1 libcap-ng0_0.8.4-2build2 libcap2_1:2.66-5ubuntu2 libcc1-0_14-20240412-0ubuntu1 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcurl3t64-gnutls_8.5.0-2ubuntu10.1 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu10 libdw1t64_0.190-1.1build4 libelf1t64_0.190-1.1build4 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfakeroot_1.34-1 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-23ubuntu4 libgcc-s1_14-20240412-0ubuntu1 libgcrypt20_1.10.3-2build1 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgmp10_2:6.3.0+dfsg-2ubuntu6 libgnutls30t64_3.8.3-1.1ubuntu3.1 libgomp1_14-20240412-0ubuntu1 libgpg-error-l10n_1.47-3build2 libgpg-error0_1.47-3build2 libgpgme11t64_1.18.0-4.1ubuntu4 libgpm2_1.20.7-11 libgprofng0_2.42-4ubuntu2 libgssapi-krb5-2_1.20.1-6ubuntu2 libhogweed6t64_3.9.1-2.2build1 libhwasan0_14-20240412-0ubuntu1 libicu-dev_74.2-1ubuntu3 libicu74_74.2-1ubuntu3 libidn2-0_2.3.7-2build1 libip4tc2_1.8.10-3ubuntu2 libisl23_0.26-3build1 libitm1_14-20240412-0ubuntu1 libjansson4_2.14-2build2 libjson-c5_0.17-1build1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3build1 libkmod2_31+20240202-2ubuntu7 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 libldap2_2.6.7+dfsg-1~exp1ubuntu8 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 liblsan0_14-20240412-0ubuntu1 liblz4-1_1.9.4-1build1 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmaus2-2_2.0.813+ds-1build1 libmaus2-dev_2.0.813+ds-1build1 libmd0_1.1.0-2build1 libmount1_2.39.3-9ubuntu6 libmpc3_1.3.1-1build1 libmpfr6_4.2.1-1build1 libncursesw6_6.4+20240113-1ubuntu2 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zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: biobambam2 Binary: biobambam2 Architecture: any Version: 2.0.185+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://gitlab.com/german.tischler/biobambam2 Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/biobambam2 Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), pkgconf, libmaus2-dev (>= 2.0.800), libxerces-c-dev Package-List: biobambam2 deb science optional arch=any Checksums-Sha1: 2776b598958c159faa1147765a37a9be788c8725 249000 biobambam2_2.0.185+ds.orig.tar.xz a6d8b9f5865c14806d595f2ac8cd188e3f9edcd2 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Checksums-Sha256: 90cc8328f4e78771cf87cc918d890d12073cbbfbcad7cf94e35b655e3ec2747a 249000 biobambam2_2.0.185+ds.orig.tar.xz 5010ff92699f48db055e33a6ddda005ed339388cc1995503e985325e4d53652c 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Files: d0c485318daa583137b98d18fd0add77 249000 biobambam2_2.0.185+ds.orig.tar.xz bc64f60dd4ccfa2477438dcd2db1131e 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Dgit: 8e56855700614f8a0ddddf4fd2cb5611e10015e4 debian archive/debian/2.0.185+ds-2 https://git.dgit.debian.org/biobambam2 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmYikWMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrX1A//dGe1VAwa3juRlsGgmA9kRTYR+J89 x2/kBqtpIS8cO7onEyZ2MDixN7hFFq9QHCh0w7q1vBpdMMmPXJ5doQIQuTVcvWia Ugv0eGCk7v6Mja6dwECg9/JZ9IKn4BDQ0Mxectx/vWqEaa1BDhX4OLA6TfiluenO bYa0mcj4zm4jtlw1MbFYLOmf3d4fkSrDCtAqacc/DfchuesLVBkBaxb6oX/RuPzP T41aTROw4wxydmqd/04LSEXvJ55mZqzjihN+o12VpSsfdjsjQn/1WV9O7MmLbzdz 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Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28281880 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28281880 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28281880 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package biobambam2 dpkg-buildpackage: info: source version 2.0.185+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean rm -f config.log make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:2: warning: The macro `AC_CANONICAL_SYSTEM' is obsolete. configure.ac:2: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:2: the top level configure.ac:3: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:3: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:3: the top level configure.ac:6: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:6: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:1089: AM_CONFIG_HEADER is expanded from... configure.ac:6: the top level configure.ac:9: warning: The macro `AC_CANONICAL_SYSTEM' is obsolete. configure.ac:9: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:9: the top level configure.ac:68: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.ac:68: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... configure.ac:68: the top level configure.ac:147: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:147: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:147: the top level configure.ac:464: warning: AC_OUTPUT should be used without arguments. configure.ac:464: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... no checking for mawk... mawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking whether we are cross compiling... no checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking dependency style of g++... none checking whether the C++ compiler supports the -fsanitize=address flag... yes configure: Adding optimisation options -O3 to C compiler gcc flags, full list now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 configure: Adding optimisation options -O3 to C++ compiler g++ flags, full list now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for egrep... (cached) /usr/bin/grep -E checking for libmaus2 >= 2.0.800... yes checking whether we can compile a program using libmaus2... yes checking whether pthread_mutexattr_settype supports PTHREAD_MUTEX_RECURSIVE_NP... yes checking whether pthread_mutexattr_settype supports PTHREAD_MUTEX_RECURSIVE... yes checking whether libmaus2 has support for io_lib... no checking for bash... /usr/bin/bash checking for base64... /usr/bin/base64 checking for xerces-c >= 3.1.1... yes configure: Using flags -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 for C compiler gcc configure: Using flags -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 for C++ compiler g++ checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating src/biobambam2/BamBamConfig.hpp config.status: creating config.h config.status: executing libtool commands config.status: executing depfiles commands dh_auto_build make -j4 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in src make[3]: Entering directory '/<>/src' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamtofastq-bamtofastq.o `test -f 'programs/bamtofastq.cpp' || echo './'`programs/bamtofastq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bammarkduplicates-bammarkduplicates.o `test -f 'programs/bammarkduplicates.cpp' || echo './'`programs/bammarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bammarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamsort-bamsort.o `test -f 'programs/bamsort.cpp' || echo './'`programs/bamsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bammaskflags-bammaskflags.o `test -f 'programs/bammaskflags.cpp' || echo './'`programs/bammaskflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bammaskflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamrecompress-bamrecompress.o `test -f 'programs/bamrecompress.cpp' || echo './'`programs/bamrecompress.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamrecompress-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamadapterfind-bamadapterfind.o `test -f 'programs/bamadapterfind.cpp' || echo './'`programs/bamadapterfind.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamadapterfind-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamadapterfind-ClipAdapters.o `test -f 'biobambam2/ClipAdapters.cpp' || echo './'`biobambam2/ClipAdapters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamadapterfind-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilteraux-bamfilteraux.o `test -f 'programs/bamfilteraux.cpp' || echo './'`programs/bamfilteraux.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilteraux-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamauxsort-bamauxsort.o `test -f 'programs/bamauxsort.cpp' || echo './'`programs/bamauxsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamauxsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamadapterclip-bamadapterclip.o `test -f 'programs/bamadapterclip.cpp' || echo './'`programs/bamadapterclip.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamadapterclip-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamadapterclip-ClipAdapters.o `test -f 'biobambam2/ClipAdapters.cpp' || echo './'`biobambam2/ClipAdapters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamcollate2-bamcollate2.o `test -f 'programs/bamcollate2.cpp' || echo './'`programs/bamcollate2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamcollate2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamcollate2-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamcollate2-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bam12auxmerge-bam12auxmerge.o `test -f 'programs/bam12auxmerge.cpp' || echo './'`programs/bam12auxmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12auxmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12auxmerge-Split12.o `test -f 'biobambam2/Split12.cpp' || echo './'`biobambam2/Split12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12auxmerge-Strip12.o `test -f 'biobambam2/Strip12.cpp' || echo './'`biobambam2/Strip12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12auxmerge-ClipReinsert.o `test -f 'biobambam2/ClipReinsert.cpp' || echo './'`biobambam2/ClipReinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12auxmerge-zzToName.o `test -f 'biobambam2/zzToName.cpp' || echo './'`biobambam2/zzToName.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bam12split-bam12split.o `test -f 'programs/bam12split.cpp' || echo './'`programs/bam12split.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12split-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12split-Split12.o `test -f 'biobambam2/Split12.cpp' || echo './'`biobambam2/Split12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bam12strip-bam12strip.o `test -f 'programs/bam12strip.cpp' || echo './'`programs/bam12strip.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12strip-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bam12strip-Strip12.o `test -f 'biobambam2/Strip12.cpp' || echo './'`biobambam2/Strip12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamreset-bamreset.o `test -f 'programs/bamreset.cpp' || echo './'`programs/bamreset.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreset-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreset-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamrank-bamrank.o `test -f 'programs/bamrank.cpp' || echo './'`programs/bamrank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamrank-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamrank-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamclipreinsert-bamclipreinsert.o `test -f 'programs/bamclipreinsert.cpp' || echo './'`programs/bamclipreinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamclipreinsert-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamclipreinsert-ClipReinsert.o `test -f 'biobambam2/ClipReinsert.cpp' || echo './'`biobambam2/ClipReinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamclipXT-bamclipXT.o `test -f 'programs/bamclipXT.cpp' || echo './'`programs/bamclipXT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamclipXT-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamzztoname-bamzztoname.o `test -f 'programs/bamzztoname.cpp' || echo './'`programs/bamzztoname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamzztoname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamzztoname-zzToName.o `test -f 'biobambam2/zzToName.cpp' || echo './'`biobambam2/zzToName.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamindex-bamindex.o `test -f 'programs/bamindex.cpp' || echo './'`programs/bamindex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamindex-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilterflags-bamfilterflags.o `test -f 'programs/bamfilterflags.cpp' || echo './'`programs/bamfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilterrg-bamfilterrg.o `test -f 'programs/bamfilterrg.cpp' || echo './'`programs/bamfilterrg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterrg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamdownsamplerandom-bamdownsamplerandom.o `test -f 'programs/bamdownsamplerandom.cpp' || echo './'`programs/bamdownsamplerandom.