https://launchpad.net/ubuntu/+source/ivar/1.4.2+dfsg-2ubuntu1/+build/26752092 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lgw01-066 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_234~642~ubuntu20.04.1 python3-lpbuildd_234~642~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 4 Oct 11:47:17 ntpdate[1774959]: adjust time server 10.211.37.1 offset -0.001528 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26752092 --image-type chroot /home/buildd/filecache-default/b4c6d1e9574dd4ae1dafde0c64e11114ad271d6f Creating target for build PACKAGEBUILD-26752092 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26752092 Starting target for build PACKAGEBUILD-26752092 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26752092 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26752092 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26752092 Updating target for build PACKAGEBUILD-26752092 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main riscv64 Packages [1339 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe riscv64 Packages [13.9 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5951 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 Packages [28.3 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [17.7 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 Packages [52.4 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [39.3 kB] Fetched 22.4 MB in 29s (772 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc-dev-bin libc6 libc6-dev libgcrypt20 linux-libc-dev 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 8849 kB of archives. After this operation, 1166 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libc6-dev riscv64 2.38-1ubuntu6 [3401 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libc-dev-bin riscv64 2.38-1ubuntu6 [19.2 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 linux-libc-dev riscv64 6.5.0-7.7 [1532 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libc6 riscv64 2.38-1ubuntu6 [2741 kB] Get:5 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libc-bin riscv64 2.38-1ubuntu6 [601 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgcrypt20 riscv64 1.10.2-3ubuntu1 [554 kB] Preconfiguring packages ... Fetched 8849 kB in 2s (5544 kB/s) (Reading database ... 13552 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.38-1ubuntu6_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.38-1ubuntu6) over (2.38-1ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.38-1ubuntu6_riscv64.deb ... Unpacking libc-dev-bin (2.38-1ubuntu6) over (2.38-1ubuntu4) ... Preparing to unpack .../linux-libc-dev_6.5.0-7.7_riscv64.deb ... Unpacking linux-libc-dev:riscv64 (6.5.0-7.7) over (6.5.0-5.5) ... Preparing to unpack .../libc6_2.38-1ubuntu6_riscv64.deb ... Unpacking libc6:riscv64 (2.38-1ubuntu6) over (2.38-1ubuntu4) ... Setting up libc6:riscv64 (2.38-1ubuntu6) ... (Reading database ... 13552 files and directories currently installed.) Preparing to unpack .../libc-bin_2.38-1ubuntu6_riscv64.deb ... Unpacking libc-bin (2.38-1ubuntu6) over (2.38-1ubuntu4) ... Setting up libc-bin (2.38-1ubuntu6) ... (Reading database ... 13552 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.2-3ubuntu1_riscv64.deb ... Unpacking libgcrypt20:riscv64 (1.10.2-3ubuntu1) over (1.10.2-2ubuntu1) ... Setting up libgcrypt20:riscv64 (1.10.2-3ubuntu1) ... Setting up linux-libc-dev:riscv64 (6.5.0-7.7) ... Setting up libc-dev-bin (2.38-1ubuntu6) ... Setting up libc6-dev:riscv64 (2.38-1ubuntu6) ... Processing triggers for libc-bin (2.38-1ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26752092 riscv64 mantic-proposed -c chroot:build-PACKAGEBUILD-26752092 --arch=riscv64 --dist=mantic-proposed --nolog ivar_1.4.2+dfsg-2ubuntu1.dsc Initiating build PACKAGEBUILD-26752092 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lgw01-066.buildd +==============================================================================+ | ivar 1.4.2+dfsg-2ubuntu1 (riscv64) Wed, 04 Oct 2023 11:50:08 +0000 | +==============================================================================+ Package: ivar Version: 1.4.2+dfsg-2ubuntu1 Source Version: 1.4.2+dfsg-2ubuntu1 Distribution: mantic-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26752092/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/ivar-gz82IC/resolver-2TNU5r' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ivar_1.4.2+dfsg-2ubuntu1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/ivar-gz82IC/ivar-1.4.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/ivar-gz82IC' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libhts-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libhts-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 [377 B] Get:5 copy:/<>/apt_archive ./ Packages [459 B] Fetched 1793 B in 0s (4379 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 liblocale-gettext-perl libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl openssl 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 intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl 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 intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 26.5 MB of archives. After this operation, 110 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [674 B] Get:2 http://ftpmaster.internal/ubuntu mantic/main riscv64 libelf1 riscv64 0.189-4 [51.9 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main riscv64 libicu72 riscv64 72.1-3ubuntu3 [10.8 MB] Get:4 http://ftpmaster.internal/ubuntu mantic/main riscv64 libxml2 riscv64 2.9.14+dfsg-1.3 [599 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmagic-mgc riscv64 1:5.44-3 [293 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmagic1 riscv64 1:5.44-3 [85.1 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main riscv64 file riscv64 1:5.44-3 [21.0 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main riscv64 gettext-base riscv64 0.21-13 [38.9 