https://launchpad.net/ubuntu/+source/kallisto/0.46.2+dfsg-3/+build/21475500 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-001 4.15.0-142-generic #146-Ubuntu SMP Tue Apr 13 01:08:49 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_195~480~ubuntu18.04.1 python3-lpbuildd_195~480~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.8 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 29 Apr 12:39:36 ntpdate[1644]: adjust time server 10.211.37.1 offset -0.008250 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-21475500 --image-type chroot /home/buildd/filecache-default/97616dc8f1f80df2f95e447b7ddaa1d0ac1b5f62 Creating target for build PACKAGEBUILD-21475500 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-21475500 Starting target for build PACKAGEBUILD-21475500 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-21475500 'deb http://ftpmaster.internal/ubuntu impish main universe' 'deb http://ftpmaster.internal/ubuntu impish-security main universe' 'deb http://ftpmaster.internal/ubuntu impish-updates main universe' 'deb http://ftpmaster.internal/ubuntu impish-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-21475500 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-21475500 Updating target for build PACKAGEBUILD-21475500 Get:1 http://ftpmaster.internal/ubuntu impish InRelease [269 kB] Get:2 http://ftpmaster.internal/ubuntu impish-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu impish-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu impish-proposed InRelease [115 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main armhf Packages [1355 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu impish/universe armhf Packages [12.8 MB] Get:8 http://ftpmaster.internal/ubuntu impish/universe Translation-en [5441 kB] Get:9 http://ftpmaster.internal/ubuntu impish-proposed/main armhf Packages [45.7 kB] Get:10 http://ftpmaster.internal/ubuntu impish-proposed/main Translation-en [17.4 kB] Get:11 http://ftpmaster.internal/ubuntu impish-proposed/universe armhf Packages [280 kB] Get:12 http://ftpmaster.internal/ubuntu impish-proposed/universe Translation-en [98.9 kB] Fetched 21.1 MB in 8s (2808 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files cpp dpkg dpkg-dev g++ gcc gcc-11-base libapt-pkg6.0 libasan6 libatomic1 libcc1-0 libdpkg-perl libgcc-s1 libgomp1 libstdc++6 libubsan1 libzstd1 linux-libc-dev sysvinit-utils 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 9503 kB of archives. After this operation, 1240 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu impish-proposed/main armhf base-files armhf 11.1ubuntu2 [60.8 kB] Get:2 http://ftpmaster.internal/ubuntu impish/main armhf dpkg armhf 1.20.9ubuntu1 [1218 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main armhf sysvinit-utils armhf 2.96-7ubuntu1 [19.2 kB] Get:4 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libasan6 armhf 11.1.0-1ubuntu1 [2002 kB] Get:5 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libubsan1 armhf 11.1.0-1ubuntu1 [810 kB] Get:6 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libgomp1 armhf 11.1.0-1ubuntu1 [91.3 kB] Get:7 http://ftpmaster.internal/ubuntu impish-proposed/main armhf gcc-11-base armhf 11.1.0-1ubuntu1 [18.8 kB] Get:8 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libgcc-s1 armhf 11.1.0-1ubuntu1 [36.3 kB] Get:9 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libcc1-0 armhf 11.1.0-1ubuntu1 [41.2 kB] Get:10 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libatomic1 armhf 11.1.0-1ubuntu1 [7232 B] Get:11 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libstdc++6 armhf 11.1.0-1ubuntu1 [499 kB] Get:12 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libzstd1 armhf 1.4.8+dfsg-2.1 [255 kB] Get:13 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libapt-pkg6.0 armhf 2.3.2 [787 kB] Get:14 http://ftpmaster.internal/ubuntu impish-proposed/main armhf apt armhf 2.3.2 [1284 kB] Get:15 http://ftpmaster.internal/ubuntu impish/main armhf g++ armhf 4:10.3.0-1ubuntu3 [1600 B] Get:16 http://ftpmaster.internal/ubuntu impish/main armhf gcc armhf 4:10.3.0-1ubuntu3 [5228 B] Get:17 http://ftpmaster.internal/ubuntu impish/main armhf cpp armhf 4:10.3.0-1ubuntu3 [27.7 kB] Get:18 http://ftpmaster.internal/ubuntu impish/main armhf dpkg-dev all 1.20.9ubuntu1 [937 kB] Get:19 http://ftpmaster.internal/ubuntu impish/main armhf libdpkg-perl all 1.20.9ubuntu1 [232 kB] Get:20 http://ftpmaster.internal/ubuntu impish/main armhf linux-libc-dev armhf 5.11.0-16.17 [1169 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9503 kB in 1s (18.9 MB/s) (Reading database ... 12870 files and directories currently installed.) Preparing to unpack .../base-files_11.1ubuntu2_armhf.deb ... Unpacking base-files (11.1ubuntu2) over (11ubuntu18) ... Setting up base-files (11.1ubuntu2) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/dpkg/origins/debian ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Updating /etc/profile to current default. (Reading database ... 12870 files and directories currently installed.) Preparing to unpack .../dpkg_1.20.9ubuntu1_armhf.deb ... Unpacking dpkg (1.20.9ubuntu1) over (1.20.7.1ubuntu4) ... Setting up dpkg (1.20.9ubuntu1) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_2.96-7ubuntu1_armhf.deb ... Unpacking sysvinit-utils (2.96-7ubuntu1) over (2.96-6ubuntu1) ... Setting up sysvinit-utils (2.96-7ubuntu1) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../libasan6_11.1.0-1ubuntu1_armhf.deb ... Unpacking libasan6:armhf (11.1.0-1ubuntu1) over (11-20210417-1ubuntu1) ... Preparing to unpack .../libubsan1_11.1.0-1ubuntu1_armhf.deb ... Unpacking libubsan1:armhf (11.1.0-1ubuntu1) over (11-20210417-1ubuntu1) ... Preparing to unpack .../libgomp1_11.1.0-1ubuntu1_armhf.deb ... Unpacking libgomp1:armhf (11.1.0-1ubuntu1) over (11-20210417-1ubuntu1) ... Preparing to unpack .../gcc-11-base_11.1.0-1ubuntu1_armhf.deb ... Unpacking gcc-11-base:armhf (11.1.0-1ubuntu1) over (11-20210417-1ubuntu1) ... Setting up gcc-11-base:armhf (11.1.0-1ubuntu1) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../libgcc-s1_11.1.0-1ubuntu1_armhf.deb ... Unpacking libgcc-s1:armhf (11.1.0-1ubuntu1) over (11-20210417-1ubuntu1) ... Setting up libgcc-s1:armhf (11.1.0-1ubuntu1) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../libcc1-0_11.1.0-1ubuntu1_armhf.deb ... Unpacking libcc1-0:armhf (11.1.0-1ubuntu1) over (11-20210417-1ubuntu1) ... Preparing to unpack .../libatomic1_11.1.0-1ubuntu1_armhf.deb ... Unpacking libatomic1:armhf (11.1.0-1ubuntu1) over (11-20210417-1ubuntu1) ... Preparing to unpack .../libstdc++6_11.1.0-1ubuntu1_armhf.deb ... Unpacking libstdc++6:armhf (11.1.0-1ubuntu1) over (11-20210417-1ubuntu1) ... Setting up libstdc++6:armhf (11.1.0-1ubuntu1) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../libzstd1_1.4.8+dfsg-2.1_armhf.deb ... Unpacking libzstd1:armhf (1.4.8+dfsg-2.1) over (1.4.8+dfsg-2build2) ... Setting up libzstd1:armhf (1.4.8+dfsg-2.1) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.3.2_armhf.deb ... Unpacking libapt-pkg6.0:armhf (2.3.2) over (2.2.3) ... Setting up libapt-pkg6.0:armhf (2.3.2) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../archives/apt_2.3.2_armhf.deb ... Unpacking apt (2.3.2) over (2.2.3) ... Setting up apt (2.3.2) ... (Reading database ... 