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamdownsamplerandom-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bammarkduplicates2-bammarkduplicates2.o `test -f 'programs/bammarkduplicates2.cpp' || echo './'`programs/bammarkduplicates2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bammarkduplicates2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamcat-bamcat.o `test -f 'programs/bamcat.cpp' || echo './'`programs/bamcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bammerge-bammerge.o `test -f 'programs/bammerge.cpp' || echo './'`programs/bammerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bammerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamsplit-bamsplit.o `test -f 'programs/bamsplit.cpp' || echo './'`programs/bamsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfastsplit-bamfastsplit.o `test -f 'programs/bamfastsplit.cpp' || echo './'`programs/bamfastsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfastsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamsplitdiv-bamsplitdiv.o `test -f 'programs/bamsplitdiv.cpp' || echo './'`programs/bamsplitdiv.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamsplitdiv-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamchecksort-bamchecksort.o `test -f 'programs/bamchecksort.cpp' || echo './'`programs/bamchecksort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamchecksort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/fastqtobam-fastqtobam.o `test -f 'programs/fastqtobam.cpp' || echo './'`programs/fastqtobam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/fastqtobam-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfixmateinformation-bamfixmateinformation.o `test -f 'programs/bamfixmateinformation.cpp' || echo './'`programs/bamfixmateinformation.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfixmateinformation-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamseqchksum-bamseqchksum.o `test -f 'programs/bamseqchksum.cpp' || echo './'`programs/bamseqchksum.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamseqchksum-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/normalisefasta-normalisefasta.o `test -f 'programs/normalisefasta.cpp' || echo './'`programs/normalisefasta.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/normalisefasta-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilterheader-bamfilterheader.o `test -f 'programs/bamfilterheader.cpp' || echo './'`programs/bamfilterheader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterheader-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilterheader2-bamfilterheader2.o `test -f 'programs/bamfilterheader2.cpp' || echo './'`programs/bamfilterheader2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterheader2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bammdnm-bammdnm.o `test -f 'programs/bammdnm.cpp' || echo './'`programs/bammdnm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bammdnm-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bammapdist-bammapdist.o `test -f 'programs/bammapdist.cpp' || echo './'`programs/bammapdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bammapdist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamvalidate-bamvalidate.o `test -f 'programs/bamvalidate.cpp' || echo './'`programs/bamvalidate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamvalidate-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamflagsplit-bamflagsplit.o `test -f 'programs/bamflagsplit.cpp' || echo './'`programs/bamflagsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamflagsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamintervalcomment-bamintervalcomment.o `test -f 'programs/bamintervalcomment.cpp' || echo './'`programs/bamintervalcomment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamintervalcomment-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamintervalcommenthist-bamintervalcommenthist.o `test -f 'programs/bamintervalcommenthist.cpp' || echo './'`programs/bamintervalcommenthist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamintervalcommenthist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o `test -f 'programs/bamstreamingmarkduplicates.cpp' || echo './'`programs/bamstreamingmarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamstreamingmarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamalignfrac-bamalignfrac.o `test -f 'programs/bamalignfrac.cpp' || echo './'`programs/bamalignfrac.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamalignfrac-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilternames-bamfilternames.o `test -f 'programs/bamfilternames.cpp' || echo './'`programs/bamfilternames.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilternames-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamsormadup-bamsormadup.o `test -f 'programs/bamsormadup.cpp' || echo './'`programs/bamsormadup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamsormadup-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamexplode-bamexplode.o `test -f 'programs/bamexplode.cpp' || echo './'`programs/bamexplode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamexplode-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamexploderef-bamexploderef.o `test -f 'programs/bamexploderef.cpp' || echo './'`programs/bamexploderef.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamexploderef-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfastexploderef-bamfastexploderef.o `test -f 'programs/bamfastexploderef.cpp' || echo './'`programs/bamfastexploderef.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfastexploderef-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfastnumextract-bamfastnumextract.o `test -f 'programs/bamfastnumextract.cpp' || echo './'`programs/bamfastnumextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfastnumextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamranksort-bamranksort.o `test -f 'programs/bamranksort.cpp' || echo './'`programs/bamranksort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamranksort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/fastaexplod-fastaexplod.o `test -f 'programs/fastaexplod.cpp' || echo './'`programs/fastaexplod.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/fastaexplod-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamrecalculatecigar-bamrecalculatecigar.o `test -f 'programs/bamrecalculatecigar.cpp' || echo './'`programs/bamrecalculatecigar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamrecalculatecigar-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfiltermc-bamfiltermc.o `test -f 'programs/bamfiltermc.cpp' || echo './'`programs/bamfiltermc.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfiltermc-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamnumericalindex-bamnumericalindex.o `test -f 'programs/bamnumericalindex.cpp' || echo './'`programs/bamnumericalindex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamnumericalindex-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamnumericalindexstats-bamnumericalindexstats.o `test -f 'programs/bamnumericalindexstats.cpp' || echo './'`programs/bamnumericalindexstats.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamnumericalindexstats-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bammarkduplicatesopt-bammarkduplicatesopt.o `test -f 'programs/bammarkduplicatesopt.cpp' || echo './'`programs/bammarkduplicatesopt.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bammarkduplicatesopt-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilterlength-bamfilterlength.o `test -f 'programs/bamfilterlength.cpp' || echo './'`programs/bamfilterlength.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterlength-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamauxmerge-bamauxmerge.o `test -f 'programs/bamauxmerge.cpp' || echo './'`programs/bamauxmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamauxmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamrefinterval-bamrefinterval.o `test -f 'programs/bamrefinterval.cpp' || echo './'`programs/bamrefinterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamrefinterval-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamscrapcount-bamscrapcount.o `test -f 'programs/bamscrapcount.cpp' || echo './'`programs/bamscrapcount.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamscrapcount-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilterrefid-bamfilterrefid.o `test -f 'programs/bamfilterrefid.cpp' || echo './'`programs/bamfilterrefid.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterrefid-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfillquery-bamfillquery.o `test -f 'programs/bamfillquery.cpp' || echo './'`programs/bamfillquery.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfillquery-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfillquery-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamrefextract-bamrefextract.o `test -f 'programs/bamrefextract.cpp' || echo './'`programs/bamrefextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamrefextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/fastqtobam2-fastqtobam2.o `test -f 'programs/fastqtobam2.cpp' || echo './'`programs/fastqtobam2.cpp programs/fastqtobam2.cpp: In member function ‘virtual void BlockReadControl::checkBgzfWriteQueue()’: programs/fastqtobam2.cpp:3861:29: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3861 | while ( ptr = bgzfGetNext() ) | ~~~~^~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/fastqtobam2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/fastqtobam2-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/fastqtobam2-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamauxmerge2-bamauxmerge2.o `test -f 'programs/bamauxmerge2.cpp' || echo './'`programs/bamauxmerge2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamauxmerge2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamauxmerge2-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamreheader-bamreheader.o `test -f 'programs/bamreheader.cpp' || echo './'`programs/bamreheader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreheader-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreheader-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreheader-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreheader-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamreplacechecksums-bamreplacechecksums.o `test -f 'programs/bamreplacechecksums.cpp' || echo './'`programs/bamreplacechecksums.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreplacechecksums-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreplacechecksums-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreplacechecksums-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfastcat-bamfastcat.o `test -f 'programs/bamfastcat.cpp' || echo './'`programs/bamfastcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfastcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfastcat-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfastcat-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/populaterefcache-populaterefcache.o `test -f 'programs/populaterefcache.cpp' || echo './'`programs/populaterefcache.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/populaterefcache-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfiltereofblocks-bamfiltereofblocks.o `test -f 'programs/bamfiltereofblocks.cpp' || echo './'`programs/bamfiltereofblocks.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfiltereofblocks-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfiltereofblocks-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamdepth-bamdepth.o `test -f 'programs/bamdepth.cpp' || echo './'`programs/bamdepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamdepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamdepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamdepthintersect-bamdepthintersect.o `test -f 'programs/bamdepthintersect.cpp' || echo './'`programs/bamdepthintersect.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamdepthintersect-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamdepthintersect-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilterk-bamfilterk.o `test -f 'programs/bamfilterk.cpp' || echo './'`programs/bamfilterk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterk-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterk-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterk-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfixpairinfo-bamfixpairinfo.o `test -f 'programs/bamfixpairinfo.cpp' || echo './'`programs/bamfixpairinfo.