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main riscv64 libuchardet0 riscv64 0.0.7-1build2 [78.9 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main riscv64 groff-base riscv64 1.23.0-2 [1017 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main riscv64 libnghttp2-14 riscv64 1.55.1-1 [82.4 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpipeline1 riscv64 1.5.7-1 [26.8 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpsl5 riscv64 0.21.2-1 [57.9 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main riscv64 man-db riscv64 2.11.2-3 [1206 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main riscv64 m4 riscv64 1.4.19-3 [243 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main riscv64 autoconf all 2.71-3 [339 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main riscv64 autotools-dev all 20220109.1 [44.9 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main riscv64 automake all 1:1.16.5-1.3 [558 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main riscv64 autopoint all 0.21-13 [422 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdebhelper-perl all 13.11.6ubuntu1 [85.4 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtool all 2.4.7-7 [166 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsub-override-perl all 0.09-4 [8706 B] Get:25 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main riscv64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:27 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdw1 riscv64 0.189-4 [234 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main riscv64 debugedit riscv64 1:5.0-5 [48.8 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main riscv64 dwz riscv64 0.15-1 [115 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main riscv64 gettext riscv64 0.21-13 [810 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main riscv64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main riscv64 debhelper all 13.11.6ubuntu1 [935 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main riscv64 libbrotli1 riscv64 1.0.9-2build8 [324 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsasl2-modules-db riscv64 2.1.28+dfsg1-3 [21.5 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsasl2-2 riscv64 2.1.28+dfsg1-3 [61.1 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main riscv64 libldap2 riscv64 2.6.6+dfsg-1~exp1ubuntu1 [201 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build4 [54.6 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main riscv64 libssh-4 riscv64 0.10.5-3ubuntu1 [195 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcurl3-gnutls riscv64 8.2.1-1ubuntu3 [323 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcurl4-gnutls-dev riscv64 8.2.1-1ubuntu3 [1031 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdeflate0 riscv64 1.18-1 [39.0 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdeflate-dev riscv64 1.18-1 [87.7 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libhtscodecs2 riscv64 1.5.1-1 [82.9 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libhts3 riscv64 1.17+ds-1 [390 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main riscv64 liblzma-dev riscv64 5.4.1-0.2 [314 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main riscv64 zlib1g-dev riscv64 1:1.2.13.dfsg-1ubuntu5 [972 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libhts-dev riscv64 1.17+ds-1 [3659 kB] Preconfiguring packages ... Fetched 26.5 MB in 5s (5228 kB/s) Selecting previously unselected package libelf1:riscv64. (Reading database ... 13552 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.189-4_riscv64.deb ... Unpacking libelf1:riscv64 (0.189-4) ... Selecting previously unselected package libicu72:riscv64. Preparing to unpack .../01-libicu72_72.1-3ubuntu3_riscv64.deb ... Unpacking libicu72:riscv64 (72.1-3ubuntu3) ... Selecting previously unselected package libxml2:riscv64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3_riscv64.deb ... Unpacking libxml2:riscv64 (2.9.14+dfsg-1.3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_riscv64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:riscv64. Preparing to unpack .../04-libmagic1_1%3a5.44-3_riscv64.deb ... Unpacking libmagic1:riscv64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_riscv64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-13_riscv64.deb ... Unpacking gettext-base (0.21-13) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../07-libuchardet0_0.0.7-1build2_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.7-1build2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-2_riscv64.deb ... Unpacking groff-base (1.23.0-2) ... Selecting previously unselected package libnghttp2-14:riscv64. Preparing to unpack .../09-libnghttp2-14_1.55.1-1_riscv64.deb ... Unpacking libnghttp2-14:riscv64 (1.55.1-1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../10-libpipeline1_1.5.7-1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.7-1) ... Selecting previously unselected package libpsl5:riscv64. 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Setting up libsasl2-modules-db:riscv64 (2.1.28+dfsg1-3) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up autopoint (0.21-13) ... Setting up libsasl2-2:riscv64 (2.1.28+dfsg1-3) ... Setting up libssh-4:riscv64 (0.10.5-3ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:riscv64 (5.4.1-0.2) ... Setting up zlib1g-dev:riscv64 (1:1.2.13.dfsg-1ubuntu5) ... Setting up libuchardet0:riscv64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libdeflate-dev:riscv64 (1.18-1) ... Setting up libelf1:riscv64 (0.189-4) ... Setting up libxml2:riscv64 (2.9.14+dfsg-1.3) ... Setting up libldap2:riscv64 (2.6.6+dfsg-1~exp1ubuntu1) ... Setting up automake (1:1.16.5-1.3) ... 