https://launchpad.net/ubuntu/+archive/test-rebuild-20200728-groovy/+build/19681090 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-012 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 2 Aug 20:49:16 ntpdate[1944]: adjust time server 10.211.37.1 offset -0.010596 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681090 --image-type chroot /home/buildd/filecache-default/6f3c84eb9e6a781060c5439a51cfc1d7c8c4fc5d Creating target for build PACKAGEBUILD-19681090 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681090 Starting target for build PACKAGEBUILD-19681090 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681090 'deb http://ftpmaster.internal/ubuntu groovy main universe' Overriding sources.list in build-PACKAGEBUILD-19681090 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681090 Updating target for build PACKAGEBUILD-19681090 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf Packages [938 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main Translation-en [510 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/universe armhf Packages [8518 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5251 kB] Fetched 15.5 MB in 6s (2481 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: base-files bsdutils build-essential ca-certificates libblkid1 libmount1 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libuuid1 mount util-linux 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1889 kB of archives. After this operation, 2048 B of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main armhf base-files armhf 11ubuntu10 [59.9 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf bsdutils armhf 1:2.35.2-9ubuntu1 [78.8 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf libselinux1 armhf 3.1-2 [60.4 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main armhf util-linux armhf 2.35.2-9ubuntu1 [984 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf mount armhf 2.35.2-9ubuntu1 [111 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf libblkid1 armhf 2.35.2-9ubuntu1 [120 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf libmount1 armhf 2.35.2-9ubuntu1 [132 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf libsemanage-common all 3.1-1 [10.2 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf libsemanage1 armhf 3.1-1 [75.0 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main armhf libsmartcols1 armhf 2.35.2-9ubuntu1 [84.4 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main armhf libuuid1 armhf 2.35.2-9ubuntu1 [21.3 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf ca-certificates all 20200601 [147 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf build-essential armhf 12.8ubuntu3 [4636 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 1889 kB in 0s (11.2 MB/s) (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu10_armhf.deb ... Unpacking base-files (11ubuntu10) over (11ubuntu9) ... Setting up base-files (11ubuntu10) ... Installing new version of config file /etc/update-motd.d/50-motd-news ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.35.2-9ubuntu1_armhf.deb ... Unpacking bsdutils (1:2.35.2-9ubuntu1) over (1:2.35.2-7ubuntu3) ... Setting up bsdutils (1:2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libselinux1_3.1-2_armhf.deb ... Unpacking libselinux1:armhf (3.1-2) over (3.0-1build2) ... Setting up libselinux1:armhf (3.1-2) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../util-linux_2.35.2-9ubuntu1_armhf.deb ... Unpacking util-linux (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up util-linux (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../mount_2.35.2-9ubuntu1_armhf.deb ... Unpacking mount (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Preparing to unpack .../libblkid1_2.35.2-9ubuntu1_armhf.deb ... Unpacking libblkid1:armhf (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libblkid1:armhf (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libmount1_2.35.2-9ubuntu1_armhf.deb ... Unpacking libmount1:armhf (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libmount1:armhf (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.1-1_all.deb ... Unpacking libsemanage-common (3.1-1) over (3.0-1build2) ... Setting up libsemanage-common (3.1-1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libsemanage1_3.1-1_armhf.deb ... Unpacking libsemanage1:armhf (3.1-1) over (3.0-1build2) ... Setting up libsemanage1:armhf (3.1-1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.35.2-9ubuntu1_armhf.deb ... Unpacking libsmartcols1:armhf (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libsmartcols1:armhf (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libuuid1_2.35.2-9ubuntu1_armhf.deb ... Unpacking libuuid1:armhf (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libuuid1:armhf (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../ca-certificates_20200601_all.deb ... Unpacking ca-certificates (20200601) over (20190110ubuntu2) ... Preparing to unpack .../build-essential_12.8ubuntu3_armhf.deb ... Unpacking build-essential (12.8ubuntu3) over (12.8ubuntu1) ... Setting up ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 13 added, 14 removed; done. Setting up mount (2.35.2-9ubuntu1) ... Setting up build-essential (12.8ubuntu3) ... Processing triggers for systemd (245.6-3ubuntu3) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... Processing triggers for ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19681090 armhf groovy -c chroot:build-PACKAGEBUILD-19681090 --arch=armhf --dist=groovy --nolog ivar_1.2.2+dfsg-3.dsc Initiating build PACKAGEBUILD-19681090 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-012.buildd +==============================================================================+ | ivar 1.2.2+dfsg-3 (armhf) 02 Aug 2020 20:49 | +==============================================================================+ Package: ivar Version: 1.2.2+dfsg-3 Source Version: 1.2.2+dfsg-3 Distribution: groovy Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/ivar-lziyZS/ivar-1.2.