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfixpairinfo-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfixpairinfo-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfixpairinfo-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamdifference-bamdifference.o `test -f 'programs/bamdifference.cpp' || echo './'`programs/bamdifference.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamdifference-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfeaturecount-bamfeaturecount.o `test -f 'programs/bamfeaturecount.cpp' || echo './'`programs/bamfeaturecount.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfeaturecount-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/blastnxmltobam-blastnxmltobam.o `test -f 'programs/blastnxmltobam.cpp' || echo './'`programs/blastnxmltobam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/blastnxmltobam-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilter-bamfilter.o `test -f 'programs/bamfilter.cpp' || echo './'`programs/bamfilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilter-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfilterbyname-bamfilterbyname.o `test -f 'programs/bamfilterbyname.cpp' || echo './'`programs/bamfilterbyname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfilterbyname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfixmatecoordinates-bamfixmatecoordinates.o `test -f 'programs/bamfixmatecoordinates.cpp' || echo './'`programs/bamfixmatecoordinates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfixmatecoordinates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfixmatecoordinatesnamesorted-bamfixmatecoordinatesnamesorted.o `test -f 'programs/bamfixmatecoordinatesnamesorted.cpp' || echo './'`programs/bamfixmatecoordinatesnamesorted.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfixmatecoordinatesnamesorted-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamtoname-bamtoname.o `test -f 'programs/bamtoname.cpp' || echo './'`programs/bamtoname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamtoname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamdisthist-bamdisthist.o `test -f 'programs/bamdisthist.cpp' || echo './'`programs/bamdisthist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamdisthist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/fastabgzfextract-fastabgzfextract.o `test -f 'programs/fastabgzfextract.cpp' || echo './'`programs/fastabgzfextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/fastabgzfextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamheap-bamheap.o `test -f 'programs/bamheap.cpp' || echo './'`programs/bamheap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamheap-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamfrontback-bamfrontback.o `test -f 'programs/bamfrontback.cpp' || echo './'`programs/bamfrontback.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfrontback-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamfrontback-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamrandomtag-bamrandomtag.o `test -f 'programs/bamrandomtag.cpp' || echo './'`programs/bamrandomtag.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamrandomtag-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamheap2-bamheap2.o `test -f 'programs/bamheap2.cpp' || echo './'`programs/bamheap2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamheap2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamheap3-bamheap3.o `test -f 'programs/bamheap3.cpp' || echo './'`programs/bamheap3.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamheap3-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamtagconversion-bamtagconversion.o `test -f 'programs/bamtagconversion.cpp' || echo './'`programs/bamtagconversion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamtagconversion-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/fastqtobampar-fastqtobampar.o `test -f 'programs/fastqtobampar.cpp' || echo './'`programs/fastqtobampar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/fastqtobampar-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bambisect-bambisect.o `test -f 'programs/bambisect.cpp' || echo './'`programs/bambisect.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bambisect-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcffilterinfo-vcffilterinfo.o `test -f 'programs/vcffilterinfo.cpp' || echo './'`programs/vcffilterinfo.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcffilterinfo-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o `test -f 'programs/vcfpatchcontigprepend.cpp' || echo './'`programs/vcfpatchcontigprepend.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcfpatchcontigprepend-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcfconcat-vcfconcat.o `test -f 'programs/vcfconcat.cpp' || echo './'`programs/vcfconcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcfconcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcfsort-vcfsort.o `test -f 'programs/vcfsort.cpp' || echo './'`programs/vcfsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcfsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/filtergtf-filtergtf.o `test -f 'programs/filtergtf.cpp' || echo './'`programs/filtergtf.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/filtergtf-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamconsensus-bamconsensus.o `test -f 'programs/bamconsensus.cpp' || echo './'`programs/bamconsensus.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamconsensus-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcfreplacecontigs-vcfreplacecontigs.o `test -f 'programs/vcfreplacecontigs.cpp' || echo './'`programs/vcfreplacecontigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcfreplacecontigs-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcffiltersamples-vcffiltersamples.o `test -f 'programs/vcffiltersamples.cpp' || echo './'`programs/vcffiltersamples.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcffiltersamples-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamexploderg-bamexploderg.o `test -f 'programs/bamexploderg.cpp' || echo './'`programs/bamexploderg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamexploderg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamexondepth-bamexondepth.o `test -f 'programs/bamexondepth.cpp' || echo './'`programs/bamexondepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamexondepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamexondepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp In file included from programs/bamexondepth.cpp:22: ./biobambam2/DepthIntervalGetter.hpp: In member function ‘uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)’: ./biobambam2/DepthIntervalGetter.hpp:210:53: warning: unused variable ‘HE’ [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ In file included from /usr/include/c++/13/cassert:44, from /usr/include/libmaus2/avl/AVLSet.hpp:24, from programs/bamexondepth.cpp:43: programs/bamexondepth.cpp: In function ‘void handleFile(const std::string&, uint64_t, const libmaus2::bambam::BamHeader&, std::ostream&, std::ostream&, const std::string&)’: programs/bamexondepth.cpp:121:44: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 121 | assert ( p < GC.e-GC.a ); | ~~^~~~~~~~~~~ programs/bamexondepth.cpp:371:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 371 | if ( d <= thresdepth ) | ~~^~~~~~~~~~~~~ programs/bamexondepth.cpp:375:52: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 375 | assert ( p < GC.e-GC.a ); | ~~^~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamheadercat-bamheadercat.o `test -f 'programs/bamheadercat.cpp' || echo './'`programs/bamheadercat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamheadercat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o `test -f 'programs/bammarkduplicatesoptdist.cpp' || echo './'`programs/bammarkduplicatesoptdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bammarkduplicatesoptdist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcfdiff-vcfdiff.o `test -f 'programs/vcfdiff.cpp' || echo './'`programs/vcfdiff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcfdiff-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamsimpledepth-bamsimpledepth.o `test -f 'programs/bamsimpledepth.cpp' || echo './'`programs/bamsimpledepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamsimpledepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamsimpledepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamdepthmerge-bamdepthmerge.o `test -f 'programs/bamdepthmerge.cpp' || echo './'`programs/bamdepthmerge.cpp In file included from programs/bamdepthmerge.cpp:23: ./biobambam2/DepthIntervalGetter.hpp: In member function ‘uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)’: ./biobambam2/DepthIntervalGetter.hpp:210:53: warning: unused variable ‘HE’ [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamdepthmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamcountflags-bamcountflags.o `test -f 'programs/bamcountflags.cpp' || echo './'`programs/bamcountflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamcountflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcffilterfilterflags-vcffilterfilterflags.o `test -f 'programs/vcffilterfilterflags.cpp' || echo './'`programs/vcffilterfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcffilterfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o `test -f 'programs/vcfreplacecontigsmap.cpp' || echo './'`programs/vcfreplacecontigsmap.cpp programs/vcfreplacecontigsmap.cpp:29:12: warning: ‘int getDefaultGZ()’ defined but not used [-Wunused-function] 29 | static int getDefaultGZ() { return 0; } | ^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/vcfreplacecontigsmap-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/fastaselectreg-fastaselectreg.o `test -f 'programs/fastaselectreg.cpp' || echo './'`programs/fastaselectreg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/fastaselectreg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamaddne-bamaddne.o `test -f 'programs/bamaddne.cpp' || echo './'`programs/bamaddne.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamaddne-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamadapterhistogram-bamadapterhistogram.o `test -f 'programs/bamadapterhistogram.cpp' || echo './'`programs/bamadapterhistogram.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamadapterhistogram-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o programs/bamsalvage-bamsalvage.o `test -f 'programs/bamsalvage.cpp' || echo './'`programs/bamsalvage.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamsalvage-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o biobambam2/bamtofastq-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicates programs/bammarkduplicates-bammarkduplicates.o biobambam2/bammarkduplicates-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicates programs/bammarkduplicates-bammarkduplicates.o biobambam2/bammarkduplicates-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcollate2 programs/bamcollate2-bamcollate2.o biobambam2/bamcollate2-Licensing.o biobambam2/bamcollate2-AttachRank.o biobambam2/bamcollate2-ResetAlignment.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bam12auxmerge programs/bam12auxmerge-bam12auxmerge.o biobambam2/bam12auxmerge-Licensing.o biobambam2/bam12auxmerge-Split12.o biobambam2/bam12auxmerge-Strip12.o biobambam2/bam12auxmerge-ClipReinsert.o biobambam2/bam12auxmerge-zzToName.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects 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-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bam12auxmerge programs/bam12auxmerge-bam12auxmerge.o biobambam2/bam12auxmerge-Licensing.o biobambam2/bam12auxmerge-Split12.o biobambam2/bam12auxmerge-Strip12.o biobambam2/bam12auxmerge-ClipReinsert.o biobambam2/bam12auxmerge-zzToName.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bam12split programs/bam12split-bam12split.o biobambam2/bam12split-Licensing.o biobambam2/bam12split-Split12.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bam12split programs/bam12split-bam12split.o biobambam2/bam12split-Licensing.o biobambam2/bam12split-Split12.