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 libdw1:riscv64 (0.189-4) ... Setting up gettext (0.21-13) ... Setting up libtool (2.4.7-7) ... Setting up libcurl3-gnutls:riscv64 (8.2.1-1ubuntu3) ... Setting up libcurl4-gnutls-dev:riscv64 (8.2.1-1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-2) ... Setting up debugedit (1:5.0-5) ... Setting up libhts3:riscv64 (1.17+ds-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:riscv64 (1.17+ds-1) ... Setting up man-db (2.11.2-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up debhelper (13.11.6ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-1ubuntu6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.41-5ubuntu1 dpkg-dev_1.22.0ubuntu1 g++-13_13.2.0-4ubuntu3 gcc-13_13.2.0-4ubuntu3 libc6-dev_2.38-1ubuntu6 libstdc++-13-dev_13.2.0-4ubuntu3 libstdc++6_13.2.0-4ubuntu3 linux-libc-dev_6.5.0-7.7 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.3 apt-utils_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 bash-completion_1:2.11-7 binutils_2.41-5ubuntu1 binutils-common_2.41-5ubuntu1 binutils-riscv64-linux-gnu_2.41-5ubuntu1 bsdextrautils_2.39.1-4ubuntu1 bsdutils_1:2.39.1-4ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:13.2.0-1ubuntu1 cpp-13_13.2.0-4ubuntu3 dash_0.5.12-6ubuntu1 debconf_1.5.82 debconf-i18n_1.5.82 debhelper_13.11.6ubuntu1 debianutils_5.8-1 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.22.0ubuntu1 dpkg-dev_1.22.0ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.1-1 file_1:5.44-3 findutils_4.9.0-5 g++_4:13.2.0-1ubuntu1 g++-13_13.2.0-4ubuntu3 gcc_4:13.2.0-1ubuntu1 gcc-13_13.2.0-4ubuntu3 gcc-13-base_13.2.0-4ubuntu3 gettext_0.21-13 gettext-base_0.21-13 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-2 groff-base_1.23.0-2 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2ubuntu1 init-system-helpers_1.65.2ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-3ubuntu1 libacl1_2.3.1-3 libapparmor1_4.0.0~alpha2-0ubuntu5 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libasan8_13.2.0-4ubuntu3 libassuan0_2.5.6-1 libatomic1_13.2.0-4ubuntu3 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-5ubuntu1 libblkid1_2.39.1-4ubuntu1 libbrotli1_1.0.9-2build8 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-1ubuntu6 libc-dev-bin_2.38-1ubuntu6 libc6_2.38-1ubuntu6 libc6-dev_2.38-1ubuntu6 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcc1-0_13.2.0-4ubuntu3 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libcryptsetup12_2:2.6.1-4ubuntu3 libctf-nobfd0_2.41-5ubuntu1 libctf0_2.41-5ubuntu1 libcurl3-gnutls_8.2.1-1ubuntu3 libcurl4-gnutls-dev_8.2.1-1ubuntu3 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270ubuntu1 libdebhelper-perl_13.11.6ubuntu1 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.0ubuntu1 libdw1_0.189-4 libelf1_0.189-4 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.32.1-1 libfdisk1_2.39.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-4ubuntu3 libgcc-s1_13.2.0-4ubuntu3 libgcrypt20_1.10.2-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.1-4ubuntu1 libgomp1_13.2.0-4ubuntu3 libgpg-error-l10n_1.47-2 libgpg-error0_1.47-2 libgpm2_1.20.7-10build1 libgssapi-krb5-2_1.20.1-3ubuntu1 libhogweed6_3.9.1-2 libhts-dev_1.17+ds-1 libhts3_1.17+ds-1 libhtscodecs2_1.5.1-1 libicu72_72.1-3ubuntu3 libidn2-0_2.3.4-1 libip4tc2_1.8.9-2ubuntu2 libisl23_0.26-3 libjansson4_2.14-2 libjson-c5_0.17-1 libk5crypto3_1.20.1-3ubuntu1 libkeyutils1_1.6.3-2 libkmod2_30+20230519-1ubuntu3 libkrb5-3_1.20.1-3ubuntu1 libkrb5support0_1.20.1-3ubuntu1 libldap2_2.6.6+dfsg-1~exp1ubuntu1 liblocale-gettext-perl_1.07-6 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma-dev_5.4.1-0.2 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.1.0-1 libmount1_2.39.1-4ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20230625-2 libnettle8_3.9.1-2 libnghttp2-14_1.55.1-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libp11-kit0_0.25.0-4ubuntu1 libpam-modules_1.5.2-6ubuntu1 libpam-modules-bin_1.5.2-6ubuntu1 libpam-runtime_1.5.2-6ubuntu1 libpam0g_1.5.2-6ubuntu1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9ubuntu1 libpipeline1_1.5.7-1 libpng16-16_1.6.40-1 libproc2-0_2:4.0.3-1ubuntu1 libpsl5_0.21.2-1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1ubuntu3 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-5ubuntu1 libsmartcols1_2.39.1-4ubuntu1 libsqlite3-0_3.42.0-1 libss2_1.47.0-2ubuntu1 libssh-4_0.10.5-3ubuntu1 libssl3_3.0.10-1ubuntu2 libstdc++-13-dev_13.2.0-4ubuntu3 libstdc++6_13.2.0-4ubuntu3 libsub-override-perl_0.09-4 libsystemd-shared_253.5-1ubuntu6 libsystemd0_253.5-1ubuntu6 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20230625-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libuchardet0_0.0.7-1build2 libudev1_253.5-1ubuntu6 libunistring2_1.0-2 libuuid1_2.39.1-4ubuntu1 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.1-1 libzstd1_1.5.5+dfsg2-1ubuntu2 linux-libc-dev_6.5.0-7.7 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_43 m4_1.4.19-3 make_4.3-4.1build1 man-db_2.11.2-3 mawk_1.3.4.20230730-1 mount_2.39.1-4ubuntu1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4+20230625-2 openssl_3.0.10-1ubuntu2 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-9ubuntu1 perl-base_5.36.0-9ubuntu1 perl-modules-5.36_5.36.0-9ubuntu1 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.3-1ubuntu1 psmisc_23.6-1 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_253.5-1ubuntu6 systemd-dev_253.5-1ubuntu6 systemd-sysv_253.5-1ubuntu6 sysvinit-utils_3.07-1ubuntu1 tar_1.34+dfsg-1.2ubuntu1 tzdata_2023c-9ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.39.1-4ubuntu1 uuid-runtime_2.39.1-4ubuntu1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1ubuntu5 zlib1g-dev_1:1.2.13.dfsg-1ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ivar Binary: ivar, ivar-doc Architecture: any all Version: 1.4.2+dfsg-2ubuntu1 Maintainer: Ubuntu Developers Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/andersen-lab/ivar Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ivar Vcs-Git: https://salsa.debian.org/med-team/ivar.