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/ivar-lziyZS' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19681090/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ivar_1.2.2+dfsg-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-UNg2Gv/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-UNg2Gv/apt_archive ./ InRelease Get:2 copy:/<>/resolver-UNg2Gv/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-UNg2Gv/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-UNg2Gv/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-UNg2Gv/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (73.5 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-UNg2Gv/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (64.5 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12532 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 13), libhts-dev Filtered Build-Depends: debhelper-compat (= 13), libhts-dev dpkg-deb: building package 'sbuild-build-depends-ivar-dummy' in '/<>/resolver-iZM2RC/apt_archive/sbuild-build-depends-ivar-dummy.deb'. Ign:1 copy:/<>/resolver-iZM2RC/apt_archive ./ InRelease Get:2 copy:/<>/resolver-iZM2RC/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-iZM2RC/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-iZM2RC/apt_archive ./ Sources [218 B] Get:5 copy:/<>/resolver-iZM2RC/apt_archive ./ Packages [533 B] Fetched 2870 B in 0s (67.0 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install ivar build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal 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 krb5-doc krb5-user 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 libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-ivar-dummy zlib1g-dev 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 23.9 MB of archives. After this operation, 74.4 MB of additional disk space will be used. Get:1 copy:/<>/resolver-iZM2RC/apt_archive ./ sbuild-build-depends-ivar-dummy 0.invalid.0 [864 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf bsdextrautils armhf 2.35.2-9ubuntu1 [70.2 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main armhf groff-base armhf 1.22.4-5 [759 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf libpipeline1 armhf 1.5.2-2build1 [23.5 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf man-db armhf 2.9.3-2 [1082 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic-mgc armhf 1:5.38-5 [218 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic1 armhf 1:5.38-5 [68.4 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf file armhf 1:5.38-5 [22.4 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main armhf libelf1 armhf 0.180-0ubuntu1 [41.1 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main armhf libglib2.0-0 armhf 2.64.4-1 [1125 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf libicu66 armhf 66.1-2ubuntu3 [8225 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf libxml2 armhf 2.9.10+dfsg-5 [546 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main armhf gettext-base armhf 0.19.8.1-10build1 [46.0 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main armhf libkrb5support0 armhf 1.17-10 [27.9 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main armhf libk5crypto3 armhf 1.17-10 [79.5 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main armhf libkeyutils1 armhf 1.6.1-2ubuntu1 [9028 B] Get:18 http://ftpmaster.internal/ubuntu groovy/main armhf libkrb5-3 armhf 1.17-10 [287 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main armhf libgssapi-krb5-2 armhf 1.17-10 [101 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main armhf libpsl5 armhf 0.21.0-1.1 [50.3 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main armhf libsigsegv2 armhf 2.12-2build1 [13.0 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main armhf m4 armhf 1.4.18-4 [187 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main armhf autoconf all 2.69-11.1 [321 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main armhf automake all 1:1.16.2-3ubuntu1 [548 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main armhf autopoint all 0.19.8.1-10build1 [412 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf libtool all 2.4.6-14 [161 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf dh-autoreconf all 19 [16.1 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main armhf libdebhelper-perl all 13.2ubuntu1 [64.2 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:32 http://ftpmaster.internal/ubuntu groovy/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main armhf dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:34 http://ftpmaster.internal/ubuntu groovy/main armhf dwz armhf 0.13-5 [153 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main armhf libcroco3 armhf 0.6.13-1 [70.5 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main armhf gettext armhf 0.19.8.1-10build1 [835 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main