12875 files and directories currently installed.) Preparing to unpack .../0-g++_4%3a10.3.0-1ubuntu3_armhf.deb ... Unpacking g++ (4:10.3.0-1ubuntu3) over (4:10.3.0-1ubuntu1) ... Preparing to unpack .../1-gcc_4%3a10.3.0-1ubuntu3_armhf.deb ... Unpacking gcc (4:10.3.0-1ubuntu3) over (4:10.3.0-1ubuntu1) ... Preparing to unpack .../2-cpp_4%3a10.3.0-1ubuntu3_armhf.deb ... Unpacking cpp (4:10.3.0-1ubuntu3) over (4:10.3.0-1ubuntu1) ... Preparing to unpack .../3-dpkg-dev_1.20.9ubuntu1_all.deb ... Unpacking dpkg-dev (1.20.9ubuntu1) over (1.20.7.1ubuntu4) ... Preparing to unpack .../4-libdpkg-perl_1.20.9ubuntu1_all.deb ... Unpacking libdpkg-perl (1.20.9ubuntu1) over (1.20.7.1ubuntu4) ... Preparing to unpack .../5-linux-libc-dev_5.11.0-16.17_armhf.deb ... Unpacking linux-libc-dev:armhf (5.11.0-16.17) over (5.11.0-14.15) ... Setting up linux-libc-dev:armhf (5.11.0-16.17) ... Setting up libgomp1:armhf (11.1.0-1ubuntu1) ... Setting up libasan6:armhf (11.1.0-1ubuntu1) ... Setting up libatomic1:armhf (11.1.0-1ubuntu1) ... Setting up libdpkg-perl (1.20.9ubuntu1) ... Setting up libubsan1:armhf (11.1.0-1ubuntu1) ... Setting up cpp (4:10.3.0-1ubuntu3) ... Setting up libcc1-0:armhf (11.1.0-1ubuntu1) ... Setting up gcc (4:10.3.0-1ubuntu3) ... Setting up dpkg-dev (1.20.9ubuntu1) ... Setting up g++ (4:10.3.0-1ubuntu3) ... Processing triggers for libc-bin (2.33-0ubuntu5) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-21475500 armhf impish-proposed -c chroot:build-PACKAGEBUILD-21475500 --arch=armhf --dist=impish-proposed --nolog kallisto_0.46.2+dfsg-3.dsc Initiating build PACKAGEBUILD-21475500 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-142-generic #146-Ubuntu SMP Tue Apr 13 01:08:49 UTC 2021 armv7l sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-001.buildd +==============================================================================+ | kallisto 0.46.2+dfsg-3 (armhf) Thu, 29 Apr 2021 12:40:10 +0000 | +==============================================================================+ Package: kallisto Version: 0.46.2+dfsg-3 Source Version: 0.46.2+dfsg-3 Distribution: impish-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-21475500/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- kallisto_0.46.2+dfsg-3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/kallisto-B2QKNG/kallisto-0.46.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/kallisto-B2QKNG' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-SdBwa1/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-SdBwa1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SdBwa1/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-SdBwa1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SdBwa1/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-SdBwa1/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (49.7 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-SdBwa1/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 (61.9 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12877 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) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), cmake, libhdf5-dev, libhts-dev Filtered Build-Depends: debhelper-compat (= 12), cmake, libhdf5-dev, libhts-dev dpkg-deb: building package 'sbuild-build-depends-kallisto-dummy' in '/<>/resolver-SdBwa1/apt_archive/sbuild-build-depends-kallisto-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-kallisto-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-SdBwa1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SdBwa1/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-SdBwa1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SdBwa1/apt_archive ./ Sources [508 B] Get:5 copy:/<>/resolver-SdBwa1/apt_archive ./ Packages [588 B] Fetched 2059 B in 0s (51.2 kB/s) Reading package lists... Reading package lists... Install kallisto 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 cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgssapi3-heimdal libhcrypto4-heimdal libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp24 libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libsz2 libtool libuchardet0 libuv1 libwind0-heimdal libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config libhdf5-doc 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 bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgssapi3-heimdal libhcrypto4-heimdal libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp24 libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libsz2 libtool libuchardet0 libuv1 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-kallisto-dummy zlib1g-dev 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 32.4 MB of archives. After this operation, 110 MB of additional disk space will be used. Get:1 copy:/<>/resolver-SdBwa1/apt_archive ./ sbuild-build-depends-kallisto-dummy 0.invalid.0 [880 B] Get:2 http://ftpmaster.internal/ubuntu impish/main armhf bsdextrautils armhf 2.36.1-7ubuntu2 [74.4 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main armhf groff-base armhf 1.22.4-6 [774 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main armhf libpipeline1 armhf 1.5.3-1 [23.3 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main armhf man-db armhf 2.9.4-2 [1118 kB] Get:7 http://ftpmaster.internal/ubuntu impish/main armhf libelf1 armhf 0.183-8 [40.0 kB] Get:8 http://ftpmaster.internal/ubuntu impish/main armhf libexpat1 armhf 2.2.10-2 [54.4 kB] Get:9 http://ftpmaster.internal/ubuntu impish/main armhf libicu67 armhf 67.1-6ubuntu2 [8301 kB] Get:10 