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 13), libhts-dev Package-List: ivar deb science optional arch=any ivar-doc deb doc optional arch=all Checksums-Sha1: 8424d860241b5fdb7cfbb71d8d8d85d6d9162962 672788 ivar_1.4.2+dfsg.orig.tar.xz 3168ebb0067dfae76b6c9f85d1c0f43efe3fd19f 46264 ivar_1.4.2+dfsg-2ubuntu1.debian.tar.xz Checksums-Sha256: 87fbc667080e95823734eeca0dfcec058ff18f1aca7aff89de7a82217a7d2968 672788 ivar_1.4.2+dfsg.orig.tar.xz 3fec41e1a67e7670c7cff180ff5e565a59f1240c9603a6642b2a3c3e1f2f7c12 46264 ivar_1.4.2+dfsg-2ubuntu1.debian.tar.xz Files: d2c0875cd8d094e11207d0d185099282 672788 ivar_1.4.2+dfsg.orig.tar.xz d5eb0ed55db68fff481c6bb5471aaba5 46264 ivar_1.4.2+dfsg-2ubuntu1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmUdT+YACgkQr8/sjmac 4cLEhg/+LHuBmMW1Ol8i1nfV2yWMvUO45FeCWDjjm9unp4WBww6mE97CVyBQG1Re Df7jEk1fCsGH3T/CgqKZedgkkNNQeWVZfPR/KZ4UIZgizcIWKl8r0JwTBGP0YkYD c4bC1DkTlGfhCn+h5QstHC+hClOqxyU0Oyy8aVjEuMKKmRHnzUBF0pH/B1ND/vLP BepRRAady1HRlnqIlIRZyMbqmgSeLRKzHKpvMiF75qfwbsuEVanneBeL34rnUbLi wz0XU0p7S7TCAsnPiUYTbqpzz5nC4rFiqYCKAZerFxARjjdU3jLxNZdbnGZJ3Uok T6QCkrDvwXrcFrNYxPWY/kdIrG9v/FPFbIe+UTcMePPPW4/3C14yIbb8sWH/L3tv ExpByLz4JVZF2o6hQDuHKXoMg3F7QCAuZ9jnwJX0HjS8DJLOUzTs8JcxUYVDS6uP EUMqeceEgYIKwexMDmO50Inoa2K1VVvd+c29pgKOo64Pf1K99flkbXFY+U6Zyimp LDXy1Jc1LT/YAf/8+sUh+ifPX531IWg3UeNxVTIdbosgP+w8ujN5uzNtTUG3KRX0 lHw7wxY1SsAM6LaT3gudux0NX1LVzN7YrdpvMry8HcAOySMmSAv5ddGu6vksNGj9 eP8NE/Iw/JjMK2VFPaG62qO2Mjwo/ENnb/Ng5JAR4b26OhUqS8E= =qDfj -----END PGP SIGNATURE----- gpgv: Signature made Wed Oct 4 11:43:34 2023 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ivar_1.4.2+dfsg-2ubuntu1.dsc: no acceptable signature found dpkg-source: info: extracting ivar in /<> dpkg-source: info: unpacking ivar_1.4.2+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.4.2+dfsg-2ubuntu1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix-warning.patch dpkg-source: info: applying forward-build-options.patch dpkg-source: info: applying privacy-breach.patch dpkg-source: info: applying gcc-13.patch dpkg-source: info: applying gcc-13-2.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 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-26752092 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26752092 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26752092 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 ivar dpkg-buildpackage: info: source version 1.4.2+dfsg-2ubuntu1 dpkg-buildpackage: info: source distribution mantic dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f data/db/test_ref.fa.fai data/test.gap.fa data/test.gap.qual.txt data/test.indel.tsv data/test.masked_primer_indices.txt data/test.trimmed.masked.bam data/test.trimmed.masked.bam.bai data/test.trimmed.sorted.bam.bai data/test.unmapped.sorted.bam.bai make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:12: installing './compile' configure.ac:58: installing './config.guess' configure.ac:58: installing './config.sub' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure -a ./configure --build=riscv64-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/riscv64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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 for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for g++... g++ 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 g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc 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 dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for main in -lhts... no checking for main in -lpthread... no checking for main in -lz... 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 unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking build system type... riscv64-unknown-linux-gnu checking host system type... riscv64-unknown-linux-gnu checking for GNU libc compatible malloc... no checking for GNU libc compatible realloc... no checking for memmove... no 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 tests/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -a make -j8 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.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o ivar.o ivar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o alignment.o alignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp Using built-in specs. Using built-in specs. COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean Using built-in specs. --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC=g++ Target: riscv64-linux-gnu COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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'-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I .COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map -I=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/bu ..ild/ivar-gz82IC/ivar-1.4.2+dfsg=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' -imultilib '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -quiet -dumpbase -v ivar.cpp -I -dumpbase-ext . .cpp -I -march=rv64imafdc_zicsr_zifencei .. -mabi=lp64d -imultilib -misa-spec=20191213 . -march=rv64imafdc_zicsr_zifencei -imultiarch -g riscv64-linux-gnu -g -D_GNU_SOURCE -O2 -D -Wdate-time HAVE_CONFIG_H -Wformat=1 -D -Werror=format-security _FORTIFY_SOURCE=2 -Wall alignment.cpp -Wextra -quiet -Werror -dumpbase -version alignment.cpp -ffile-prefix-map=/<>=. -dumpbase-ext -fstack-protector-strong .cpp -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -march=rv64imafdc_zicsr_zifencei -Wformat-security -mabi=lp64d -o -misa-spec=20191213 /tmp/cct0ssAU.s -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/ccQbLtmq.sUsing built-in specs. COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -dumpbase-ext .cpp -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -WallUsing built-in specs. -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/ccyT4p3p.s COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -dumpbase-ext .cpp -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/ccYs9EyE.s Using built-in specs. COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/cccYlFpD.s Using built-in specs. COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/ccWwYXxS.s GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" #include "..." search starts here: #include "..." search starts here: #include <...