armhf po-debconf all 1.0.21 [233 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main armhf debhelper all 13.2ubuntu1 [878 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main armhf libroken18-heimdal armhf 7.7.0+dfsg-2 [34.5 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main armhf libasn1-8-heimdal armhf 7.7.0+dfsg-2 [140 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main armhf libbrotli1 armhf 1.0.7-7 [259 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main armhf libheimbase1-heimdal armhf 7.7.0+dfsg-2 [24.3 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main armhf libhcrypto4-heimdal armhf 7.7.0+dfsg-2 [78.5 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main armhf libwind0-heimdal armhf 7.7.0+dfsg-2 [47.2 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main armhf libhx509-5-heimdal armhf 7.7.0+dfsg-2 [88.8 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main armhf libkrb5-26-heimdal armhf 7.7.0+dfsg-2 [170 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main armhf libheimntlm0-heimdal armhf 7.7.0+dfsg-2 [13.2 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main armhf libgssapi3-heimdal armhf 7.7.0+dfsg-2 [79.9 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2 [13.4 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main armhf libsasl2-2 armhf 2.1.27+dfsg-2 [42.7 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main armhf libldap-common all 2.4.50+dfsg-1ubuntu3 [16.9 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main armhf libldap-2.4-2 armhf 2.4.50+dfsg-1ubuntu3 [133 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main armhf libnghttp2-14 armhf 1.41.0-2 [55.5 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build2 [48.9 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main armhf libssh-4 armhf 0.9.4-1ubuntu1 [147 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main armhf libcurl3-gnutls armhf 7.68.0-1ubuntu4 [200 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/universe armhf libdeflate0 armhf 1.6-1 [46.1 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/universe armhf libhts3 armhf 1.10.2-4 [308 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main armhf liblzma-dev armhf 5.2.4-1 [139 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu1 [150 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/universe armhf libhts-dev armhf 1.10.2-4 [4775 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.9 MB in 1s (25.3 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12532 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.35.2-9ubuntu1_armhf.deb ... Unpacking bsdextrautils (2.35.2-9ubuntu1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_armhf.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.2-2build1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_armhf.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.38-5_armhf.deb ... Unpacking libmagic-mgc (1:5.38-5) ... 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Setting up libkeyutils1:armhf (1.6.1-2ubuntu1) ... Setting up libpsl5:armhf (0.21.0-1.1) ... Setting up bsdextrautils (2.35.2-9ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.64.4-1) ... No schema files found: doing nothing. Setting up libicu66:armhf (66.1-2ubuntu3) ... Setting up libdebhelper-perl (13.2ubuntu1) ... Setting up libbrotli1:armhf (1.0.7-7) ... Setting up libnghttp2-14:armhf (1.41.0-2) ... Setting up libmagic1:armhf (1:5.38-5) ... Setting up libdeflate0:armhf (1.6-1) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up libldap-common (2.4.50+dfsg-1ubuntu3) ... Setting up libkrb5support0:armhf (1.17-10) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:armhf (2.12-2build1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libk5crypto3:armhf (1.17-10) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2) ... Setting up libroken18-heimdal:armhf (7.7.0+dfsg-2) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:armhf (1.17-10) ... Setting up libelf1:armhf (0.180-0ubuntu1) ... Setting up libxml2:armhf (2.9.10+dfsg-5) ... Setting up libheimbase1-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:armhf (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-4) ... Setting up libhcrypto4-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libwind0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libgssapi-krb5-2:armhf (1.17-10) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up libssh-4:armhf (0.9.4-1ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up automake (1:1.16.2-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10build1) ... Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-2) ... Setting up man-db (2.9.3-2) ... 