http://ftpmaster.internal/ubuntu impish/main armhf libxml2 armhf 2.9.10+dfsg-6.3build2 [529 kB] Get:11 http://ftpmaster.internal/ubuntu impish/main armhf libmagic-mgc armhf 1:5.39-3 [228 kB] Get:12 http://ftpmaster.internal/ubuntu impish/main armhf libmagic1 armhf 1:5.39-3 [71.7 kB] Get:13 http://ftpmaster.internal/ubuntu impish/main armhf file armhf 1:5.39-3 [22.7 kB] Get:14 http://ftpmaster.internal/ubuntu impish/main armhf gettext-base armhf 0.21-3ubuntu2 [36.2 kB] Get:15 http://ftpmaster.internal/ubuntu impish/main armhf libpsl5 armhf 0.21.0-1.2 [52.3 kB] Get:16 http://ftpmaster.internal/ubuntu impish/main armhf libuv1 armhf 1.40.0-1 [68.7 kB] Get:17 http://ftpmaster.internal/ubuntu impish/main armhf libsigsegv2 armhf 2.13-1ubuntu1 [13.4 kB] Get:18 http://ftpmaster.internal/ubuntu impish/main armhf m4 armhf 1.4.18-5 [187 kB] Get:19 http://ftpmaster.internal/ubuntu impish/main armhf autoconf all 2.69-14 [293 kB] Get:20 http://ftpmaster.internal/ubuntu impish/main armhf autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:21 http://ftpmaster.internal/ubuntu impish/main armhf automake all 1:1.16.3-2ubuntu1 [552 kB] Get:22 http://ftpmaster.internal/ubuntu impish/main armhf autopoint all 0.21-3ubuntu2 [422 kB] Get:23 http://ftpmaster.internal/ubuntu impish/main armhf cmake-data all 3.18.4-2ubuntu1 [1705 kB] Get:24 http://ftpmaster.internal/ubuntu impish/main armhf libarchive13 armhf 3.4.3-2 [294 kB] Get:25 http://ftpmaster.internal/ubuntu impish/main armhf libbrotli1 armhf 1.0.9-2build2 [259 kB] Get:26 http://ftpmaster.internal/ubuntu impish/main armhf libroken18-heimdal armhf 7.7.0+dfsg-2 [34.5 kB] Get:27 http://ftpmaster.internal/ubuntu impish/main armhf libasn1-8-heimdal armhf 7.7.0+dfsg-2 [140 kB] Get:28 http://ftpmaster.internal/ubuntu impish/main armhf libheimbase1-heimdal armhf 7.7.0+dfsg-2 [24.3 kB] Get:29 http://ftpmaster.internal/ubuntu impish/main armhf libhcrypto4-heimdal armhf 7.7.0+dfsg-2 [78.5 kB] Get:30 http://ftpmaster.internal/ubuntu impish/main armhf libwind0-heimdal armhf 7.7.0+dfsg-2 [47.2 kB] Get:31 http://ftpmaster.internal/ubuntu impish/main armhf libhx509-5-heimdal armhf 7.7.0+dfsg-2 [88.8 kB] Get:32 http://ftpmaster.internal/ubuntu impish/main armhf libkrb5-26-heimdal armhf 7.7.0+dfsg-2 [170 kB] Get:33 http://ftpmaster.internal/ubuntu impish/main armhf libheimntlm0-heimdal armhf 7.7.0+dfsg-2 [13.2 kB] Get:34 http://ftpmaster.internal/ubuntu impish/main armhf libgssapi3-heimdal armhf 7.7.0+dfsg-2 [79.9 kB] Get:35 http://ftpmaster.internal/ubuntu impish/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2ubuntu1 [13.2 kB] Get:36 http://ftpmaster.internal/ubuntu impish/main armhf libsasl2-2 armhf 2.1.27+dfsg-2ubuntu1 [42.4 kB] Get:37 http://ftpmaster.internal/ubuntu impish/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-2ubuntu1 [134 kB] Get:38 http://ftpmaster.internal/ubuntu impish/main armhf libnghttp2-14 armhf 1.43.0-1 [61.2 kB] Get:39 http://ftpmaster.internal/ubuntu impish/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build2 [48.9 kB] Get:40 http://ftpmaster.internal/ubuntu impish/main armhf libssh-4 armhf 0.9.5-1 [147 kB] Get:41 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impish/main armhf libcurl3-gnutls armhf 7.74.0-1ubuntu2 [211 kB] Get:62 http://ftpmaster.internal/ubuntu impish/main armhf libcurl4-gnutls-dev armhf 7.74.0-1ubuntu2 [304 kB] Get:63 http://ftpmaster.internal/ubuntu impish/main armhf libdeflate0 armhf 1.7-1ubuntu1 [42.9 kB] Get:64 http://ftpmaster.internal/ubuntu impish/main armhf libdeflate-dev armhf 1.7-1ubuntu1 [38.4 kB] Get:65 http://ftpmaster.internal/ubuntu impish-proposed/main armhf libgfortran5 armhf 11.1.0-1ubuntu1 [254 kB] Get:66 http://ftpmaster.internal/ubuntu impish/universe armhf libsz2 armhf 1.0.4-1 [5048 B] Get:67 http://ftpmaster.internal/ubuntu impish/universe armhf libhdf5-103-1 armhf 1.10.6+repack-2 [1191 kB] Get:68 http://ftpmaster.internal/ubuntu impish/universe armhf libhdf5-cpp-103-1 armhf 1.10.6+repack-2 [103 kB] Get:69 http://ftpmaster.internal/ubuntu impish/universe armhf libhdf5-fortran-102 armhf 1.10.6+repack-2 [64.7 kB] Get:70 http://ftpmaster.internal/ubuntu impish/universe armhf libhdf5-hl-100 armhf 1.10.6+repack-2 [51.3 kB] Get:71 http://ftpmaster.internal/ubuntu impish/universe armhf libhdf5-hl-fortran-100 armhf 1.10.6+repack-2 [22.2 kB] Get:72 http://ftpmaster.internal/ubuntu impish/universe armhf libhdf5-hl-cpp-100 armhf 1.10.6+repack-2 [9696 B] Get:73 http://ftpmaster.internal/ubuntu impish/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu6 [149 kB] Get:74 http://ftpmaster.internal/ubuntu impish/main armhf libjpeg-turbo8 armhf 2.0.6-0ubuntu2 [89.3 kB] Get:75 http://ftpmaster.internal/ubuntu impish/main armhf libjpeg-turbo8-dev armhf 2.0.6-0ubuntu2 [202 kB] Get:76 http://ftpmaster.internal/ubuntu impish/main armhf libjpeg8 armhf 8c-2ubuntu8 [2202 B] Get:77 http://ftpmaster.internal/ubuntu impish/main armhf libjpeg8-dev armhf 8c-2ubuntu8 [1554 B] Get:78 http://ftpmaster.internal/ubuntu impish/main armhf libjpeg-dev armhf 8c-2ubuntu8 [1554 B] Get:79 http://ftpmaster.internal/ubuntu impish/universe armhf libaec-dev armhf 1.0.4-1 [16.7 kB] Get:80 http://ftpmaster.internal/ubuntu impish/universe armhf libhdf5-dev armhf 1.10.6+repack-2 [2454 kB] Get:81 http://ftpmaster.internal/ubuntu impish/universe armhf libhts3 armhf 1.11-4 [307 kB] Get:82 http://ftpmaster.internal/ubuntu impish/main armhf liblzma-dev armhf 5.2.5-1.0build2 [142 kB] Get:83 http://ftpmaster.internal/ubuntu impish/universe armhf libhts-dev armhf 1.11-4 [3795 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.4 MB in 1s (23.2 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12877 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7ubuntu2_armhf.deb ... Unpacking bsdextrautils (2.36.1-7ubuntu2) ... 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_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../05-libelf1_0.183-8_armhf.deb ... Unpacking libelf1:armhf (0.183-8) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4ubuntu1) ... Setting up libbrotli1:armhf (1.0.9-2build2) ... Setting up libnghttp2-14:armhf (1.43.