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle 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-fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bam12strip programs/bam12strip-bam12strip.o biobambam2/bam12strip-Licensing.o biobambam2/bam12strip-Strip12.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreset programs/bamreset-bamreset.o biobambam2/bamreset-Licensing.o biobambam2/bamreset-ResetAlignment.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrank programs/bamrank-bamrank.o biobambam2/bamrank-Licensing.o biobambam2/bamrank-AttachRank.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: 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-O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrank programs/bamrank-bamrank.o biobambam2/bamrank-Licensing.o biobambam2/bamrank-AttachRank.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamclipreinsert programs/bamclipreinsert-bamclipreinsert.o biobambam2/bamclipreinsert-Licensing.o biobambam2/bamclipreinsert-ClipReinsert.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamclipreinsert programs/bamclipreinsert-bamclipreinsert.o biobambam2/bamclipreinsert-Licensing.o biobambam2/bamclipreinsert-ClipReinsert.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash 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-D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamclipXT programs/bamclipXT-bamclipXT.o biobambam2/bamclipXT-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamzztoname programs/bamzztoname-bamzztoname.o biobambam2/bamzztoname-Licensing.o biobambam2/bamzztoname-zzToName.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamindex programs/bamindex-bamindex.o biobambam2/bamindex-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects 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-Wl,relro -Wl,-z -Wl,now -rdynamic -o bamindex programs/bamindex-bamindex.o biobambam2/bamindex-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterflags programs/bamfilterflags-bamfilterflags.o biobambam2/bamfilterflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterflags programs/bamfilterflags-bamfilterflags.o biobambam2/bamfilterflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicates2 programs/bammarkduplicates2-bammarkduplicates2.o biobambam2/bammarkduplicates2-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicates2 programs/bammarkduplicates2-bammarkduplicates2.o biobambam2/bammarkduplicates2-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcat programs/bamcat-bamcat.o biobambam2/bamcat-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong 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programs/bammerge-bammerge.o biobambam2/bammerge-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammerge programs/bammerge-bammerge.o biobambam2/bammerge-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 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-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsplit programs/bamsplit-bamsplit.o biobambam2/bamsplit-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfastsplit programs/bamfastsplit-bamfastsplit.o biobambam2/bamfastsplit-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastsplit programs/bamfastsplit-bamfastsplit.o biobambam2/bamfastsplit-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsplitdiv programs/bamsplitdiv-bamsplitdiv.o biobambam2/bamsplitdiv-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsplitdiv programs/bamsplitdiv-bamsplitdiv.o biobambam2/bamsplitdiv-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamchecksort programs/bamchecksort-bamchecksort.o biobambam2/bamchecksort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamchecksort programs/bamchecksort-bamchecksort.o biobambam2/bamchecksort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobam programs/fastqtobam-fastqtobam.o biobambam2/fastqtobam-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfixmateinformation programs/bamfixmateinformation-bamfixmateinformation.o biobambam2/bamfixmateinformation-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobam programs/fastqtobam-fastqtobam.o biobambam2/fastqtobam-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfixmateinformation programs/bamfixmateinformation-bamfixmateinformation.o biobambam2/bamfixmateinformation-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp In function 'allocate', inlined from 'allocateArray' at /usr/include/libmaus2/autoarray/AutoArray.hpp:637:58, inlined from '__ct ' at /usr/include/libmaus2/autoarray/AutoArray.hpp:918:18, inlined from 'bamsplitmod' at programs/bamsplitdiv.cpp:92:94: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In function 'bamsplitmod': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamseqchksum programs/bamseqchksum-bamseqchksum.o biobambam2/bamseqchksum-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception 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normalisefasta programs/normalisefasta-normalisefasta.o biobambam2/normalisefasta-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterheader programs/bamfilterheader-bamfilterheader.o biobambam2/bamfilterheader-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterheader programs/bamfilterheader-bamfilterheader.o biobambam2/bamfilterheader-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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biobambam2/bamfilterheader2-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bammdnm programs/bammdnm-bammdnm.o biobambam2/bammdnm-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer 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-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bammapdist programs/bammapdist-bammapdist.o biobambam2/bammapdist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamvalidate programs/bamvalidate-bamvalidate.o biobambam2/bamvalidate-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch 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biobambam2/bamflagsplit-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamflagsplit programs/bamflagsplit-bamflagsplit.o biobambam2/bamflagsplit-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 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-fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamintervalcomment programs/bamintervalcomment-bamintervalcomment.o biobambam2/bamintervalcomment-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamintervalcommenthist programs/bamintervalcommenthist-bamintervalcommenthist.o biobambam2/bamintervalcommenthist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamintervalcommenthist programs/bamintervalcommenthist-bamintervalcommenthist.o biobambam2/bamintervalcommenthist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamstreamingmarkduplicates programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o biobambam2/bamstreamingmarkduplicates-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamstreamingmarkduplicates programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o biobambam2/bamstreamingmarkduplicates-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamalignfrac 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-D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilternames programs/bamfilternames-bamfilternames.o biobambam2/bamfilternames-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsormadup programs/bamsormadup-bamsormadup.o biobambam2/bamsormadup-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray 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bamexplode programs/bamexplode-bamexplode.o biobambam2/bamexplode-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexploderef programs/bamexploderef-bamexploderef.o biobambam2/bamexploderef-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz 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biobambam2/bamfastexploderef-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfastnumextract programs/bamfastnumextract-bamfastnumextract.o biobambam2/bamfastnumextract-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastnumextract programs/bamfastnumextract-bamfastnumextract.o biobambam2/bamfastnumextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamranksort programs/bamranksort-bamranksort.o biobambam2/bamranksort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamranksort programs/bamranksort-bamranksort.o biobambam2/bamranksort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp In function 'allocate', inlined from 'allocateArray' at /usr/include/libmaus2/autoarray/AutoArray.hpp:637:58, inlined from '__ct ' at /usr/include/libmaus2/autoarray/AutoArray.hpp:918:18, inlined from 'loadBlock' at /usr/include/libmaus2/bambam/ReadEndsBlockDecoderBase.hpp:99:31, inlined from 'get' at /usr/include/libmaus2/bambam/ReadEndsBlockDecoderBase.hpp:186:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'get': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ 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-fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrecalculatecigar programs/bamrecalculatecigar-bamrecalculatecigar.o biobambam2/bamrecalculatecigar-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 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-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfiltermc programs/bamfiltermc-bamfiltermc.o biobambam2/bamfiltermc-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamnumericalindex programs/bamnumericalindex-bamnumericalindex.o biobambam2/bamnumericalindex-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamnumericalindex programs/bamnumericalindex-bamnumericalindex.o biobambam2/bamnumericalindex-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto 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-ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamnumericalindexstats programs/bamnumericalindexstats-bamnumericalindexstats.o biobambam2/bamnumericalindexstats-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicatesopt programs/bammarkduplicatesopt-bammarkduplicatesopt.o biobambam2/bammarkduplicatesopt-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicatesopt programs/bammarkduplicatesopt-bammarkduplicatesopt.o biobambam2/bammarkduplicatesopt-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer 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-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxmerge programs/bamauxmerge-bamauxmerge.o biobambam2/bamauxmerge-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterlength programs/bamfilterlength-bamfilterlength.o biobambam2/bamfilterlength-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxmerge programs/bamauxmerge-bamauxmerge.o biobambam2/bamauxmerge-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat 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biobambam2/bamrefinterval-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamscrapcount programs/bamscrapcount-bamscrapcount.o biobambam2/bamscrapcount-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterrefid programs/bamfilterrefid-bamfilterrefid.o biobambam2/bamfilterrefid-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfillquery programs/bamfillquery-bamfillquery.o biobambam2/bamfillquery-Licensing.o biobambam2/bamfillquery-AttachRank.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamscrapcount programs/bamscrapcount-bamscrapcount.o biobambam2/bamscrapcount-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterrefid programs/bamfilterrefid-bamfilterrefid.o biobambam2/bamfilterrefid-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfillquery programs/bamfillquery-bamfillquery.o biobambam2/bamfillquery-Licensing.o biobambam2/bamfillquery-AttachRank.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrefextract programs/bamrefextract-bamrefextract.o biobambam2/bamrefextract-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrefextract programs/bamrefextract-bamrefextract.o biobambam2/bamrefextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobam2 programs/fastqtobam2-fastqtobam2.o biobambam2/fastqtobam2-Licensing.o biobambam2/fastqtobam2-KmerPoisson.o biobambam2/fastqtobam2-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobam2 programs/fastqtobam2-fastqtobam2.o biobambam2/fastqtobam2-Licensing.o biobambam2/fastqtobam2-KmerPoisson.o biobambam2/fastqtobam2-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxmerge2 programs/bamauxmerge2-bamauxmerge2.o biobambam2/bamauxmerge2-Licensing.o biobambam2/bamauxmerge2-KmerPoisson.