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 intltool-debian (0.35.0+20060710.5) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:armhf (2.4.50+dfsg-1ubuntu3) ... Setting up libcurl3-gnutls:armhf (7.68.0-1ubuntu4) ... Setting up libhts3:armhf (1.10.2-4) ... Setting up libhts-dev:armhf (1.10.2-4) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.2ubuntu1) ... Setting up sbuild-build-depends-ivar-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (armv7l) Toolchain package versions: binutils_2.35-1ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-10_10.2.0-3ubuntu1 gcc-10_10.2.0-3ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-10-dev_10.2.0-3ubuntu1 libstdc++6_10.2.0-3ubuntu1 linux-libc-dev_5.4.0-42.46 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.7 autoconf_2.69-11.1 automake_1:1.16.2-3ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu10 base-passwd_3.5.47 bash_5.0-6ubuntu2 binutils_2.35-1ubuntu1 binutils-arm-linux-gnueabihf_2.35-1ubuntu1 binutils-common_2.35-1ubuntu1 bsdextrautils_2.35.2-9ubuntu1 bsdutils_1:2.35.2-9ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.30-3ubuntu3 cpp_4:10.1.0-1ubuntu1 cpp-10_10.2.0-3ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3build1 dpkg_1.19.7ubuntu4 dpkg-dev_1.19.7ubuntu4 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:10.1.0-1ubuntu1 g++-10_10.2.0-3ubuntu1 gcc_4:10.1.0-1ubuntu1 gcc-10_10.2.0-3ubuntu1 gcc-10-base_10.2.0-3ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.0-3ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.2.0-3ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.35-1ubuntu1 libblkid1_2.35.2-9ubuntu1 libbrotli1_1.0.7-7 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.31-0ubuntu10 libc-dev-bin_2.31-0ubuntu10 libc6_2.31-0ubuntu10 libc6-dev_2.31-0ubuntu10 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcc1-0_10.2.0-3ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1ubuntu1 libcrypt1_1:4.4.16-1ubuntu1 libcryptsetup12_2:2.3.3-1ubuntu3 libctf-nobfd0_2.35-1ubuntu1 libctf0_2.35-1ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu4 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.252ubuntu1 libdebhelper-perl_13.2ubuntu1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.19.7ubuntu4 libelf1_0.180-0ubuntu1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-3ubuntu1 libgcc-s1_10.2.0-3ubuntu1 libgcrypt20_1.8.5-5ubuntu2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.13-4ubuntu4 libgomp1_10.2.0-3ubuntu1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.10.2-4 libhts3_1.10.2-4 libhx509-5-heimdal_7.7.0+dfsg-2 libicu66_66.1-2ubuntu3 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libldap-2.4-2_2.4.50+dfsg-1ubuntu3 libldap-common_2.4.50+dfsg-1ubuntu3 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-9ubuntu1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1build1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu5 libpam-modules-bin_1.3.1-5ubuntu5 libpam-runtime_1.3.1-5ubuntu5 libpam0g_1.3.1-5ubuntu5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-5ubuntu1 libpsl5_0.21.0-1.1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1ubuntu4 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.35.2-9ubuntu1 libsqlite3-0_3.32.3-1 libss2_1.45.6-1ubuntu1 libssh-4_0.9.4-1ubuntu1 libssl1.1_1.1.1f-1ubuntu3 libstdc++-10-dev_10.2.0-3ubuntu1 libstdc++6_10.2.0-3ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.6-3ubuntu3 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.2.0-3ubuntu1 libuchardet0_0.0.7-1 libudev1_245.6-3ubuntu3 libunistring2_0.9.10-4 libuuid1_2.35.2-9ubuntu1 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.5+dfsg-3 linux-libc-dev_5.4.0-42.46 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-9ubuntu1 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1f-1ubuntu3 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ivar-dummy_0.invalid.0 sed_4.7-1build1 sensible-utils_0.0.12+nmu1 systemd_245.6-3ubuntu3 systemd-sysv_245.6-3ubuntu3 systemd-timesyncd_245.6-3ubuntu3 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.35.2-9ubuntu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Jun 16 17:23:33 2020 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ivar_1.2.2+dfsg-3.dsc dpkg-source: info: extracting ivar in ivar-1.2.2+dfsg dpkg-source: info: unpacking ivar_1.2.2+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.2.2+dfsg-3.debian.tar.xz Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19681090 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19681090 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19681090 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.2.2+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/ivar-1.2.2+dfsg' 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 '/<>/ivar-1.2.2+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:12: installing './compile' 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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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 thread-safe mkdir -p... /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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... 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 for stdlib.h... (cached) yes checking for GNU libc compatible malloc... no checking for stdlib.h... (cached) yes 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 -j4 make[1]: Entering directory '/<>/ivar-1.2.2+dfsg' make all-recursive make[2]: Entering directory '/<>/ivar-1.2.2+dfsg' Making all in src make[3]: Entering directory '/<>/ivar-1.2.2+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ivar.o ivar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -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 -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -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 -std=c++11 -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 -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp In file included from /usr/include/c++/10/vector:67, from /usr/include/c++/10/regex:51, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:558:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 558 | std::__uninitialized_copy_a(__x.begin(), __x.end(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 