> search starts here: #include <...> search starts here: . . .. .. ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" /usr/include/c++/13 /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include/riscv64-linux-gnu /usr/include /usr/include ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" End of search list. End of search list. ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include End of search list. Using built-in specs. GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward COLLECT_GCC=g++ /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu Target: riscv64-linux-gnu /usr/include Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-1End of search list. 3 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/ccU91plw.s GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include End of search list. GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include End of search list. Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" Compiler executable checksum: 06ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" 114c18db20ec265cignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" 0cb887fcceignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" 6f7d ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include End of search list. Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include End of search list. Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o alignment.o /tmp/ccQbLtmq.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'alignment.' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp Using built-in specs. COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -dumpbase-ext .cpp -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/ccUovFYM.s GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include End of search list. Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o remove_reads_from_amplicon.o /tmp/cccYlFpD.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'remove_reads_from_amplicon.' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp Using built-in specs. COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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'-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'call_variants.' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp Using built-in specs. COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' 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COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -dumpbase-ext .cpp -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/ccD0W41S.s GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include End of search list. MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'primer_bed.' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o call_consensus_pileup.o /tmp/ccGPuf9p.s Using built-in specs. COLLECT_GCC=g++ Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' /usr/libexec/gcc/riscv64-linux-gnu/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch riscv64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -march=rv64imafdc_zicsr_zifencei -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<>=. -fstack-protector-strong -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -fstack-protector-strong -Wformat-security -o /tmp/ccRq8uiW.s Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 GNU C++17 (Ubuntu 13.2.0-4ubuntu3) version 13.2.0 (riscv64-linux-gnu) compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/riscv64-linux-gnu/c++/13" ignoring nonexistent directory "/usr/local/include/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed/riscv64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/riscv64-linux-gnu/13/../../../../riscv64-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/13 /usr/include/riscv64-linux-gnu/c++/13 /usr/include/c++/13/backward /usr/lib/gcc/riscv64-linux-gnu/13/include /usr/local/include /usr/include/riscv64-linux-gnu /usr/include End of search list. Compiler executable checksum: 06114c18db20ec265c0cb887fcce6f7d COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o trim_primer_quality.o /tmp/ccyT4p3p.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'call_consensus_pileup.' MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'trim_primer_quality.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o get_masked_amplicons.o /tmp/ccdYTTdl.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'get_masked_amplicons.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o allele_functions.o /tmp/ccUovFYM.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'allele_functions.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o interval_tree.o /tmp/ccRq8uiW.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'interval_tree.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o get_common_variants.o /tmp/cc9wotL6.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'get_common_variants.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o ref_seq.o /tmp/ccD0W41S.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'ref_seq.