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreheader programs/bamreheader-bamreheader.o biobambam2/bamreheader-Licensing.o biobambam2/bamreheader-ReadHeader.o biobambam2/bamreheader-RunEOFFilter.o biobambam2/bamreheader-UpdateNumericalIndex.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamreheader programs/bamreheader-bamreheader.o biobambam2/bamreheader-Licensing.o biobambam2/bamreheader-ReadHeader.o biobambam2/bamreheader-RunEOFFilter.o biobambam2/bamreheader-UpdateNumericalIndex.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxmerge2 programs/bamauxmerge2-bamauxmerge2.o biobambam2/bamauxmerge2-Licensing.o biobambam2/bamauxmerge2-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreplacechecksums programs/bamreplacechecksums-bamreplacechecksums.o biobambam2/bamreplacechecksums-Licensing.o biobambam2/bamreplacechecksums-ReadHeader.o biobambam2/bamreplacechecksums-RunEOFFilter.o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamreplacechecksums programs/bamreplacechecksums-bamreplacechecksums.o biobambam2/bamreplacechecksums-Licensing.o biobambam2/bamreplacechecksums-ReadHeader.o biobambam2/bamreplacechecksums-RunEOFFilter.o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfastcat programs/bamfastcat-bamfastcat.o biobambam2/bamfastcat-Licensing.o biobambam2/bamfastcat-ReadHeader.o biobambam2/bamfastcat-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o populaterefcache programs/populaterefcache-populaterefcache.o biobambam2/populaterefcache-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastcat programs/bamfastcat-bamfastcat.o biobambam2/bamfastcat-Licensing.o biobambam2/bamfastcat-ReadHeader.o biobambam2/bamfastcat-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfiltereofblocks programs/bamfiltereofblocks-bamfiltereofblocks.o biobambam2/bamfiltereofblocks-Licensing.o biobambam2/bamfiltereofblocks-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o populaterefcache programs/populaterefcache-populaterefcache.o biobambam2/populaterefcache-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfiltereofblocks programs/bamfiltereofblocks-bamfiltereofblocks.o biobambam2/bamfiltereofblocks-Licensing.o biobambam2/bamfiltereofblocks-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepth programs/bamdepth-bamdepth.o biobambam2/bamdepth-Licensing.o biobambam2/bamdepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepth programs/bamdepth-bamdepth.o biobambam2/bamdepth-Licensing.o biobambam2/bamdepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepthintersect programs/bamdepthintersect-bamdepthintersect.o biobambam2/bamdepthintersect-Licensing.o biobambam2/bamdepthintersect-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepthintersect programs/bamdepthintersect-bamdepthintersect.o biobambam2/bamdepthintersect-Licensing.o biobambam2/bamdepthintersect-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterk programs/bamfilterk-bamfilterk.o biobambam2/bamfilterk-Licensing.o biobambam2/bamfilterk-DepthInterval.o biobambam2/bamfilterk-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterk programs/bamfilterk-bamfilterk.o biobambam2/bamfilterk-Licensing.o biobambam2/bamfilterk-DepthInterval.o biobambam2/bamfilterk-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer 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-Wl,-z,now -rdynamic -o bamdifference programs/bamdifference-bamdifference.o biobambam2/bamdifference-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdifference programs/bamdifference-bamdifference.o biobambam2/bamdifference-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfeaturecount programs/bamfeaturecount-bamfeaturecount.o biobambam2/bamfeaturecount-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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biobambam2/blastnxmltobam-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz -lxerces-c libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o blastnxmltobam programs/blastnxmltobam-blastnxmltobam.o biobambam2/blastnxmltobam-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -lxerces-c -fopenmp /bin/bash ../libtool --tag=CXX 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-std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilter programs/bamfilter-bamfilter.o biobambam2/bamfilter-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterbyname programs/bamfilterbyname-bamfilterbyname.o biobambam2/bamfilterbyname-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterbyname programs/bamfilterbyname-bamfilterbyname.o biobambam2/bamfilterbyname-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto 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-Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfixmatecoordinates programs/bamfixmatecoordinates-bamfixmatecoordinates.o biobambam2/bamfixmatecoordinates-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfixmatecoordinatesnamesorted programs/bamfixmatecoordinatesnamesorted-bamfixmatecoordinatesnamesorted.o biobambam2/bamfixmatecoordinatesnamesorted-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfixmatecoordinatesnamesorted programs/bamfixmatecoordinatesnamesorted-bamfixmatecoordinatesnamesorted.o biobambam2/bamfixmatecoordinatesnamesorted-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 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-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtoname programs/bamtoname-bamtoname.o biobambam2/bamtoname-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdisthist programs/bamdisthist-bamdisthist.o biobambam2/bamdisthist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdisthist programs/bamdisthist-bamdisthist.o biobambam2/bamdisthist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o fastabgzfextract programs/fastabgzfextract-fastabgzfextract.o biobambam2/fastabgzfextract-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastabgzfextract programs/fastabgzfextract-fastabgzfextract.o biobambam2/fastabgzfextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamheap programs/bamheap-bamheap.o biobambam2/bamheap-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheap programs/bamheap-bamheap.o biobambam2/bamheap-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfrontback programs/bamfrontback-bamfrontback.o biobambam2/bamfrontback-Licensing.o biobambam2/bamfrontback-ResetAlignment.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfrontback programs/bamfrontback-bamfrontback.o biobambam2/bamfrontback-Licensing.o biobambam2/bamfrontback-ResetAlignment.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrandomtag programs/bamrandomtag-bamrandomtag.o biobambam2/bamrandomtag-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamheap2 programs/bamheap2-bamheap2.o biobambam2/bamheap2-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrandomtag programs/bamrandomtag-bamrandomtag.o biobambam2/bamrandomtag-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheap2 programs/bamheap2-bamheap2.o biobambam2/bamheap2-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamheap3 programs/bamheap3-bamheap3.o biobambam2/bamheap3-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheap3 programs/bamheap3-bamheap3.o biobambam2/bamheap3-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtagconversion programs/bamtagconversion-bamtagconversion.o biobambam2/bamtagconversion-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtagconversion programs/bamtagconversion-bamtagconversion.o biobambam2/bamtagconversion-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffilterinfo programs/vcffilterinfo-vcffilterinfo.o biobambam2/vcffilterinfo-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffilterinfo programs/vcffilterinfo-vcffilterinfo.o biobambam2/vcffilterinfo-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfpatchcontigprepend programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o biobambam2/vcfpatchcontigprepend-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfpatchcontigprepend programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o biobambam2/vcfpatchcontigprepend-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfconcat programs/vcfconcat-vcfconcat.o biobambam2/vcfconcat-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfconcat programs/vcfconcat-vcfconcat.o biobambam2/vcfconcat-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfsort programs/vcfsort-vcfsort.o biobambam2/vcfsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfsort programs/vcfsort-vcfsort.o biobambam2/vcfsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o filtergtf programs/filtergtf-filtergtf.o biobambam2/filtergtf-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o filtergtf programs/filtergtf-filtergtf.o biobambam2/filtergtf-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfreplacecontigs programs/vcfreplacecontigs-vcfreplacecontigs.o biobambam2/vcfreplacecontigs-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfreplacecontigs programs/vcfreplacecontigs-vcfreplacecontigs.o biobambam2/vcfreplacecontigs-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffiltersamples programs/vcffiltersamples-vcffiltersamples.o biobambam2/vcffiltersamples-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffiltersamples programs/vcffiltersamples-vcffiltersamples.o biobambam2/vcffiltersamples-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexploderg programs/bamexploderg-bamexploderg.o biobambam2/bamexploderg-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexondepth programs/bamexondepth-bamexondepth.o biobambam2/bamexondepth-Licensing.o biobambam2/bamexondepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamexploderg programs/bamexploderg-bamexploderg.o biobambam2/bamexploderg-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamexondepth programs/bamexondepth-bamexondepth.o biobambam2/bamexondepth-Licensing.o biobambam2/bamexondepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamheadercat programs/bamheadercat-bamheadercat.o biobambam2/bamheadercat-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheadercat programs/bamheadercat-bamheadercat.o biobambam2/bamheadercat-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfdiff programs/vcfdiff-vcfdiff.o biobambam2/vcfdiff-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfdiff programs/vcfdiff-vcfdiff.o biobambam2/vcfdiff-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsimpledepth programs/bamsimpledepth-bamsimpledepth.o biobambam2/bamsimpledepth-Licensing.o biobambam2/bamsimpledepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsimpledepth programs/bamsimpledepth-bamsimpledepth.o biobambam2/bamsimpledepth-Licensing.o biobambam2/bamsimpledepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepthmerge programs/bamdepthmerge-bamdepthmerge.o biobambam2/bamdepthmerge-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepthmerge programs/bamdepthmerge-bamdepthmerge.o biobambam2/bamdepthmerge-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcountflags programs/bamcountflags-bamcountflags.o biobambam2/bamcountflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcountflags programs/bamcountflags-bamcountflags.o biobambam2/bamcountflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffilterfilterflags programs/vcffilterfilterflags-vcffilterfilterflags.o biobambam2/vcffilterfilterflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffilterfilterflags programs/vcffilterfilterflags-vcffilterfilterflags.o biobambam2/vcffilterfilterflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfreplacecontigsmap programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o biobambam2/vcfreplacecontigsmap-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfreplacecontigsmap programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o biobambam2/vcfreplacecontigsmap-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o fastaselectreg programs/fastaselectreg-fastaselectreg.o biobambam2/fastaselectreg-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastaselectreg programs/fastaselectreg-fastaselectreg.o biobambam2/fastaselectreg-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp In function 'allocate', inlined from 'reallocate' at /usr/include/libmaus2/autoarray/AutoArray.hpp:406:50, inlined from 'resize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:736:53, inlined from 'bump' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1110:11, inlined from 'ensureSize' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1116:10, inlined from 'push.constprop' at /usr/include/libmaus2/autoarray/AutoArray.hpp:1121:15: /usr/include/libmaus2/autoarray/AutoArray.hpp:266:49: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | N * p = new N[n]; | ^ /usr/include/c++/13/new: In member function 'push.