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up libdeflate0:armhf (1.7-1ubuntu1) ... Setting up gettext-base (0.21-3ubuntu2) ... Setting up file (1:5.39-3) ... Setting up libaec0:armhf (1.0.4-1) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2ubuntu1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:armhf (1.40.0-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:armhf (2.13-1ubuntu1) ... Setting up autopoint (0.21-3ubuntu2) ... Setting up libjpeg-turbo8:armhf (2.0.6-0ubuntu2) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:armhf (0.9.5-1) ... Setting up libgfortran5:armhf (11.1.0-1ubuntu1) ... Setting up libroken18-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libjsoncpp24:armhf (1.9.4-4) ... Setting up liblzma-dev:armhf (5.2.5-1.0build2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu6) ... Setting up librhash0:armhf (1.4.1-1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up cmake-data (3.18.4-2ubuntu1) ... Setting up libdeflate-dev:armhf (1.7-1ubuntu1) ... Setting up libelf1:armhf (0.183-8) ... Setting up libxml2:armhf (2.9.10+dfsg-6.3build2) ... Setting up libsz2:armhf (1.0.4-1) ... Setting up libheimbase1-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libdw1:armhf (0.183-8) ... Setting up libjpeg-turbo8-dev:armhf (2.0.6-0ubuntu2) ... Setting up gettext (0.21-3ubuntu2) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:armhf (3.4.3-2) ... Setting up libasn1-8-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libaec-dev:armhf (1.0.4-1) ... Setting up m4 (1.4.18-5) ... Setting up libhcrypto4-heimdal:armhf (7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libwind0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up libhdf5-103-1:armhf (1.10.6+repack-2) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhdf5-cpp-103-1:armhf (1.10.6+repack-2) ... Setting up debugedit (1:0.1-0ubuntu2) ... Setting up libjpeg8-dev:armhf (8c-2ubuntu8) ... Setting up libhdf5-hl-100:armhf (1.10.6+repack-2) ... Setting up automake (1:1.16.3-2ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:armhf (8c-2ubuntu8) ... Setting up man-db (2.9.4-2) ... 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 dh-autoreconf (20) ... Setting up libhdf5-hl-cpp-100:armhf (1.10.6+repack-2) ... Setting up libhdf5-fortran-102:armhf (1.10.6+repack-2) ... Setting up libhdf5-hl-fortran-100:armhf (1.10.6+repack-2) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-2) ... Setting up debhelper (13.3.4ubuntu1) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libhdf5-dev (1.10.6+repack-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libldap-2.4-2:armhf (2.4.57+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:armhf (7.74.0-1ubuntu2) ... Setting up libcurl4-gnutls-dev:armhf (7.74.0-1ubuntu2) ... Setting up libcurl4:armhf (7.74.0-1ubuntu2) ... Setting up libhts3:armhf (1.11-4) ... Setting up libhts-dev:armhf (1.11-4) ... Setting up cmake (3.18.4-2ubuntu1) ... Setting up sbuild-build-depends-kallisto-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.33-0ubuntu5) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-142-generic arm64 (armv7l) Toolchain package versions: binutils_2.36.1-6ubuntu1 dpkg-dev_1.20.9ubuntu1 g++-10_10.3.0-1ubuntu1 gcc-10_10.3.0-1ubuntu1 libc6-dev_2.33-0ubuntu5 libstdc++-10-dev_10.3.0-1ubuntu1 libstdc++6_11.1.0-1ubuntu1 linux-libc-dev_5.11.0-16.17 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1build1 apt_2.3.2 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3ubuntu2 autotools-dev_20180224.1+nmu1 base-files_11.1ubuntu2 base-passwd_3.5.49 bash_5.1-2ubuntu1 binutils_2.36.1-6ubuntu1 binutils-arm-linux-gnueabihf_2.36.1-6ubuntu1 binutils-common_2.36.1-6ubuntu1 bsdextrautils_2.36.1-7ubuntu2 bsdutils_1:2.36.1-7ubuntu2 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu3 ca-certificates_20210119build1 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libdeflate-dev_1.7-1ubuntu1 libdeflate0_1.7-1ubuntu1 libdevmapper1.02.1_2:1.02.175-2ubuntu4 libdpkg-perl_1.20.9ubuntu1 libdw1_0.183-8 libelf1_0.183-8 libexpat1_2.2.10-2 libext2fs2_1.45.7-1ubuntu2 libfakeroot_1.25.3-1.1ubuntu2 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu5 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.3.0-1ubuntu1 libgcc-s1_11.1.0-1ubuntu1 libgcrypt20_1.8.7-2ubuntu2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_11.1.0-1ubuntu1 libgmp10_2:6.2.1+dfsg-1ubuntu2 libgnutls30_3.7.1-3ubuntu1 libgomp1_11.1.0-1ubuntu1 libgpg-error0_1.38-2build1 libgssapi-krb5-2_1.18.3-4 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.7-2.1ubuntu1 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libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpcre2-8-0_10.36-2ubuntu5 libpcre3_2:8.39-13build3 libperl5.32_5.32.1-3ubuntu2 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3build3 libprocps8_2:3.3.16-5ubuntu3 libpsl5_0.21.0-1.2 libreadline8_8.1-1 librhash0_1.4.1-1 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27+dfsg-2ubuntu1 libseccomp2_2.5.1-1ubuntu1 libselinux1_3.1-3build1 libsemanage-common_3.1-1ubuntu1 libsemanage1_3.1-1ubuntu1 libsepol1_3.1-1ubuntu1 libsigsegv2_2.13-1ubuntu1 libsmartcols1_2.36.1-7ubuntu2 libsqlite3-0_3.34.1-3 libss2_1.45.7-1ubuntu2 libssh-4_0.9.5-1 libssl1.1_1.1.1j-1ubuntu3 libstdc++-10-dev_10.3.0-1ubuntu1 libstdc++6_11.1.0-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_247.3-3ubuntu3 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2build1 libtirpc-common_1.3.1-1build1 libtirpc-dev_1.3.1-1build1 libtirpc3_1.3.1-1build1 libtool_2.4.6-15 libubsan1_11.1.0-1ubuntu1 libuchardet0_0.0.7-1 libudev1_247.3-3ubuntu3 libunistring2_0.9.10-4 libuuid1_2.36.1-7ubuntu2 libuv1_1.40.0-1 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-6.3build2 libxxhash0_0.8.0-2 libzstd1_1.4.8+dfsg-2.1 linux-libc-dev_5.11.0-16.17 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu8 logsave_1.45.7-1ubuntu2 lsb-base_11.1.0ubuntu2 lto-disabled-list_7 m4_1.4.18-5 make_4.3-4ubuntu1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-7ubuntu2 ncurses-base_6.2+20201114-2build1 ncurses-bin_6.2+20201114-2build1 openssl_1.1.1j-1ubuntu3 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu8 patch_2.7.6-7 perl_5.32.1-3ubuntu2 perl-base_5.32.1-3ubuntu2 perl-modules-5.32_5.32.1-3ubuntu2 pinentry-curses_1.1.0-4build1 pkgbinarymangler_147 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu3 readline-common_8.1-1 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-kallisto-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.14 systemd_247.3-3ubuntu3 systemd-sysv_247.3-3ubuntu3 systemd-timesyncd_247.3-3ubuntu3 sysvinit-utils_2.96-7ubuntu1 tar_1.34+dfsg-1build1 tzdata_2021a-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_24ubuntu3 util-linux_2.36.1-7ubuntu2 xz-utils_5.2.5-1.0build2 zlib1g_1:1.2.11.dfsg-2ubuntu6 zlib1g-dev_1:1.2.11.dfsg-2ubuntu6 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Mar 4 18:30:33 2021 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kallisto_0.46.2+dfsg-3.dsc dpkg-source: info: extracting kallisto in /<>/kallisto-0.46.2+dfsg dpkg-source: info: unpacking kallisto_0.46.2+dfsg.orig.tar.xz dpkg-source: info: unpacking kallisto_0.46.2+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_htslib.patch dpkg-source: info: applying spelling dpkg-source: info: applying htslib1.3 dpkg-source: info: applying Check_busOptions.seq_length_before_accessing.patch dpkg-source: info: applying gcc11.