559 | this->_M_impl._M_start, | ~~~~~~~~~~~~~~~~~~~~~~~ 560 | _M_get_Tp_allocator()); | ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’: /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 325 | { return std::uninitialized_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/regex:51, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*]’: /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 125 | uninitialized_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 147 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/regex:51, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator]’: /usr/include/c++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 346 | return std::__uninitialized_copy_a | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’: /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’: /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 325 | { return std::uninitialized_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*]’: /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 125 | uninitialized_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 147 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’: /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 g++ -g -std=c++11 -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 -lhts -lz -lpthread -lhts -lz -lpthread make[3]: Leaving directory '/<>/ivar-1.2.2+dfsg/src' Making all in tests make[3]: Entering directory '/<>/ivar-1.2.2+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/ivar-1.2.2+dfsg/tests' make[3]: Entering directory '/<>/ivar-1.2.2+dfsg' make[3]: Leaving directory '/<>/ivar-1.2.2+dfsg' make[2]: Leaving directory '/<>/ivar-1.2.2+dfsg' make[1]: Leaving directory '/<>/ivar-1.2.2+dfsg' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/<>/ivar-1.2.2+dfsg' Making check in src make[2]: Entering directory '/<>/ivar-1.2.2+dfsg/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/ivar-1.2.2+dfsg/src' Making check in tests make[2]: Entering directory '/<>/ivar-1.2.2+dfsg/tests' make check_primer_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases make[3]: Entering directory '/<>/ivar-1.2.2+dfsg/tests' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_getmasked.o test_getmasked.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_removereads.o test_removereads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_variants.o test_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_variants.o ../src/call_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_common_variants.o test_common_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp In file included from /usr/include/c++/10/vector:67, from /usr/include/c++/10/regex:51, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:558:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 558 | std::__uninitialized_copy_a(__x.begin(), __x.end(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 559 | this->_M_impl._M_start, | ~~~~~~~~~~~~~~~~~~~~~~~ 560 | _M_get_Tp_allocator()); | ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’: /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 325 | { return std::uninitialized_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/regex:51, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*]’: /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 125 | uninitialized_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 147 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/regex:51, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator]’: /usr/include/c++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 346 | return std::__uninitialized_copy_a | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’: /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’: /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 325 | { return std::uninitialized_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*]’: /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 125 | uninitialized_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 147 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’: /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_common_variants test_common_variants.o ../src/get_common_variants.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_allele_depth test_allele_depth.o ../src/allele_functions.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_primer_bed test_primer_bed.o ../src/primer_bed.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o -lhts -lz -lpthread g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o -lhts -lz -lpthread make[3]: Leaving directory '/<>/ivar-1.2.2+dfsg/tests' make check-TESTS make[3]: Entering directory '/<>/ivar-1.2.2+dfsg/tests' make[4]: Entering directory '/<>/ivar-1.2.2+dfsg/tests' PASS: check_consensus FAIL: check_primer_trim PASS: check_allele_depth PASS: check_consensus_threshold PASS: check_quality_trim PASS: check_primer_bed PASS: check_getmasked PASS: check_consensus_min_depth PASS: check_common_variants FAIL: check_unpaired_trim PASS: check_removereads PASS: check_primer_trim_edge_cases PASS: check_variants ====================================== ivar 1.2.2: tests/test-suite.log ====================================== # TOTAL: 13 # PASS: 11 # SKIP: 0 # XFAIL: 0 # FAIL: 2 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 FAIL: check_primer_trim ======================= Found 8 primers in BED file [E::idx_find_and_load] Could not retrieve index file for '../data/test.unmapped.sorted.bam' test_outside_primer ---- test_20_381_1:0:0_6:0:0_1_150 0-6 6-1 0-5 1-1 0-139 Condensing cigar ... 