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterhistogram programs/bamadapterhistogram-bamadapterhistogram.o biobambam2/bamadapterhistogram-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsalvage programs/bamsalvage-bamsalvage.o biobambam2/bamsalvage-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterhistogram programs/bamadapterhistogram-bamadapterhistogram.o biobambam2/bamadapterhistogram-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtofastq programs/bamtofastq-bamtofastq.o biobambam2/bamtofastq-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsalvage programs/bamsalvage-bamsalvage.o biobambam2/bamsalvage-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtofastq programs/bamtofastq-bamtofastq.o biobambam2/bamtofastq-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp make[3]: Leaving directory '/<>/src' Making all in test make[3]: Entering directory '/<>/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/test' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/<>' Making check in src make[2]: Entering directory '/<>/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/src' Making check in test make[2]: Entering directory '/<>/test' make bamcmp bamtosam make[3]: Entering directory '/<>/test' g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o bamcmp-bamcmp.o `test -f 'bamcmp.cpp' || echo './'`bamcmp.cpp g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=3 -W -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -c -o bamtosam-bamtosam.o `test -f 'bamtosam.cpp' || echo './'`bamtosam.cpp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtosam bamtosam-bamtosam.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcmp bamcmp-bamcmp.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtosam bamtosam-bamtosam.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/biobambam2-2.0.185+ds-2 -O3 -D_FORTIFY_SOURCE=3 -fopenmp -std=c++17 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcmp bamcmp-bamcmp.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp make[3]: Leaving directory '/<>/test' make check-TESTS make[3]: Entering directory '/<>/test' make[4]: Entering directory '/<>/test' PASS: testshortsortqueryname.sh PASS: testshortsortcoordinate.sh PASS: testshortsort.sh PASS: testdupsinglemarkedsortedqreset.sh PASS: testdupsingle.sh PASS: testfastqbamloop.sh ============================================================================ Testsuite summary for biobambam2 2.0.185 ============================================================================ # TOTAL: 6 # PASS: 6 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/<>/test' make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>/test' make[2]: Entering directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/biobambam2/ make -j1 install DESTDIR=/<>/biobambam2-2.0.185\+ds/debian/biobambam2 AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' Making install in src make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src' /usr/bin/mkdir -p '/<>/debian/biobambam2/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress bamadapterfind bamfilteraux bamauxsort bamadapterclip bamcollate2 bam12auxmerge bam12split bam12strip bamreset bamrank bamclipreinsert bamclipXT bamzztoname bamindex bamfilterflags bamfilterrg bamdownsamplerandom bammarkduplicates2 bamcat bammerge bamsplit bamfastsplit bamsplitdiv bamchecksort fastqtobam bamfixmateinformation bamseqchksum normalisefasta bamfilterheader bamfilterheader2 bammdnm bammapdist bamvalidate bamflagsplit bamintervalcomment bamintervalcommenthist bamstreamingmarkduplicates bamalignfrac bamfilternames bamsormadup bamexplode bamexploderef bamfastexploderef bamfastnumextract bamranksort fastaexplod bamrecalculatecigar bamfiltermc bamnumericalindex bamnumericalindexstats bammarkduplicatesopt bamfilterlength bamauxmerge bamrefinterval bamscrapcount bamfilterrefid bamfillquery bamrefextract fastqtobam2 bamauxmerge2 bamreheader bamreplacechecksums bamfastcat populaterefcache bamfiltereofblocks bamdepth bamdepthintersect bamfilterk bamfixpairinfo bamdifference bamfeaturecount '/<>/debian/biobambam2/usr/bin' libtool: install: /usr/bin/install -c bamtofastq /<>/debian/biobambam2/usr/bin/bamtofastq libtool: install: /usr/bin/install -c bammarkduplicates /<>/debian/biobambam2/usr/bin/bammarkduplicates libtool: install: /usr/bin/install -c bamsort /<>/debian/biobambam2/usr/bin/bamsort libtool: install: /usr/bin/install -c bammaskflags /<>/debian/biobambam2/usr/bin/bammaskflags libtool: install: /usr/bin/install -c bamrecompress /<>/debian/biobambam2/usr/bin/bamrecompress libtool: install: /usr/bin/install -c bamadapterfind /<>/debian/biobambam2/usr/bin/bamadapterfind libtool: install: /usr/bin/install -c bamfilteraux /<>/debian/biobambam2/usr/bin/bamfilteraux libtool: install: /usr/bin/install -c bamauxsort /<>/debian/biobambam2/usr/bin/bamauxsort libtool: install: /usr/bin/install -c bamadapterclip /<>/debian/biobambam2/usr/bin/bamadapterclip libtool: install: /usr/bin/install -c bamcollate2 /<>/debian/biobambam2/usr/bin/bamcollate2 libtool: install: /usr/bin/install -c bam12auxmerge /<>/debian/biobambam2/usr/bin/bam12auxmerge libtool: install: /usr/bin/install -c bam12split /<>/debian/biobambam2/usr/bin/bam12split libtool: install: /usr/bin/install -c bam12strip /<>/debian/biobambam2/usr/bin/bam12strip libtool: install: /usr/bin/install -c bamreset /<>/debian/biobambam2/usr/bin/bamreset libtool: install: /usr/bin/install -c bamrank /<>/debian/biobambam2/usr/bin/bamrank libtool: install: /usr/bin/install -c bamclipreinsert /<>/debian/biobambam2/usr/bin/bamclipreinsert libtool: install: /usr/bin/install -c bamclipXT /<>/debian/biobambam2/usr/bin/bamclipXT libtool: install: /usr/bin/install -c bamzztoname /<>/debian/biobambam2/usr/bin/bamzztoname libtool: install: /usr/bin/install -c bamindex /<>/debian/biobambam2/usr/bin/bamindex libtool: install: /usr/bin/install -c bamfilterflags /<>/debian/biobambam2/usr/bin/bamfilterflags libtool: install: /usr/bin/install -c bamfilterrg /<>/debian/biobambam2/usr/bin/bamfilterrg libtool: install: /usr/bin/install -c bamdownsamplerandom /<>/debian/biobambam2/usr/bin/bamdownsamplerandom libtool: install: /usr/bin/install -c bammarkduplicates2 /<>/debian/biobambam2/usr/bin/bammarkduplicates2 libtool: install: /usr/bin/install -c bamcat /<>/debian/biobambam2/usr/bin/bamcat libtool: install: /usr/bin/install -c bammerge /<>/debian/biobambam2/usr/bin/bammerge libtool: install: /usr/bin/install -c bamsplit /<>/debian/biobambam2/usr/bin/bamsplit libtool: install: /usr/bin/install -c bamfastsplit /<>/debian/biobambam2/usr/bin/bamfastsplit libtool: install: /usr/bin/install -c bamsplitdiv /<>/debian/biobambam2/usr/bin/bamsplitdiv libtool: install: /usr/bin/install -c bamchecksort /<>/debian/biobambam2/usr/bin/bamchecksort libtool: install: /usr/bin/install -c fastqtobam /<>/debian/biobambam2/usr/bin/fastqtobam libtool: install: /usr/bin/install -c bamfixmateinformation /<>/debian/biobambam2/usr/bin/bamfixmateinformation libtool: install: /usr/bin/install -c bamseqchksum /<>/debian/biobambam2/usr/bin/bamseqchksum libtool: install: /usr/bin/install -c normalisefasta /<>/debian/biobambam2/usr/bin/normalisefasta libtool: install: /usr/bin/install -c bamfilterheader /<>/debian/biobambam2/usr/bin/bamfilterheader libtool: install: /usr/bin/install -c bamfilterheader2 /<>/debian/biobambam2/usr/bin/bamfilterheader2 libtool: install: /usr/bin/install -c bammdnm /<>/debian/biobambam2/usr/bin/bammdnm libtool: install: /usr/bin/install -c bammapdist /<>/debian/biobambam2/usr/bin/bammapdist libtool: install: /usr/bin/install -c bamvalidate /<>/debian/biobambam2/usr/bin/bamvalidate libtool: install: /usr/bin/install -c bamflagsplit /<>/debian/biobambam2/usr/bin/bamflagsplit libtool: install: /usr/bin/install -c bamintervalcomment /<>/debian/biobambam2/usr/bin/bamintervalcomment libtool: install: /usr/bin/install -c bamintervalcommenthist /<>/debian/biobambam2/usr/bin/bamintervalcommenthist libtool: install: /usr/bin/install -c bamstreamingmarkduplicates /<>/debian/biobambam2/usr/bin/bamstreamingmarkduplicates libtool: install: /usr/bin/install -c bamalignfrac /<>/debian/biobambam2/usr/bin/bamalignfrac libtool: install: /usr/bin/install -c bamfilternames /<>/debian/biobambam2/usr/bin/bamfilternames libtool: install: /usr/bin/install -c bamsormadup /<>/debian/biobambam2/usr/bin/bamsormadup libtool: install: /usr/bin/install -c bamexplode /<>/debian/biobambam2/usr/bin/bamexplode libtool: install: /usr/bin/install -c bamexploderef /<>/debian/biobambam2/usr/bin/bamexploderef libtool: install: /usr/bin/install -c bamfastexploderef /<>/debian/biobambam2/usr/bin/bamfastexploderef libtool: install: /usr/bin/install -c bamfastnumextract /<>/debian/biobambam2/usr/bin/bamfastnumextract libtool: install: /usr/bin/install -c bamranksort /<>/debian/biobambam2/usr/bin/bamranksort libtool: install: /usr/bin/install -c fastaexplod /<>/debian/biobambam2/usr/bin/fastaexplod libtool: install: /usr/bin/install -c bamrecalculatecigar /<>/debian/biobambam2/usr/bin/bamrecalculatecigar libtool: install: /usr/bin/install -c bamfiltermc /<>/debian/biobambam2/usr/bin/bamfiltermc libtool: install: /usr/bin/install -c bamnumericalindex /<>/debian/biobambam2/usr/bin/bamnumericalindex libtool: install: /usr/bin/install -c bamnumericalindexstats /<>/debian/biobambam2/usr/bin/bamnumericalindexstats libtool: install: /usr/bin/install -c bammarkduplicatesopt /<>/debian/biobambam2/usr/bin/bammarkduplicatesopt libtool: install: /usr/bin/install -c bamfilterlength /<>/debian/biobambam2/usr/bin/bamfilterlength libtool: install: /usr/bin/install -c bamauxmerge /<>/debian/biobambam2/usr/bin/bamauxmerge libtool: install: /usr/bin/install -c bamrefinterval /<>/debian/biobambam2/usr/bin/bamrefinterval libtool: install: /usr/bin/install -c bamscrapcount /<>/debian/biobambam2/usr/bin/bamscrapcount libtool: install: /usr/bin/install -c bamfilterrefid /<>/debian/biobambam2/usr/bin/bamfilterrefid libtool: install: /usr/bin/install -c bamfillquery /<>/debian/biobambam2/usr/bin/bamfillquery libtool: install: /usr/bin/install -c bamrefextract /<>/debian/biobambam2/usr/bin/bamrefextract libtool: install: /usr/bin/install -c fastqtobam2 /<>/debian/biobambam2/usr/bin/fastqtobam2 libtool: install: /usr/bin/install -c bamauxmerge2 /<>/debian/biobambam2/usr/bin/bamauxmerge2 libtool: install: /usr/bin/install -c bamreheader /<>/debian/biobambam2/usr/bin/bamreheader libtool: install: /usr/bin/install -c bamreplacechecksums /<>/debian/biobambam2/usr/bin/bamreplacechecksums libtool: install: /usr/bin/install -c bamfastcat /<>/debian/biobambam2/usr/bin/bamfastcat libtool: install: /usr/bin/install -c populaterefcache /<>/debian/biobambam2/usr/bin/populaterefcache libtool: install: /usr/bin/install -c bamfiltereofblocks /<>/debian/biobambam2/usr/bin/bamfiltereofblocks libtool: install: /usr/bin/install -c bamdepth /<>/debian/biobambam2/usr/bin/bamdepth libtool: install: /usr/bin/install -c bamdepthintersect /<>/debian/biobambam2/usr/bin/bamdepthintersect libtool: install: /usr/bin/install -c bamfilterk /<>/debian/biobambam2/usr/bin/bamfilterk libtool: install: /usr/bin/install -c bamfixpairinfo /<>/debian/biobambam2/usr/bin/bamfixpairinfo libtool: install: /usr/bin/install -c bamdifference /<>/debian/biobambam2/usr/bin/bamdifference libtool: install: /usr/bin/install -c bamfeaturecount /<>/debian/biobambam2/usr/bin/bamfeaturecount /usr/bin/mkdir -p '/<>/debian/biobambam2/usr/share/man/man1' /usr/bin/install -c -m 644 programs/bamtofastq.1 programs/bamsort.1 programs/bammarkduplicates.1 programs/bammarkduplicatesopt.1 programs/bammaskflags.1 programs/bamrecompress.1 programs/bamadapterfind.1 programs/bamfilteraux.1 programs/bamauxsort.1 programs/bamadapterclip.1 programs/bamcollate2.1 programs/bam12auxmerge.1 programs/bam12split.1 programs/bam12strip.1 programs/bamreset.1 programs/bamrank.1 programs/bamclipreinsert.1 programs/bamzztoname.1 programs/bamindex.1 programs/bamfilterflags.1 programs/bamfilterrg.1 programs/bamdownsamplerandom.1 programs/bammarkduplicates2.1 programs/bamcat.1 programs/bammerge.1 programs/bamsplit.1 