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-21475500 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-21475500 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-21475500 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package kallisto dpkg-buildpackage: info: source version 0.46.2+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/kallisto-0.46.2+dfsg' dh_auto_configure -- -DDEBIAN_BUILD=1 -DLINK=shared cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DDEBIAN_BUILD=1 -DLINK=shared .. -- The C compiler identification is GNU 10.3.0 -- The CXX compiler identification is GNU 10.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf make[1]: Leaving directory '/<>/kallisto-0.46.2+dfsg' dh_auto_build -a cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<>/kallisto-0.46.2+dfsg -B/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend make[3]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/kallisto-0.46.2+dfsg /<>/kallisto-0.46.2+dfsg/src /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake --color= Dependee "/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake" is newer than depender "/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto_core.dir/depend.internal". Dependee "/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto_core.dir/depend.internal". Scanning dependencies of target kallisto_core make[3]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build make[3]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' [ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o [ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o [ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/BUSTools.cpp cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/BUSData.cpp [ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/Bootstrap.cpp cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/GeneModel.cpp [ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/H5Writer.cpp [ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/Kmer.cpp [ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/KmerIndex.cpp In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:10, from /<>/kallisto-0.46.2+dfsg/src/GeneModel.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.h:7, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/GeneModel.cpp:1: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function ‘std::size_t std::hash >::operator()(const std::pair&) const’: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:10, from /<>/kallisto-0.46.2+dfsg/src/GeneModel.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:13, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:2: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function ‘std::size_t std::hash >::operator()(const std::pair&) const’: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.h:7, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ [ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/KmerIterator.cpp In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ [ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/Merge.cpp /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:218:13: required from ‘void KmerHashTable::reserve(size_t, bool) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:848:32: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] In file included from /usr/include/c++/10/vector:72, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.h:7, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.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 = {const double&}; _Tp = double; _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/vector:67, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.h:7, from /<>/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = int]’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/MinCollector.cpp In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/Merge.cpp:11: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/MinCollector.h:12, from /<>/kallisto-0.46.2+dfsg/src/MinCollector.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ [ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] In file included from /usr/include/c++/10/vector:72, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.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 = {const Kmer&}; _Tp = Kmer; _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 /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:12, from /<>/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:13, from /<>/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function ‘std::size_t std::hash >::operator()(const std::pair&) const’: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:12, from /<>/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ /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 = {Kmer}; _Tp = Kmer; _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 In file included from /usr/include/c++/10/vector:67, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void KmerIndex::BuildDeBruijnGraph(const ProgramOptions&, const std::vector >&)’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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/vector:72, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1: /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp [ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/PseudoBam.cpp In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/MinCollector.h:12, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /usr/include/c++/10/vector:72, from /<>/kallisto-0.46.2+dfsg/src/Merge.cpp:5: /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 long long int&}; _Tp = long long