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' as -v -I . -I .. --gdwarf-5 --traditional-format -fpic -march=rv64imafdc_zicsr_zifencei -march=rv64imafdc_zicsr_zifencei -mabi=lp64d -misa-spec=20191213 -o parse_gff.o /tmp/cctMfDV5.s GNU assembler version 2.41 (riscv64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.41 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'parse_gff.' g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1 -v -g -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/riscv64-linux-gnu/13/lto-wrapper Target: riscv64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.2.0-4ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=riscv64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --disable-multilib --with-arch=rv64gc --with-abi=lp64d --enable-checking=release --build=riscv64-linux-gnu --host=riscv64-linux-gnu --target=riscv64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 13.2.0 (Ubuntu 13.2.0-4ubuntu3) MAKEFLAGS=w -j8 COMPILER_PATH=/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/13/:/usr/libexec/gcc/riscv64-linux-gnu/:/usr/lib/gcc/riscv64-linux-gnu/13/:/usr/lib/gcc/riscv64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/riscv64-linux-gnu/13/:/lib/riscv64-linux-gnu/:/lib/:/usr/lib/riscv64-linux-gnu/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'ivar.' /usr/libexec/gcc/riscv64-linux-gnu/13/collect2 -plugin /usr/libexec/gcc/riscv64-linux-gnu/13/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/riscv64-linux-gnu/13/lto-wrapper -plugin-opt=-fresolution=/tmp/cc2gGY79.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -hash-style=gnu --as-needed -melf64lriscv -dynamic-linker /lib/ld-linux-riscv64-lp64d.so.1 -pie -z now -z relro -o ivar /lib/riscv64-linux-gnu/Scrt1.o /usr/lib/gcc/riscv64-linux-gnu/13/crti.o /usr/lib/gcc/riscv64-linux-gnu/13/crtbeginS.o -L/usr/lib/gcc/riscv64-linux-gnu/13 -L/lib/riscv64-linux-gnu -L/usr/lib/riscv64-linux-gnu -Bsymbolic-functions -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/riscv64-linux-gnu/13/crtendS.o /usr/lib/gcc/riscv64-linux-gnu/13/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-fdebug-prefix-map=/<>=/usr/src/ivar-1.4.2+dfsg-2ubuntu1' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-march=rv64imafdc_zicsr_zifencei' '-mabi=lp64d' '-misa-spec=20191213' '-march=rv64imafdc_zicsr_zifencei' '-dumpdir' 'ivar.' make[3]: Leaving directory '/<>/src' Making all in tests make[3]: Entering directory '/<>/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules execute_before_dh_auto_install make[1]: Entering directory '/<>' chmod -x /<>/data/primer_pair_test/test_primer_pair.bed make[1]: Leaving directory '/<>' dh_auto_install -a make -j8 install DESTDIR=/<>/ivar-1.4.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' Making install in src make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c ivar '/<>/debian/tmp/usr/bin' make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making install in tests make[2]: Entering directory '/<>/tests' make[3]: Entering directory '/<>/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/tests' make[2]: Leaving directory '/<>/tests' 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_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a 516f757e445a42f854fc29174b5aa1cb52f6b634 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing ivar (in debian/ivar); do_strip: , oemstrip: pkgstriptranslations: processing ivar-dbgsym (in debian/.debhelper/ivar/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/ivar/dbgsym-root/DEBIAN/control, package ivar-dbgsym, directory debian/.debhelper/ivar/dbgsym-root dpkg-deb: building package 'ivar-dbgsym' in 'debian/.debhelper/scratch-space/build-ivar/ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.deb'. pkgstripfiles: processing control file: debian/ivar/DEBIAN/control, package ivar, directory debian/ivar pkgstripfiles: Truncating usr/share/doc/ivar/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 8 cpus) for package ivar ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ivar' in '../ivar_1.4.2+dfsg-2ubuntu1_riscv64.deb'. Renaming ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.deb to ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.ddeb dpkg-genbuildinfo --build=any -O../ivar_1.4.2+dfsg-2ubuntu1_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../ivar_1.4.2+dfsg-2ubuntu1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-10-04T11:58:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ ivar_1.4.2+dfsg-2ubuntu1_riscv64.changes: ----------------------------------------- Format: 1.8 Date: Wed, 27 Sep 2023 12:41:50 -0300 Source: ivar Binary: ivar Built-For-Profiles: noudeb Architecture: riscv64 Version: 1.4.2+dfsg-2ubuntu1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Mateus Rodrigues de Morais Description: ivar - functions broadly useful for viral amplicon-based sequencing Launchpad-Bugs-Fixed: 2037769 Changes: ivar (1.4.2+dfsg-2ubuntu1) mantic; urgency=medium . * d/rules: disable LTO to fix failure to build from source on amd64 and arm64 on Ubuntu. (LP: #2037769) Checksums-Sha1: b2a437c6ad2ab076ee2e67cbc3262e51117ca929 1198942 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.ddeb 18172a2c2c95cde821d2bc7346661e481e8155e0 6175 ivar_1.4.2+dfsg-2ubuntu1_riscv64.buildinfo c971c922d5b1c9517dc872c8c0a76fec8fb73cdf 214096 ivar_1.4.2+dfsg-2ubuntu1_riscv64.deb Checksums-Sha256: 7142f0d526cc17bef998df7e60eec677393d3493ca13e37cbc4dd1db81c2d0ca 1198942 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.ddeb e0ba167c678af64b17f94ddb251cb1fae158b032f5bbf0cc45ef98e5715cd4f8 6175 ivar_1.4.2+dfsg-2ubuntu1_riscv64.buildinfo 5ecb07093d9213ad57ccae42db681720b3a856e308a7064dc5b96cd59be0012b 214096 ivar_1.4.2+dfsg-2ubuntu1_riscv64.deb Files: 3c3bd6c44caf7a13541425b11dcc76d6 1198942 debug optional ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.ddeb 39ae489a6d6af4b3cf76f5665e9510d1 6175 science optional ivar_1.4.2+dfsg-2ubuntu1_riscv64.buildinfo b81d4fd452befaecfc0acbb651c03fd6 214096 science optional ivar_1.4.2+dfsg-2ubuntu1_riscv64.deb Original-Maintainer: Debian Med Packaging Team /<>/ivar_1.4.2+dfsg-2ubuntu1_riscv64.changes.new could not be renamed to /<>/ivar_1.4.2+dfsg-2ubuntu1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: ivar Binary: ivar ivar-dbgsym Architecture: riscv64 Version: 1.4.2+dfsg-2ubuntu1 Checksums-Md5: 3c3bd6c44caf7a13541425b11dcc76d6 1198942 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.ddeb