programs/bamsplitdiv.1 programs/bamchecksort.1 programs/fastqtobam.1 programs/bamfixmateinformation.1 programs/normalisefasta.1 programs/bamfilterheader.1 programs/bamfilterheader2.1 programs/bammdnm.1 programs/bamseqchksum.1 programs/bamvalidate.1 programs/bamflagsplit.1 programs/bamintervalcomment.1 programs/bamstreamingmarkduplicates.1 programs/bamsormadup.1 '/<>/debian/biobambam2/usr/share/man/man1' /usr/bin/install -c -m 644 programs/fastaexplod.1 programs/bamrecalculatecigar.1 programs/bamfiltermc.1 programs/bamfillquery.1 programs/bamalignfrac.1 programs/bamauxmerge.1 programs/bamauxmerge2.1 programs/bambisect.1 programs/bamclipXT.1 programs/bamconsensus.1 programs/filtergtf.1 programs/bamfeaturecount.1 '/<>/debian/biobambam2/usr/share/man/man1' make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making install in test make[2]: Entering directory '/<>/test' make[3]: Entering directory '/<>/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>/test' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/biobambam2/usr/bin/bamflagsplit: Unknown DWARF DW_FORM_0x1f20 ac73132b1e3a28b3461d575757635e9435103bd1 debugedit: debian/biobambam2/usr/bin/bamintervalcommenthist: Unknown DWARF DW_FORM_0x1f20 6fba62d1d9a680c4048a8bd6baf8b688142df148 debugedit: debian/biobambam2/usr/bin/bammarkduplicates2: Unknown DWARF DW_FORM_0x1f20 341b8318cd4c547d2f6ddb77d4eac95870a5db3c debugedit: debian/biobambam2/usr/bin/bammarkduplicatesopt: Unknown DWARF DW_FORM_0x1f20 40b16b1fdf32196bc330476d8e1418f2806d1ada debugedit: debian/biobambam2/usr/bin/bamrefextract: Unknown DWARF DW_FORM_0x1f20 c49c22d069cdbf61658c621af67a57bacb2672c9 debugedit: debian/biobambam2/usr/bin/bamfastcat: Unknown DWARF DW_FORM_0x1f20 020306fce4a0eeb684708beaa1f2484738172f1b debugedit: debian/biobambam2/usr/bin/bamdepth: Unknown DWARF DW_FORM_0x1f20 cd234261e41346bd8242485cd20b9320d42bb0a4 debugedit: debian/biobambam2/usr/bin/bamcat: Unknown DWARF DW_FORM_0x1f20 7e98f635225bd72b58a963c28308774b2100e238 debugedit: debian/biobambam2/usr/bin/bamalignfrac: Unknown DWARF DW_FORM_0x1f20 fa4da0ce3715d48bc7aeb49d20153d4ac2324a4b debugedit: debian/biobambam2/usr/bin/bamclipXT: Unknown DWARF DW_FORM_0x1f20 3a2d3283aa9cfbe0a60a5d6188a3146763ce7a1a debugedit: debian/biobambam2/usr/bin/bamranksort: Unknown DWARF DW_FORM_0x1f21 d05ca5dd318e433fe29318953221f35296759dc8 debugedit: debian/biobambam2/usr/bin/bam12strip: Unknown DWARF DW_FORM_0x1f21 69e23ea18dd0b8ec160ddabc90a3d1e74bbaa20d debugedit: debian/biobambam2/usr/bin/bammerge: Unknown DWARF DW_FORM_0x1f20 948f4047f959f59499f596ed7a029853be5eced9 debugedit: debian/biobambam2/usr/bin/bammdnm: Unknown DWARF DW_FORM_0x1f20 89c44c54b20a112586a60190d94d5ca8856c1bf0 debugedit: debian/biobambam2/usr/bin/bamzztoname: Unknown DWARF DW_FORM_0x1f20 d62c491f0a974612013bfd53d42b5672e69e209b debugedit: debian/biobambam2/usr/bin/bamchecksort: Unknown DWARF DW_FORM_0x1f20 75004aec97c787f1d324af9b088afd33558dac8e debugedit: debian/biobambam2/usr/bin/bam12auxmerge: Unknown DWARF DW_FORM_0x1f21 869f4793a1b1771df1dc05cf9640099398b61eab debugedit: debian/biobambam2/usr/bin/bamstreamingmarkduplicates: Unknown DWARF DW_FORM_0x1f20 9caf05793f32e4ad8a56cdc8bb2e1a83623cf303 debugedit: debian/biobambam2/usr/bin/fastqtobam2: Unknown DWARF DW_FORM_0x1f20 337b0d2781714164a0563812f4859d955ad19760 debugedit: debian/biobambam2/usr/bin/fastaexplod: Unknown DWARF DW_FORM_0x1f20 9c1a0aebc9d272938e9e8b78e4ef3dae76fd0694 debugedit: debian/biobambam2/usr/bin/normalisefasta: Unknown DWARF DW_FORM_0x1f20 5d9b13640bec2ae912aec4221ee41856173cffa1 debugedit: debian/biobambam2/usr/bin/bamclipreinsert: Unknown DWARF DW_FORM_0x1f21 a8d247576125f69d42068126c3fd71c64b0f0631 debugedit: debian/biobambam2/usr/bin/populaterefcache: Unknown DWARF DW_FORM_0x1f20 5eeda329a73408207d5b6ef3f6b9eac23550cfd3 debugedit: debian/biobambam2/usr/bin/bamfilterrg: Unknown DWARF DW_FORM_0x1f20 74b0caff8b79298bdf9646860a2f41857a409799 debugedit: debian/biobambam2/usr/bin/bamreset: Unknown DWARF DW_FORM_0x1f20 5f25e03b2c5473510b43400ffc5efcfbf6368d1a debugedit: debian/biobambam2/usr/bin/bamfilterlength: Unknown DWARF DW_FORM_0x1f20 9d3d6e1873be0ffa4ceb6383328f65747ba8cc91 debugedit: debian/biobambam2/usr/bin/bamcollate2: Unknown DWARF DW_FORM_0x1f20 d8e4f136fff087676d34379aad5af9f3a7f7f42d debugedit: debian/biobambam2/usr/bin/bamscrapcount: Unknown DWARF DW_FORM_0x1f20 281e5484ec10ec2dbdcf0697fecbcd32188e9d7e debugedit: debian/biobambam2/usr/bin/bamtofastq: Unknown DWARF DW_FORM_0x1f20 d19e307fb570daf41310e614dafa83d8f7553994 debugedit: debian/biobambam2/usr/bin/bamseqchksum: Unknown DWARF DW_FORM_0x1f20 51aa6e218bd4a73eec61fddb8191262131b50639 debugedit: debian/biobambam2/usr/bin/bamfillquery: Unknown DWARF DW_FORM_0x1f21 59bb41932fcf62f1098a7725e39e6087e46a751e debugedit: debian/biobambam2/usr/bin/bamadapterfind: Unknown DWARF DW_FORM_0x1f20 8ccfa1e282d845eb29b3b4dd0897698a8d7b84bd debugedit: debian/biobambam2/usr/bin/bamreheader: Unknown DWARF DW_FORM_0x1f20 1f58388dda35868c0bdf45a2ff5293d723e18f1f debugedit: debian/biobambam2/usr/bin/bamexploderef: Unknown DWARF DW_FORM_0x1f20 2642482f2ba45e138bc6107c991002ff37e1320f debugedit: debian/biobambam2/usr/bin/bamauxmerge2: Unknown DWARF DW_FORM_0x1f20 c226ae70186fa3e2cb66c1037b074c57c47efbe2 debugedit: debian/biobambam2/usr/bin/bamadapterclip: Unknown DWARF DW_FORM_0x1f20 377a849393d41ee32af68ceb66fc5a07a417933a debugedit: debian/biobambam2/usr/bin/bamfiltereofblocks: Unknown DWARF DW_FORM_0x1f20 1c7c6a6839930e61f0b92ebeb9589a9ca760a66d debugedit: debian/biobambam2/usr/bin/bamfilterheader: Unknown DWARF DW_FORM_0x1f20 c00a6d992cd74f2f7a858b232341d41325a7af36 debugedit: debian/biobambam2/usr/bin/bamsplitdiv: Unknown DWARF DW_FORM_0x1f20 6f2cdcbe666bbfbea72e7e64d0ffbc2ab1e92d9b debugedit: debian/biobambam2/usr/bin/bamfilterheader2: Unknown DWARF DW_FORM_0x1f20 41d5a96b0e87445e46708877e81ffe69535f7bd7 debugedit: debian/biobambam2/usr/bin/bamnumericalindexstats: Unknown DWARF DW_FORM_0x1f21 2b410acdb708529feeb8a87e0d325629e25b0db1 debugedit: debian/biobambam2/usr/bin/bamfixpairinfo: Unknown DWARF DW_FORM_0x1f20 af9a54ebcfa63d12d47dcc23cf19404a2ef9c37c debugedit: debian/biobambam2/usr/bin/bam12split: Unknown DWARF DW_FORM_0x1f21 0e3bf8c50005efcd0490c9d8adc01380101d7e88 debugedit: debian/biobambam2/usr/bin/bamauxsort: Unknown DWARF DW_FORM_0x1f20 f899ff2013061ab6bd1034e168a4f36eff720890 debugedit: debian/biobambam2/usr/bin/bamrecompress: Unknown DWARF DW_FORM_0x1f20 03ba54eb7747647c2e70cfd984cd8ac1a131ea4c debugedit: debian/biobambam2/usr/bin/bamauxmerge: Unknown DWARF DW_FORM_0x1f20 8c3936c1836e80290b38e7e2435383644d1124f3 debugedit: debian/biobambam2/usr/bin/bamdownsamplerandom: Unknown DWARF DW_FORM_0x1f20 e42c64872179f5201fed208dff4ab780e48b408b debugedit: debian/biobambam2/usr/bin/bamdifference: Unknown DWARF DW_FORM_0x1f20 8c0b2b5cfefa6d50b11522a6256cd6c9e8e24714 debugedit: debian/biobambam2/usr/bin/fastqtobam: Unknown DWARF DW_FORM_0x1f20 5b67f8a97c8293eaf332facfc9cef072514936d8 debugedit: debian/biobambam2/usr/bin/bammarkduplicates: Unknown DWARF DW_FORM_0x1f20 362c04e1e8ba0ee732c957b9e836633ae8011396 debugedit: debian/biobambam2/usr/bin/bamfastsplit: Unknown DWARF DW_FORM_0x1f21 c6cc5aff9bfc9bed0cbda6c77a1a346c9f66c5b1 debugedit: debian/biobambam2/usr/bin/bamdepthintersect: Unknown DWARF DW_FORM_0x1f20 7c8c071caeb04d981e0ce12364a881bf72623218 debugedit: debian/biobambam2/usr/bin/bamfiltermc: Unknown DWARF DW_FORM_0x1f20 252151be95b603d7f5545dcca81136d8849c4567 debugedit: debian/biobambam2/usr/bin/bamfeaturecount: Unknown DWARF DW_FORM_0x1f20 2ff24392ffa8277d7b9186ebd4defa924185a2df debugedit: debian/biobambam2/usr/bin/bammaskflags: Unknown DWARF DW_FORM_0x1f20 6a3257e3f81d88d3a9e77812a7462cb812be2bed debugedit: debian/biobambam2/usr/bin/bamintervalcomment: Unknown DWARF DW_FORM_0x1f20 0ac86917c8b2f827c67cd6008add46d9000b55d6 debugedit: debian/biobambam2/usr/bin/bamrefinterval: Unknown DWARF DW_FORM_0x1f21 a19fe040cb6a16237a235192feed9fcf430a2891 debugedit: debian/biobambam2/usr/bin/bamexplode: Unknown DWARF DW_FORM_0x1f20 17711f9ba0c6fd291de14b4c4509e19608db3bd6 debugedit: debian/biobambam2/usr/bin/bamreplacechecksums: Unknown DWARF DW_FORM_0x1f20 60f3f18a9f39bae398a286918fcd6e4d1104422e debugedit: debian/biobambam2/usr/bin/bamfilterflags: Unknown DWARF DW_FORM_0x1f20 7b157b38f44b9bb9d4de47e93e5d99ee5eb05f05 debugedit: debian/biobambam2/usr/bin/bamrank: Unknown DWARF DW_FORM_0x1f21 3f842062cbbc811355f20e6cd1eff253a534f159 debugedit: debian/biobambam2/usr/bin/bamrecalculatecigar: Unknown DWARF DW_FORM_0x1f20 45391626d846017798311122ecc2f6e5bb469929 debugedit: debian/biobambam2/usr/bin/bamfastexploderef: Unknown DWARF DW_FORM_0x1f20 e86fa0d31209972d70ce90e9cc4fe0831c461100 debugedit: debian/biobambam2/usr/bin/bamvalidate: Unknown DWARF DW_FORM_0x1f20 32a3569eced78b162ea0830c9902f0ef235cd145 debugedit: debian/biobambam2/usr/bin/bamfilterk: Unknown DWARF DW_FORM_0x1f20 ffb793245d4a2b61276d4a00fbc808e33e04981a debugedit: debian/biobambam2/usr/bin/bamfixmateinformation: Unknown DWARF DW_FORM_0x1f20 648b058ef9008562457c85430310d3a9bf1ac051 debugedit: debian/biobambam2/usr/bin/bamfilterrefid: Unknown DWARF DW_FORM_0x1f20 120ede0f5327d9980f1cc28a1dd67a96d970e4e1 debugedit: debian/biobambam2/usr/bin/bammapdist: Unknown DWARF DW_FORM_0x1f20 c6fc3a3c2177f821d8535fda56f078d57d83b2a3 debugedit: debian/biobambam2/usr/bin/bamfilternames: Unknown DWARF DW_FORM_0x1f20 40ddb32cb9749b926c01b65a8b77d7f151e0ef56 debugedit: debian/biobambam2/usr/bin/bamnumericalindex: Unknown DWARF DW_FORM_0x1f20 dcb8918cd15c0f46743f9362e6b2fd57f51fe8ca debugedit: debian/biobambam2/usr/bin/bamsplit: Unknown DWARF DW_FORM_0x1f20 8a606b3ba21c10846c4f768e984b1d2a34af303b debugedit: debian/biobambam2/usr/bin/bamsormadup: Unknown DWARF DW_FORM_0x1f21 93461267654c40d02c6c7032cec4dcd9616953a0 debugedit: debian/biobambam2/usr/bin/bamfastnumextract: Unknown DWARF DW_FORM_0x1f20 3628f2a4d3d6bba99e1c8b3b6a6d89aabd027d5a debugedit: debian/biobambam2/usr/bin/bamsort: Unknown DWARF DW_FORM_0x1f21 0b4cb2b6a6969c2e5b3c4cb62cd500e7afdc64a2 debugedit: debian/biobambam2/usr/bin/bamindex: Unknown DWARF DW_FORM_0x1f20 24125b93b15fe7b522cb406e2da0bce3ae45847e debugedit: debian/biobambam2/usr/bin/bamfilteraux: Unknown DWARF DW_FORM_0x1f20 b5ccea5f422f576c123f24727a3cc77996e77dbb dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamrefextract debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamfilterrg debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bamrecalculatecigar debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/bamfilterheader debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bamreplacechecksums were not linked against libmaus2_simd_align_128.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamrefextract debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamfilterrg debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bamrecalculatecigar debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/bamfilterheader debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bamreplacechecksums were not linked against libmaus2_simd_align_256.so.2 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing biobambam2 (in debian/biobambam2); do_strip: , oemstrip: pkgstriptranslations: processing biobambam2-dbgsym (in debian/.debhelper/biobambam2/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/biobambam2/DEBIAN/control, package biobambam2, directory debian/biobambam2 pkgstripfiles: processing control file: debian/.debhelper/biobambam2/dbgsym-root/DEBIAN/control, package biobambam2-dbgsym, directory debian/.debhelper/biobambam2/dbgsym-root dpkg-deb: building package 'biobambam2-dbgsym' in 'debian/.debhelper/scratch-space/build-biobambam2/biobambam2-dbgsym_2.0.185+ds-2_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/biobambam2/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package biobambam2 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'biobambam2' in '../biobambam2_2.0.185+ds-2_amd64.deb'. Renaming biobambam2-dbgsym_2.0.185+ds-2_amd64.deb to biobambam2-dbgsym_2.0.185+ds-2_amd64.ddeb dpkg-genbuildinfo --build=binary -O../biobambam2_2.0.185+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../biobambam2_2.0.185+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-05-03T02:08:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ biobambam2_2.0.185+ds-2_amd64.changes: -------------------------------------- Format: 1.8 Date: Fri, 19 Apr 2024 17:24:26 +0200 Source: biobambam2 Binary: biobambam2 Built-For-Profiles: noudeb Architecture: amd64 Version: 2.0.185+ds-2 Distribution: oracular-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: biobambam2 - tools for early stage alignment file processing Changes: biobambam2 (2.0.185+ds-2) unstable; urgency=medium . * d/watch: repair gitlab watch file. This instructs uscan to use git ls-remote mode. * d/control: declare compliance to standards version 4.7.0. * d/control: move from pkg-config to pkgconf. 