int; _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 /<>/kallisto-0.46.2+dfsg/src/PseudoBam.h:13, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:21, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function ‘std::size_t std::hash >::operator()(const std::pair&) const’: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.h:12, from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.cpp:3: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.h:13, from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.cpp:3: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function ‘std::size_t std::hash >::operator()(const std::pair&) const’: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.h:12, from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.cpp:3: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/MinCollector.h:12, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /usr/include/c++/10/vector:72, from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.h:5, from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.cpp:3: /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 = {PseudoAlignmentInfo}; _Tp = PseudoAlignmentInfo; _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>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘void readPseudoAlignmentBatch(std::ifstream&, PseudoAlignmentBatch&)’: /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/common.cpp [ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/h5utils.cpp [ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/hash.cpp [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/main.cpp [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/weights.cpp In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/weights.h:4, from /<>/kallisto-0.46.2+dfsg/src/weights.cpp:1: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/MinCollector.h:12, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:17: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.h:13, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:21, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:17: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function ‘std::size_t std::hash >::operator()(const std::pair&) const’: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] In file included from /usr/include/c++/10/vector:72, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/weights.h:4, from /<>/kallisto-0.46.2+dfsg/src/weights.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 = {const double&}; _Tp = double; _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/vector:67, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/weights.h:4, from /<>/kallisto-0.46.2+dfsg/src/weights.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector calc_eff_lens(const std::vector&, double)’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector calc_eff_lens(const std::vector&, const std::vector&)’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector get_frag_len_means(const std::vector&, const std::vector&)’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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/vector:72, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/weights.h:4, from /<>/kallisto-0.46.2+dfsg/src/weights.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/weights.h:4, from /<>/kallisto-0.46.2+dfsg/src/weights.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector update_eff_lens(const std::vector&, const MinCollector&, const KmerIndex&, const std::vector&, const std::vector&, std::vector&, const ProgramOptions&)’: /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:9, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, std::pair)> >]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:9, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter, std::pair)> >]’: /usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1824 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, std::pair)> >]’: /usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1844 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.2+dfsg/src/weights.h:4, from /<>/kallisto-0.46.2+dfsg/src/weights.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 = {double}; _Tp = double; _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>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘WeightMap calc_weights(const std::vector&, const EcMap&, const std::vector&)’: /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/MinCollector.h:12, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:17: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter, std::pair)> >]’: /usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1950 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /<>/kallisto-0.46.2+dfsg/src/Merge.cpp:5: /usr/include/c++/10/bits/stl_vector.h: In function ‘bool MergeBatchDirectories(const ProgramOptions&, int&, int64_t&, int64_t&, int64_t&, int&)’: /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/vector:72, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /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 bam1_t&}; _Tp = bam1_t; _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>:: | ^~~~~~~~~~~~~~~~~~~ /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 BUSData&}; _Tp = BUSData; _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 /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 = {std::pair}; _Tp = std::pair; _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 /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 = {PseudoAlignmentInfo}; _Tp = PseudoAlignmentInfo; _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 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PseudoAlignmentInfo}; _Tp = PseudoAlignmentInfo; _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 = {std::pair}; _Tp = std::pair; _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>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void MasterProcessor::processAln(const EMAlgorithm&, bool)’: /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/vector:72, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:9, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1979 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1980 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1981 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1896 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void