4-12 0-139 ---- test_20_381_1_softclip:0:0_6:0:0_1_150 4-24 0-3 2-2 0-1 1-1 0-4 2-1 6-1 2-1 0-114 Condensing cigar ... 4-33 0-114 ---- test_67_308_2:0:0_2:0:0_0_100 ---- test_67_308_2:0:0_2:0:0_0_100 ---- test_200_349_0:0:0_6:0:0_2_25 ---- test_200_349_0:0:0_6:0:0_2_25 ---- test_20_381_1:0:0_6:0:0_1_150 0-121 6-1 2-4 0-4 2-1 0-1 6-1 0-1 2-1 0-11 4-6 Condensing cigar ... 0-121 4-23 ---- test_20_381_1_softclip:0:0_6:0:0_1_150 0-103 1-1 0-10 1-1 0-13 4-24 Condensing cigar ... 0-103 4-49 ---- test_outside_primer 0-41 2-3 0-57 6-1 0-10 6-1 0-39 Incorrect start position Cigar flag didn't match for 6 ! Expected 2 Got 0 Cigar length didn't match for test_outside_primer ! Expected 3 Got 57 Cigar flag didn't match for 6 ! Expected 0 Got 6 Cigar length didn't match for test_outside_primer ! Expected 57 Got 1 Cigar flag didn't match for 6 ! Expected 6 Got 0 Cigar length didn't match for test_outside_primer ! Expected 1 Got 10 Cigar flag didn't match for 6 ! Expected 0 Got 6 Cigar length didn't match for test_outside_primer ! Expected 10 Got 1 Cigar flag didn't match for 6 ! Expected 6 Got 0 Cigar length didn't match for test_outside_primer ! Expected 1 Got 39 Condensing cigar ... 4-23 0-75 6-1 0-10 6-1 0-39 Cigar length didn't match after condense! Expected 18 Got 75 Cigar flag didn't match! Expected  Got 6 Cigar length didn't match after condense! Expected 3 Got 1 Cigar length didn't match after condense! Expected 57 Got 10 Cigar length didn't match after condense! Expected 10 Got 39 ---- FAIL check_primer_trim (exit status: 255) FAIL: check_unpaired_trim ========================= Found 8 primers in BED file test_72_280_12:1:0_11:0:0_2 Forward Reverse Cigar flag didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 0 Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 1 Cigar flag didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 0 Got 4 Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 1 Got 3 Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 3 Got 2 Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 8 Condensing cigar ... Cigar length didn't match after condense! Expected 93 Got 94 Cigar flag didn't match! Expected  Got 4 Cigar length didn't match after condense! Expected 2 Got 13 test_92_337_8:0:0_10:0:0_21 Forward Reverse Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 56 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 56 Got 1 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 6 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 3 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 3 Got 99 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 99 Got 2 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 2 Got 65 Condensing cigar ... Cigar length didn't match after condense! Expected 19 Got 75 Cigar length didn't match after condense! Expected 56 Got 6 Cigar length didn't match after condense! Expected 1 Got 3 Cigar length didn't match after condense! Expected 6 Got 99 Cigar length didn't match after condense! Expected 3 Got 2 Cigar length didn't match after condense! Expected 99 Got 65 test_147_337_11:1:0_11:1:0_11 Forward Reverse Condensing cigar ... test_149_298_7:0:0_11:0:0_d Forward Reverse Condensing cigar ... test_184_379_11:1:0_8:1:0_26 Forward Reverse Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 6 Got 0 Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 2 Got 89 Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 0 Got 4 Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 89 Got 18 Condensing cigar ... Cigar length didn't match after condense! Expected 71 Got 160 Cigar flag didn't match! Expected  Got 4 Cigar length didn't match after condense! Expected 2 Got 18 FAIL check_unpaired_trim (exit status: 255) ============================================================================ Testsuite summary for ivar 1.2.2 ============================================================================ # TOTAL: 13 # PASS: 11 # SKIP: 0 # XFAIL: 0 # FAIL: 2 # XPASS: 0 # ERROR: 0 ============================================================================ See tests/test-suite.log Please report to gkarthik@scripps.edu ============================================================================ make[4]: *** [Makefile:826: test-suite.log] Error 1 make[4]: Leaving directory '/<>/ivar-1.2.2+dfsg/tests' make[3]: *** [Makefile:934: check-TESTS] Error 2 make[3]: Leaving directory '/<>/ivar-1.2.2+dfsg/tests' make[2]: *** [Makefile:1092: check-am] Error 2 make[2]: Leaving directory '/<>/ivar-1.2.2+dfsg/tests' make[1]: *** [Makefile:360: check-recursive] Error 1 make[1]: Leaving directory '/<>/ivar-1.2.2+dfsg' dh_auto_test: error: make -j4 check VERBOSE=1 returned exit code 2 make: *** [debian/rules:9: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200802-2051 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 23088 Build-Time: 73 Distribution: groovy Fail-Stage: build Host Architecture: armhf Install-Time: 27 Job: ivar_1.2.2+dfsg-3.dsc Machine Architecture: arm64 Package: ivar Package-Time: 103 Source-Version: 1.2.2+dfsg-3 Space: 23088 Status: attempted Version: 1.2.2+dfsg-3 -------------------------------------------------------------------------------- Finished at 20200802-2051 Build needed 00:01:43, 23088k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681090 Scanning for processes to kill in build PACKAGEBUILD-19681090