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/<>/biobambam2_2.0.185+ds-2_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: biobambam2 Binary: biobambam2 biobambam2-dbgsym Architecture: amd64 Version: 2.0.185+ds-2 Checksums-Md5: be29b4bc586ca26ea6925f80cd6841f7 187426596 biobambam2-dbgsym_2.0.185+ds-2_amd64.ddeb 64532fa7bc202c33e51190b4c45b86fb 9657548 biobambam2_2.0.185+ds-2_amd64.deb Checksums-Sha1: bb1508342a8a743f0c2ed04151934ffd2fff4c93 187426596 biobambam2-dbgsym_2.0.185+ds-2_amd64.ddeb 95fe548a85dd0500e40642db2a1d56a2dfc31ba7 9657548 biobambam2_2.0.185+ds-2_amd64.deb Checksums-Sha256: b2cc64aab1c0d0d9bf1c9b4095bcd9c1ad104659420fe264291a0e32de49c192 187426596 biobambam2-dbgsym_2.0.185+ds-2_amd64.ddeb a70db95937849d108aaf27e2b204f52190731b5edc286f821e711fdeb34d82e4 9657548 biobambam2_2.0.185+ds-2_amd64.deb Build-Origin: 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(= 1.8.1-2build1), pkgconf-bin (= 1.8.1-2build1), po-debconf (= 1.0.21+nmu1), readline-common (= 8.2-4build1), rpcsvc-proto (= 1.4.2-0ubuntu7), sed (= 4.9-2build1), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu3), tar (= 1.35+dfsg-3build1), util-linux (= 2.39.3-9ubuntu6), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1713540266" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ biobambam2_2.0.185+ds-2_amd64.deb --------------------------------- new Debian package, version 2.0. size 9657548 bytes: control archive=4335 bytes. 1364 bytes, 26 lines control 8813 bytes, 139 lines md5sums Package: biobambam2 Version: 2.0.185+ds-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 54402 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.4), libgomp1 (>= 6), libmaus2-2 (>= 2.0.813+ds), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://gitlab.com/german.tischler/biobambam2 Description: tools for early stage alignment file processing This package contains some tools for processing BAM files, including . bamsormadup: parallel sorting and duplicate marking bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. bamsort: reads BAM and writes BAM resorted by coordinates or query name bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name drwxr-xr-x root/root 0 2024-04-19 15:24 ./ drwxr-xr-x root/root 0 2024-04-19 15:24 ./usr/ drwxr-xr-x root/root 0 2024-04-19 15:24 ./usr/bin/ -rwxr-xr-x root/root 871944 2024-04-19 15:24 ./usr/bin/bam12auxmerge -rwxr-xr-x root/root 785928 2024-04-19 15:24 ./usr/bin/bam12split -rwxr-xr-x root/root 785928 2024-04-19 15:24 ./usr/bin/bam12strip -rwxr-xr-x root/root 794120 2024-04-19 15:24 ./usr/bin/bamadapterclip -rwxr-xr-x root/root 900616 2024-04-19 15:24 ./usr/bin/bamadapterfind -rwxr-xr-x root/root 708104 2024-04-19 15:24 ./usr/bin/bamalignfrac -rwxr-xr-x root/root 839176 2024-04-19 15:24 ./usr/bin/bamauxmerge -rwxr-xr-x root/root 526848 2024-04-19 15:24 ./usr/bin/bamauxmerge2 -rwxr-xr-x root/root 790024 2024-04-19 15:24 ./usr/bin/bamauxsort -rwxr-xr-x root/root 773640 2024-04-19 15:24 ./usr/bin/bamcat -rwxr-xr-x root/root 683528 2024-04-19 15:24 ./usr/bin/bamchecksort -rwxr-xr-x root/root 749064 2024-04-19 15:24 ./usr/bin/bamclipXT -rwxr-xr-x root/root 802312 2024-04-19 15:24 ./usr/bin/bamclipreinsert -rwxr-xr-x root/root 982536 2024-04-19 15:24 ./usr/bin/bamcollate2 -rwxr-xr-x root/root 695816 2024-04-19 15:24 ./usr/bin/bamdepth -rwxr-xr-x root/root 749064 2024-04-19 15:24 ./usr/bin/bamdepthintersect -rwxr-xr-x root/root 777736 2024-04-19 15:24 ./usr/bin/bamdifference -rwxr-xr-x root/root 917000 2024-04-19 15:24 ./usr/bin/bamdownsamplerandom -rwxr-xr-x root/root 744968 2024-04-19 15:24 ./usr/bin/bamexplode -rwxr-xr-x root/root 511496 2024-04-19 15:24 ./usr/bin/bamexploderef -rwxr-xr-x root/root 355848 2024-04-19 15:24 ./usr/bin/bamfastcat -rwxr-xr-x root/root 704008 2024-04-19 15:24 ./usr/bin/bamfastexploderef -rwxr-xr-x root/root 347656 2024-04-19 15:24 ./usr/bin/bamfastnumextract -rwxr-xr-x root/root 347656 2024-04-19 15:24 ./usr/bin/bamfastsplit -rwxr-xr-x root/root 1052264 2024-04-19 15:24 ./usr/bin/bamfeaturecount -rwxr-xr-x root/root 839176 2024-04-19 15:24 ./usr/bin/bamfillquery -rwxr-xr-x root/root 785928 2024-04-19 15:24 ./usr/bin/bamfilteraux -rwxr-xr-x root/root 51624 2024-04-19 15:24 ./usr/bin/bamfiltereofblocks -rwxr-xr-x root/root 839176 2024-04-19 15:24 ./usr/bin/bamfilterflags -rwxr-xr-x root/root 830984 2024-04-19 15:24 ./usr/bin/bamfilterheader -rwxr-xr-x root/root 186872 2024-04-19 15:24 ./usr/bin/bamfilterheader2 -rwxr-xr-x root/root 794120 2024-04-19 15:24 ./usr/bin/bamfilterk -rwxr-xr-x root/root 822792 2024-04-19 15:24 ./usr/bin/bamfilterlength -rwxr-xr-x root/root 830984 2024-04-19 15:24 ./usr/bin/bamfiltermc -rwxr-xr-x root/root 785928 2024-04-19 15:24 ./usr/bin/bamfilternames -rwxr-xr-x root/root 785928 2024-04-19 15:24 ./usr/bin/bamfilterrefid -rwxr-xr-x root/root 785928 2024-04-19 15:24 ./usr/bin/bamfilterrg -rwxr-xr-x root/root 765448 2024-04-19 15:24 ./usr/bin/bamfixmateinformation -rwxr-xr-x root/root 826888 2024-04-19 15:24 ./usr/bin/bamfixpairinfo -rwxr-xr-x root/root 753160 2024-04-19 15:24 ./usr/bin/bamflagsplit -rwxr-xr-x root/root 347656 2024-04-19 15:24 ./usr/bin/bamindex -rwxr-xr-x root/root 892424 2024-04-19 15:24 ./usr/bin/bamintervalcomment -rwxr-xr-x root/root 699912 2024-04-19 15:24 ./usr/bin/bamintervalcommenthist -rwxr-xr-x root/root 699912 2024-04-19 15:24 ./usr/bin/bammapdist -rwxr-xr-x root/root 1080840 2024-04-19 15:24 ./usr/bin/bammarkduplicates -rwxr-xr-x root/root 1121800 2024-04-19 15:24 ./usr/bin/bammarkduplicates2 -rwxr-xr-x root/root 1187336 2024-04-19 15:24 ./usr/bin/bammarkduplicatesopt -rwxr-xr-x root/root 790024 2024-04-19 15:24 ./usr/bin/bammaskflags -rwxr-xr-x root/root 503304 2024-04-19 15:24 ./usr/bin/bammdnm -rwxr-xr-x root/root 830984 2024-04-19 15:24 ./usr/bin/bammerge -rwxr-xr-x root/root 282120 2024-04-19 15:24 ./usr/bin/bamnumericalindex -rwxr-xr-x root/root 273928 2024-04-19 15:24 ./usr/bin/bamnumericalindexstats -rwxr-xr-x root/root 785928 2024-04-19 15:24 ./usr/bin/bamrank -rwxr-xr-x root/root 761352 2024-04-19 15:24 ./usr/bin/bamranksort -rwxr-xr-x root/root 843272 2024-04-19 15:24 ./usr/bin/bamrecalculatecigar -rwxr-xr-x root/root 413192 2024-04-19 15:24 ./usr/bin/bamrecompress -rwxr-xr-x root/root 753160 2024-04-19 15:24 ./usr/bin/bamrefextract -rwxr-xr-x root/root 818696 2024-04-19 15:24 ./usr/bin/bamrefinterval -rwxr-xr-x root/root 310792 2024-04-19 15:24 ./usr/bin/bamreheader -rwxr-xr-x root/root 310792 2024-04-19 15:24 ./usr/bin/bamreplacechecksums -rwxr-xr-x root/root 790024 2024-04-19 15:24 ./usr/bin/bamreset -rwxr-xr-x root/root 679432 2024-04-19 15:24 ./usr/bin/bamscrapcount -rwxr-xr-x root/root 753160 2024-04-19 15:24 ./usr/bin/bamseqchksum -rwxr-xr-x root/root 1887752 2024-04-19 15:24 ./usr/bin/bamsormadup -rwxr-xr-x root/root 1351176 2024-04-19 15:24 ./usr/bin/bamsort -rwxr-xr-x root/root 744968 2024-04-19 15:24 ./usr/bin/bamsplit -rwxr-xr-x root/root 704008 2024-04-19 15:24 ./usr/bin/bamsplitdiv -rwxr-xr-x root/root 978440 2024-04-19 15:24 ./usr/bin/bamstreamingmarkduplicates -rwxr-xr-x root/root 1027592 2024-04-19 15:24 ./usr/bin/bamtofastq -rwxr-xr-x root/root 835080 2024-04-19 15:24 ./usr/bin/bamvalidate -rwxr-xr-x root/root 785928 2024-04-19 15:24 ./usr/bin/bamzztoname -rwxr-xr-x root/root 72184 2024-04-19 15:24 ./usr/bin/fastaexplod -rwxr-xr-x root/root 301568 2024-04-19 15:24 ./usr/bin/fastqtobam -rwxr-xr-x root/root 596480 2024-04-19 15:24 ./usr/bin/fastqtobam2 -rwxr-xr-x root/root 187912 2024-04-19 15:24 ./usr/bin/normalisefasta -rwxr-xr-x root/root 216584 2024-04-19 15:24 ./usr/bin/populaterefcache drwxr-xr-x root/root 0 2024-04-19 15:24 ./usr/share/ drwxr-xr-x root/root 0 2024-04-19 15:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-19 15:24 ./usr/share/doc/biobambam2/ lrwxrwxrwx root/root 0 2024-04-19 15:24 ./usr/share/doc/biobambam2/README.gz -> README.md.gz -rw-r--r-- root/root 2465 2022-12-11 19:21 ./usr/share/doc/biobambam2/README.md.gz -rw-r--r-- root/root 278 2024-04-19 15:24 ./usr/share/doc/biobambam2/README.test -rw-r--r-- root/root 623 2024-04-19 15:24 ./usr/share/doc/biobambam2/README.test-data -rw-r--r-- root/root 1408 2024-04-19 15:24 ./usr/share/doc/biobambam2/changelog.Debian.gz -rw-r--r-- root/root 3250 2024-04-19 15:24 ./usr/share/doc/biobambam2/copyright drwxr-xr-x root/root 0 2024-04-19 15:24 ./usr/share/doc/biobambam2/examples/ -rw-r--r-- root/root 623 2024-04-19 15:24 ./usr/share/doc/biobambam2/examples/README.test-data -rw-r--r-- root/root 659193 2024-04-19 15:24 ./usr/share/doc/biobambam2/examples/SRR11728627.bam -rw-r--r-- root/root 365817 2024-04-19 15:24 ./usr/share/doc/biobambam2/examples/SRR11728641.bam -rw-r--r-- root/root 1764 2024-04-19 15:24 ./usr/share/doc/biobambam2/run-unit-test drwxr-xr-x root/root 0 2024-04-19 15:24 ./usr/share/man/ drwxr-xr-x root/root 0 2024-04-19 15:24 ./usr/share/man/man1/ -rw-r--r-- root/root 1777 2024-04-19 15:24 ./usr/share/man/man1/bam12auxmerge.1.gz -rw-r--r-- root/root 1110 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15:24 ./usr/share/man/man1/bamfixmateinformation.1.gz -rw-r--r-- root/root 1625 2024-04-19 15:24 ./usr/share/man/man1/bamflagsplit.1.gz -rw-r--r-- root/root 568 2024-04-19 15:24 ./usr/share/man/man1/bamindex.1.gz -rw-r--r-- root/root 1955 2024-04-19 15:24 ./usr/share/man/man1/bamintervalcomment.1.gz -rw-r--r-- root/root 2552 2024-04-19 15:24 ./usr/share/man/man1/bammarkduplicates.1.gz -rw-r--r-- root/root 2672 2024-04-19 15:24 ./usr/share/man/man1/bammarkduplicates2.1.gz -rw-r--r-- root/root 2729 2024-04-19 15:24 ./usr/share/man/man1/bammarkduplicatesopt.1.gz -rw-r--r-- root/root 1508 2024-04-19 15:24 ./usr/share/man/man1/bammaskflags.1.gz -rw-r--r-- root/root 1625 2024-04-19 15:24 ./usr/share/man/man1/bammdnm.1.gz -rw-r--r-- root/root 1458 2024-04-19 15:24 ./usr/share/man/man1/bammerge.1.gz -rw-r--r-- root/root 1147 2024-04-19 15:24 ./usr/share/man/man1/bamrank.1.gz -rw-r--r-- root/root 1204 2024-04-19 15:24 ./usr/share/man/man1/bamranksort.1.gz -rw-r--r-- root/root 1507 2024-04-19 15:24 ./usr/share/man/man1/bamrecalculatecigar.1.gz -rw-r--r-- root/root 1065 2024-04-19 15:24 ./usr/share/man/man1/bamrecompress.1.gz -rw-r--r-- root/root 1732 2024-04-19 15:24 ./usr/share/man/man1/bamreset.1.gz -rw-r--r-- root/root 2194 2024-04-19 15:24 ./usr/share/man/man1/bamseqchksum.1.gz -rw-r--r-- root/root 2006 2024-04-19 15:24 ./usr/share/man/man1/bamsormadup.1.gz -rw-r--r-- root/root 3834 2024-04-19 15:24 ./usr/share/man/man1/bamsort.1.gz -rw-r--r-- root/root 951 2024-04-19 15:24 ./usr/share/man/man1/bamsplit.1.gz -rw-r--r-- root/root 982 2024-04-19 15:24 ./usr/share/man/man1/bamsplitdiv.1.gz -rw-r--r-- root/root 2096 2024-04-19 15:24 ./usr/share/man/man1/bamstreamingmarkduplicates.1.gz -rw-r--r-- root/root 1011 2024-04-19 15:24 ./usr/share/man/man1/bamtagconversion.1.gz -rw-r--r-- root/root 3269 2024-04-19 15:24 ./usr/share/man/man1/bamtofastq.1.gz -rw-r--r-- root/root 2033 2024-04-19 15:24 ./usr/share/man/man1/bamvalidate.1.gz -rw-r--r-- root/root 1088 2024-04-19 15:24 ./usr/share/man/man1/bamzztoname.1.gz -rw-r--r-- root/root 967 2024-04-19 15:24 ./usr/share/man/man1/fastaexplod.1.gz -rw-r--r-- root/root 2592 2024-04-19 15:24 ./usr/share/man/man1/fastqtobam.1.gz -rw-r--r-- root/root 671 2024-04-19 15:24 ./usr/share/man/man1/filtergtf.1.gz -rw-r--r-- root/root 1076 2024-04-19 15:24 ./usr/share/man/man1/normalisefasta.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 5879208 Build-Time: 1823 Distribution: oracular-proposed Host Architecture: amd64 Install-Time: 5 Job: biobambam2_2.0.185+ds-2.dsc Machine Architecture: amd64 Package: biobambam2 Package-Time: 1829 Source-Version: 2.0.185+ds-2 Space: 5879208 Status: successful Version: 2.0.185+ds-2 -------------------------------------------------------------------------------- Finished at 2024-05-03T02:08:21Z Build needed 00:30:29, 5879208k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28281880 Scanning for processes to kill in build PACKAGEBUILD-28281880