BUSProcessor::processBuffer()’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void AlnProcessor::processBufferTrans()’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void MasterProcessor::update(const std::vector&, const std::vector >&, std::vector > >&, std::vector, std::__cxx11::basic_string > >&, int, std::vector&, std::vector&, const PseudoAlignmentBatch&, std::vector&, std::vector > >, int*, int*, int, int)’: /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/vector:72, from /usr/include/c++/10/bits/random.h:34, from /usr/include/c++/10/random:49, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void AlnProcessor::processBufferGenome()’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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 = {std::pair}; _Tp = std::pair; _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>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ 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 double&}; _Tp = double; _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/vector:67, from /usr/include/c++/10/bits/random.h:34, from /usr/include/c++/10/random:49, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:3: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = int]’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘int main(int, char**)’: /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 90%] Linking CXX static library libkallisto_core.a cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto_core.dir/link.txt --verbose=1 /usr/bin/ar qc libkallisto_core.a CMakeFiles/kallisto_core.dir/BUSData.cpp.o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o CMakeFiles/kallisto_core.dir/Kmer.cpp.o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o CMakeFiles/kallisto_core.dir/Merge.cpp.o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o CMakeFiles/kallisto_core.dir/common.cpp.o CMakeFiles/kallisto_core.dir/h5utils.cpp.o CMakeFiles/kallisto_core.dir/hash.cpp.o CMakeFiles/kallisto_core.dir/main.cpp.o CMakeFiles/kallisto_core.dir/weights.cpp.o /usr/bin/ranlib libkallisto_core.a make[3]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' [ 90%] Built target kallisto_core make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend make[3]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/kallisto-0.46.2+dfsg /<>/kallisto-0.46.2+dfsg/src /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto.dir/DependInfo.cmake --color= Dependee "/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto.dir/DependInfo.cmake" is newer than depender "/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto.dir/depend.internal". Dependee "/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto.dir/depend.internal". Scanning dependencies of target kallisto make[3]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build make[3]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' [ 95%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<>/kallisto-0.46.2+dfsg/src -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto.dir/main.cpp.o -c /<>/kallisto-0.46.2+dfsg/src/main.cpp In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/MinCollector.h:12, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:17: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function ‘size_t KmerHashTable::rndup(size_t)’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/PseudoBam.h:13, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:21, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:17: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function ‘std::size_t std::hash >::operator()(const std::pair&) const’: /<>/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.2+dfsg/src/MinCollector.h:12, from /<>/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:17: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of ‘size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’: /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from ‘void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]’ /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from ‘KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]’ /<>/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/bits/random.h:34, from /usr/include/c++/10/random:49, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /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 = {std::pair}; _Tp = std::pair; _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>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ 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 double&}; _Tp = double; _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/vector:67, from /usr/include/c++/10/bits/random.h:34, from /usr/include/c++/10/random:49, from /<>/kallisto-0.46.2+dfsg/src/main.cpp:3: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = int]’: /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘int main(int, char**)’: /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable kallisto cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kallisto.dir/main.cpp.o -o kallisto libkallisto_core.a -lpthread -lhts libkallisto_core.a -lz -lrt make[3]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' [100%] Built target kallisto make[2]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<>/kallisto-0.46.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<>/kallisto-0.46.2+dfsg -B/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend make[3]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/kallisto-0.46.2+dfsg /<>/kallisto-0.46.2+dfsg/src /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build make[3]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/CMakeFiles/kallisto_core.dir/build'. make[3]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' [ 90%] Built target kallisto_core make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend make[3]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' cd /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/kallisto-0.46.2+dfsg /<>/kallisto-0.46.2+dfsg/src /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build make[3]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/CMakeFiles/kallisto.dir/build'. make[3]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' [100%] Built target kallisto make[2]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/kallisto-0.46.2+dfsg/debian/tmp/usr/bin/kallisto make[1]: Leaving directory '/<>/kallisto-0.46.2+dfsg/obj-arm-linux-gnueabihf' dh_install -a dh_installdocs -a dh_installchangelogs -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 be586ca540be608aa707a73624e8a6d80db28bde dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/kallisto/usr/bin/kallisto contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 147 INFO: pkgstriptranslations version 147 pkgstriptranslations: processing kallisto (in debian/kallisto); do_strip: , oemstrip: pkgstriptranslations: processing kallisto-dbgsym (in debian/.debhelper/kallisto/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/kallisto/DEBIAN/control, package kallisto, directory debian/kallisto pkgstripfiles: Running PNG optimization (using 4 cpus) for package kallisto ... pkgstripfiles: No PNG files. dpkg-deb: building package 'kallisto' in '../kallisto_0.46.2+dfsg-3_armhf.