b81d4fd452befaecfc0acbb651c03fd6 214096 ivar_1.4.2+dfsg-2ubuntu1_riscv64.deb Checksums-Sha1: b2a437c6ad2ab076ee2e67cbc3262e51117ca929 1198942 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.ddeb c971c922d5b1c9517dc872c8c0a76fec8fb73cdf 214096 ivar_1.4.2+dfsg-2ubuntu1_riscv64.deb Checksums-Sha256: 7142f0d526cc17bef998df7e60eec677393d3493ca13e37cbc4dd1db81c2d0ca 1198942 ivar-dbgsym_1.4.2+dfsg-2ubuntu1_riscv64.ddeb 5ecb07093d9213ad57ccae42db681720b3a856e308a7064dc5b96cd59be0012b 214096 ivar_1.4.2+dfsg-2ubuntu1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Wed, 04 Oct 2023 11:58:22 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-13), autotools-dev (= 20220109.1), base-files (= 13ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.41-5ubuntu1), binutils-common (= 2.41-5ubuntu1), binutils-riscv64-linux-gnu (= 2.41-5ubuntu1), bsdextrautils (= 2.39.1-4ubuntu1), bsdutils (= 1:2.39.1-4ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu2), cpp (= 4:13.2.0-1ubuntu1), cpp-13 (= 13.2.0-4ubuntu3), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.6ubuntu1), debianutils (= 5.8-1), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.22.0ubuntu1), dpkg-dev (= 1.22.0ubuntu1), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-5), g++ (= 4:13.2.0-1ubuntu1), g++-13 (= 13.2.0-4ubuntu3), gcc (= 4:13.2.0-1ubuntu1), gcc-13 (= 13.2.0-4ubuntu3), gcc-13-base (= 13.2.0-4ubuntu3), gettext (= 0.21-13), gettext-base (= 0.21-13), grep (= 3.11-2), groff-base (= 1.23.0-2), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.2.0-4ubuntu3), libatomic1 (= 13.2.0-4ubuntu3), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1), libaudit1 (= 1:3.1.1-1), libbinutils (= 2.41-5ubuntu1), libblkid1 (= 2.39.1-4ubuntu1), libbrotli1 (= 1.0.9-2build8), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-1ubuntu6), libc-dev-bin (= 2.38-1ubuntu6), libc6 (= 2.38-1ubuntu6), libc6-dev (= 2.38-1ubuntu6), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-4ubuntu3), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41-5ubuntu1), libctf0 (= 2.41-5ubuntu1), libcurl3-gnutls (= 8.2.1-1ubuntu3), libcurl4-gnutls-dev (= 8.2.1-1ubuntu3), libdb5.3 (= 5.3.28+dfsg2-2), libdebconfclient0 (= 0.270ubuntu1), libdebhelper-perl (= 13.11.6ubuntu1), libdeflate-dev (= 1.18-1), libdeflate0 (= 1.18-1), libdpkg-perl (= 1.22.0ubuntu1), libdw1 (= 0.189-4), libelf1 (= 0.189-4), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-4ubuntu3), libgcc-s1 (= 13.2.0-4ubuntu3), libgcrypt20 (= 1.10.2-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.1-4ubuntu1), libgomp1 (= 13.2.0-4ubuntu3), libgpg-error0 (= 1.47-2), libgssapi-krb5-2 (= 1.20.1-3ubuntu1), libhogweed6 (= 3.9.1-2), libhts-dev (= 1.17+ds-1), libhts3 (= 1.17+ds-1), libhtscodecs2 (= 1.5.1-1), libicu72 (= 72.1-3ubuntu3), libidn2-0 (= 2.3.4-1), libisl23 (= 0.26-3), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-3ubuntu1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-3ubuntu1), libkrb5support0 (= 1.20.1-3ubuntu1), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu1), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.1-0.2), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.1.0-1), libmount1 (= 2.39.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.55.1-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.25.0-4ubuntu1), libpam-modules (= 1.5.2-6ubuntu1), libpam-modules-bin (= 1.5.2-6ubuntu1), libpam-runtime (= 1.5.2-6ubuntu1), libpam0g (= 1.5.2-6ubuntu1), libpcre2-8-0 (= 10.42-4), libperl5.36 (= 5.36.0-9ubuntu1), libpipeline1 (= 1.5.7-1), libpsl5 (= 0.21.2-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-3), libsasl2-modules-db (= 2.1.28+dfsg1-3), libselinux1 (= 3.5-1), libsframe1 (= 2.41-5ubuntu1), libsmartcols1 (= 2.39.1-4ubuntu1), libssh-4 (= 0.10.5-3ubuntu1), libssl3 (= 3.0.10-1ubuntu2), libstdc++-13-dev (= 13.2.0-4ubuntu3), libstdc++6 (= 13.2.0-4ubuntu3), libsub-override-perl (= 0.09-4), libsystemd0 (= 253.5-1ubuntu6), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20230625-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-7), libuchardet0 (= 0.0.7-1build2), libudev1 (= 253.5-1ubuntu6), libunistring2 (= 1.0-2), libuuid1 (= 2.39.1-4ubuntu1), libxml2 (= 2.9.14+dfsg-1.3), libzstd1 (= 1.5.5+dfsg2-1ubuntu2), linux-libc-dev (= 6.5.0-7.7), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 43), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-3), mawk (= 1.3.4.20230730-1), ncurses-base (= 6.4+20230625-2), ncurses-bin (= 6.4+20230625-2), patch (= 2.7.6-7build2), perl (= 5.36.0-9ubuntu1), perl-base (= 5.36.0-9ubuntu1), perl-modules-5.36 (= 5.36.0-9ubuntu1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.07-1ubuntu1), tar (= 1.34+dfsg-1.2ubuntu1), util-linux (= 2.39.1-4ubuntu1), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu5), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu5) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1695829310" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ ivar_1.4.2+dfsg-2ubuntu1_riscv64.deb ------------------------------------ new Debian package, version 2.0. size 214096 bytes: control archive=2130 bytes. 1257 bytes, 25 lines control 3732 bytes, 45 lines md5sums Package: ivar Version: 1.4.2+dfsg-2ubuntu1 Architecture: riscv64 Maintainer: Ubuntu Developers Installed-Size: 1391 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.4), libhts3 (>= 1.17), libstdc++6 (>= 13.1) Recommends: samtools Section: science Priority: optional Homepage: https://github.com/andersen-lab/ivar Description: functions broadly useful for viral amplicon-based sequencing iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. iVar provided the following functions: . 1. trimming of primers and low-quality bases, 2. consensus calling, 3. variant calling - both iSNVs and insertions/deletions, and 4. identifying mismatches to primer sequences and excluding the corresponding reads from alignment files. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2023-09-27 15:41 ./ drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/ drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/bin/ -rwxr-xr-x root/root 262752 2023-09-27 15:41 ./usr/bin/ivar drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/share/ drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/share/doc/ivar/ -rw-r--r-- root/root 1592 2023-03-28 23:10 ./usr/share/doc/ivar/COOKBOOK.md -rw-r--r-- root/root 6802 2023-03-28 23:10 ./usr/share/doc/ivar/MANUAL.md.gz -rw-r--r-- root/root 3456 2023-03-28 23:10 ./usr/share/doc/ivar/README -rw-r--r-- root/root 2697 2023-03-28 23:10 ./usr/share/doc/ivar/README.md.gz -rw-r--r-- root/root 278 2023-09-27 15:41 ./usr/share/doc/ivar/README.test -rw-r--r-- root/root 141 2023-09-27 15:41 ./usr/share/doc/ivar/README.test_data -rw-r--r-- root/root 1418 2023-09-27 15:41 ./usr/share/doc/ivar/changelog.Debian.gz -rw-r--r-- root/root 1851 2023-09-27 15:41 ./usr/share/doc/ivar/copyright drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ drwxr-xr-x root/root 0 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/ drwxr-xr-x root/root 0 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/db/ -rw-r--r-- root/root 407 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/db/test_ref.fa -rw-r--r-- root/root 4133 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/pair_info_2.tsv -rw-r--r-- root/root 93 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/pair_information.tsv drwxr-xr-x root/root 0 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/primer_only/ -rw-r--r-- root/root 495 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/primer_only/primer_edge_cases.bam -rw-r--r-- root/root 96 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/primer_only/primer_edge_cases.bam.bai drwxr-xr-x root/root 0 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/primer_pair_test/ -rw-r--r-- root/root 769 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/primer_pair_test/test_primer_pair.bed -rw-r--r-- root/root 284 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/primer_pair_test/test_primer_pair_trim.tsv -rw-r--r-- root/root 731 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/primer_pair_test/test_primer_pair_trim.untrimmed.bam -rw-r--r-- root/root 441 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.bed -rw-r--r-- root/root 314 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.filtered.tsv -rw-r--r-- root/root 984 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.gap.sorted.bam -rw-r--r-- root/root 96 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.gap.sorted.bam.bai -rw-r--r-- root/root 6002 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.gap.sorted.mpileup -rw-r--r-- root/root 594 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.gff -rw-r--r-- root/root 27 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.indel.mpileup -rw-r--r-- root/root 822 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.sim.merged.sorted.bam -rw-r--r-- root/root 96 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.sim.merged.sorted.bam.bai -rw-r--r-- root/root 1210 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.sorted.bam -rw-r--r-- root/root 96 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.sorted.bam.bai -rw-r--r-- root/root 15617 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.trimmed.sorted.bam -rw-r--r-- root/root 1500 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test.unmapped.sorted.bam -rw-r--r-- root/root 1000 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test_amplicon.sorted.bam -rw-r--r-- root/root 10275 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test_isize.bed -rw-r--r-- root/root 1316 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test_isize.sorted.bam -rw-r--r-- root/root 447 2023-03-28 23:10 ./usr/share/doc/ivar/examples/data/test_merged.bed drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/ -rw-r--r-- root/root 141 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/README.test_data -rw-r--r-- root/root 405 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/out-consensus.fa -rw-r--r-- root/root 357 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/out-consensus.qual.txt -rw-r--r-- root/root 515910 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/out-filtered.tsv -rw-r--r-- root/root 82 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/out-getmasked.txt -rw-r--r-- root/root 413 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/out-removereads.sam -rw-r--r-- root/root 413 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/out-trim.sam -rw-r--r-- root/root 828 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/out-trim2.sam -rw-r--r-- root/root 532543 2023-09-27 15:41 ./usr/share/doc/ivar/examples/ref/out-variants.tsv -rw-r--r-- root/root 2040 2023-09-27 15:41 ./usr/share/doc/ivar/run-unit-test drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/share/man/ drwxr-xr-x root/root 0 2023-09-27 15:41 ./usr/share/man/man1/ -rw-r--r-- root/root 741 2023-09-27 15:41 ./usr/share/man/man1/ivar.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 40868 Build-Time: 367 Distribution: mantic-proposed Host Architecture: riscv64 Install-Time: 109 Job: ivar_1.4.2+dfsg-2ubuntu1.dsc Machine Architecture: riscv64 Package: ivar Package-Time: 498 Source-Version: 1.4.2+dfsg-2ubuntu1 Space: 40868 Status: successful Version: 1.4.2+dfsg-2ubuntu1 -------------------------------------------------------------------------------- Finished at 2023-10-04T11:58:26Z Build needed 00:08:18, 40868k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26752092 Scanning for processes to kill in build PACKAGEBUILD-26752092 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26752092 Stopping target for build PACKAGEBUILD-26752092 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26752092 Removing build PACKAGEBUILD-26752092