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/kallisto/dbgsym-root/DEBIAN/control, package kallisto-dbgsym, directory debian/.debhelper/kallisto/dbgsym-root dpkg-deb: building package 'kallisto-dbgsym' in 'debian/.debhelper/scratch-space/build-kallisto/kallisto-dbgsym_0.46.2+dfsg-3_armhf.deb'. Renaming kallisto-dbgsym_0.46.2+dfsg-3_armhf.deb to kallisto-dbgsym_0.46.2+dfsg-3_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../kallisto_0.46.2+dfsg-3_armhf.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 2021-04-29T12:42:38Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kallisto_0.46.2+dfsg-3_armhf.changes: ------------------------------------- Format: 1.8 Date: Thu, 04 Mar 2021 23:54:34 +0530 Source: kallisto Binary: kallisto Built-For-Profiles: noudeb Architecture: armhf Version: 0.46.2+dfsg-3 Distribution: impish-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nilesh Patra Description: kallisto - near-optimal RNA-Seq quantification Closes: 984073 Changes: kallisto (0.46.2+dfsg-3) unstable; urgency=medium . * Team Upload. * debian/patches/gcc11.patch: Fix gcc-11 FTBFS (Closes: #984073) Checksums-Sha1: 0932331c575c11033e8674f7113612c739bef0b6 3715428 kallisto-dbgsym_0.46.2+dfsg-3_armhf.ddeb b2800743757a3ba0e076d89809f1afae229d9496 7813 kallisto_0.46.2+dfsg-3_armhf.buildinfo 9923ff619be0c89cec206f6b451ecffda4f14d40 214468 kallisto_0.46.2+dfsg-3_armhf.deb Checksums-Sha256: 8529473641b667239d2a7e020c5dc8403a1866671ceb32559d0150c710185817 3715428 kallisto-dbgsym_0.46.2+dfsg-3_armhf.ddeb 4b7459c563ee1251cf56dc108454f4d21951fb4c27141f9cb529b6902bbe598b 7813 kallisto_0.46.2+dfsg-3_armhf.buildinfo 1d886c9f514ed74ba19c7343e3242f9470f567c82bc11ebbc65e5465d4d98ff8 214468 kallisto_0.46.2+dfsg-3_armhf.deb Files: 089fa95dc4a92cd239cc5722a39b4ea4 3715428 debug optional kallisto-dbgsym_0.46.2+dfsg-3_armhf.ddeb 9f3a14d9de1b6a26fe4343cf9d446a17 7813 science optional kallisto_0.46.2+dfsg-3_armhf.buildinfo 463c7c7c61ceecdfe51f1edf052adbb4 214468 science optional kallisto_0.46.2+dfsg-3_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kallisto Binary: kallisto kallisto-dbgsym Architecture: armhf Version: 0.46.2+dfsg-3 Checksums-Md5: 089fa95dc4a92cd239cc5722a39b4ea4 3715428 kallisto-dbgsym_0.46.2+dfsg-3_armhf.ddeb 463c7c7c61ceecdfe51f1edf052adbb4 214468 kallisto_0.46.2+dfsg-3_armhf.deb Checksums-Sha1: 0932331c575c11033e8674f7113612c739bef0b6 3715428 kallisto-dbgsym_0.46.2+dfsg-3_armhf.ddeb 9923ff619be0c89cec206f6b451ecffda4f14d40 214468 kallisto_0.46.2+dfsg-3_armhf.deb Checksums-Sha256: 8529473641b667239d2a7e020c5dc8403a1866671ceb32559d0150c710185817 3715428 kallisto-dbgsym_0.46.2+dfsg-3_armhf.ddeb 1d886c9f514ed74ba19c7343e3242f9470f567c82bc11ebbc65e5465d4d98ff8 214468 kallisto_0.46.2+dfsg-3_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Thu, 29 Apr 2021 12:42:37 +0000 Build-Path: /<>/kallisto-0.46.2+dfsg Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-14), automake (= 1:1.16.3-2ubuntu1), autopoint (= 0.21-3ubuntu2), autotools-dev (= 20180224.1+nmu1), base-files (= 11.1ubuntu2), base-passwd (= 3.5.49), bash (= 5.1-2ubuntu1), binutils (= 2.36.1-6ubuntu1), binutils-arm-linux-gnueabihf (= 2.36.1-6ubuntu1), binutils-common (= 2.36.1-6ubuntu1), bsdextrautils (= 2.36.1-7ubuntu2), bsdutils (= 1:2.36.1-7ubuntu2), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu3), cmake (= 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2.36.1-7ubuntu2), xz-utils (= 5.2.5-1.0build2), zlib1g (= 1:1.2.11.dfsg-2ubuntu6), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu6) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1614882274" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ kallisto_0.46.2+dfsg-3_armhf.deb -------------------------------- new Debian package, version 2.0. size 214468 bytes: control archive=1164 bytes. 1374 bytes, 24 lines control 264 bytes, 4 lines md5sums Package: kallisto Version: 0.46.2+dfsg-3 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 448 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.5), libhts3 (>= 1.10), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://pachterlab.github.io/kallisto Description: near-optimal RNA-Seq quantification Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate than existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools. drwxr-xr-x root/root 0 2021-03-04 18:24 ./ drwxr-xr-x root/root 0 2021-03-04 18:24 ./usr/ drwxr-xr-x root/root 0 2021-03-04 18:24 ./usr/bin/ -rwxr-xr-x root/root 445628 2021-03-04 18:24 ./usr/bin/kallisto drwxr-xr-x root/root 0 2021-03-04 18:24 ./usr/share/ drwxr-xr-x root/root 0 2021-03-04 18:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-03-04 18:24 ./usr/share/doc/kallisto/ -rw-r--r-- root/root 323 2021-03-04 16:50 ./usr/share/doc/kallisto/README.test -rw-r--r-- root/root 754 2021-03-04 18:24 ./usr/share/doc/kallisto/changelog.Debian.gz -rw-r--r-- root/root 2910 2021-03-04 16:50 ./usr/share/doc/kallisto/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: n/a Build-Time: 114 Distribution: impish-proposed Host Architecture: armhf Install-Time: 31 Job: kallisto_0.46.2+dfsg-3.dsc Machine Architecture: arm64 Package: kallisto Package-Time: 148 Source-Version: 0.46.2+dfsg-3 Space: n/a Status: successful Version: 0.46.2+dfsg-3 -------------------------------------------------------------------------------- Finished at 2021-04-29T12:42:38Z Build needed 00:02:28, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=impish --arch=armhf PACKAGEBUILD-21475500 Scanning for processes to kill in build PACKAGEBUILD-21475500