sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | kallisto 0.46.0+dfsg-1 (armhf) Sat, 10 Aug 2019 20:11:56 +0000 | +==============================================================================+ Package: kallisto Version: 0.46.0+dfsg-1 Source Version: 0.46.0+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-80681b51-07df-48b9-9434-fde1a6fc6dd3' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [149 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-10-0815.42.pdiff [5767 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-10-1415.28.pdiff [13.1 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-10-1415.28.pdiff [13.1 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-10-0815.42.pdiff [4706 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-10-1415.28.pdiff [8673 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-10-1415.28.pdiff [8673 B] Get:8 http://debian.oregonstate.edu/debian unstable/main armhf Packages [8155 kB] Fetched 8391 kB in 2s (4279 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'kallisto' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kallisto.git Please use: git clone https://salsa.debian.org/med-team/kallisto.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 853 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main kallisto 0.46.0+dfsg-1 (dsc) [2108 B] Get:2 http://debian.oregonstate.edu/debian unstable/main kallisto 0.46.0+dfsg-1 (tar) [846 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main kallisto 0.46.0+dfsg-1 (diff) [5060 B] Fetched 853 kB in 0s (17.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/kallisto-eyaEmI/kallisto-0.46.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/kallisto-eyaEmI' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-L5gqZs/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-L5gqZs/apt_archive ./ InRelease Get:2 copy:/<>/resolver-L5gqZs/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-L5gqZs/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-L5gqZs/apt_archive ./ Sources [363 B] Get:5 copy:/<>/resolver-L5gqZs/apt_archive ./ Packages [452 B] Fetched 1772 B in 0s (93.2 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 additional packages will be installed: binutils-arm-linux-gnueabihf cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf dpkg-cross file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-cross-base gcc-9-cross-base gcc-arm-linux-gnueabihf libasan5-armhf-cross libatomic1-armhf-cross libc6-armhf-cross libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-armhf-cross libgcc1-armhf-cross libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-armhf-cross libstdc++6-armhf-cross libubsan1-armhf-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armhf-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch gcc-8-doc libstdc++6-8-dbg-armhf-cross libgcc1-dbg-armhf-cross libgomp1-dbg-armhf-cross libitm1-dbg-armhf-cross libatomic1-dbg-armhf-cross libasan5-dbg-armhf-cross liblsan0-dbg-armhf-cross libtsan0-dbg-armhf-cross libubsan1-dbg-armhf-cross libmpx2-dbg-armhf-cross libquadmath0-dbg-armhf-cross manpages-dev autoconf automake libtool flex bison gdb-arm-linux-gnueabihf gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-arm-linux-gnueabihf cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf dpkg-cross file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-cross-base gcc-9-cross-base gcc-arm-linux-gnueabihf libasan5-armhf-cross libatomic1-armhf-cross libc6-armhf-cross libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-armhf-cross libgcc1-armhf-cross libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-armhf-cross libstdc++6-armhf-cross libubsan1-armhf-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armhf-cross sbuild-build-depends-core-dummy:armhf sensible-utils ucf 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 42.3 MB of archives. After this operation, 154 MB of additional disk space will be used. Get:1 copy:/<>/resolver-L5gqZs/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [872 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-5 [253 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-5 [119 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-5 [67.1 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.32.51.20190727-1 [2914 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabihf-base amd64 8.3.0-19cross1 [192 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-arm-linux-gnueabihf amd64 8.3.0-19cross1 [6549 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-19cross1 [187 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.1.0-8cross1 [185 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.28-10cross3 [1172 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armhf-cross all 1:9.1.0-8cross1 [37.3 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 9.1.0-8cross1 [73.2 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 9.1.0-8cross1 [6692 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armhf-cross all 9.1.0-8cross1 [363 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 9.1.0-8cross1 [392 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 9.1.0-8cross1 [112 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-armhf-cross all 8.3.0-19cross1 [614 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabihf amd64 8.3.0-19cross1 [6979 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:8.3.0-1 [1456 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 4.19.37-5cross3 [1255 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.28-10cross3 [2150 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-armhf-cross all 8.3.0-19cross1 [1561 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-arm-linux-gnueabihf amd64 8.3.0-19cross1 [7130 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:8.3.0-1 [1180 B] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.6 [6572 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.3 MB in 1s (67.5 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11990 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.37-5_amd64.deb ... Unpacking libmagic-mgc (1:5.37-5) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.37-5_amd64.deb ... Unpacking libmagic1:amd64 (1:5.37-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.37-5_amd64.deb ... Unpacking file (1:5.37-5) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... 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Selecting previously unselected package dpkg-cross. Preparing to unpack .../42-dpkg-cross_2.6.15-3_all.deb ... Unpacking dpkg-cross (2.6.15-3) ... Selecting previously unselected package crossbuild-essential-armhf. Preparing to unpack .../43-crossbuild-essential-armhf_12.6_all.deb ... Unpacking crossbuild-essential-armhf (12.6) ... Selecting previously unselected package sbuild-build-depends-core-dummy:armhf. Preparing to unpack .../44-sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy:armhf (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libc6-armhf-cross (2.28-10cross3) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up gcc-8-cross-base (8.3.0-19cross1) ... Setting up libmagic1:amd64 (1:5.37-5) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up file (1:5.37-5) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-3) ... Setting up gcc-8-arm-linux-gnueabihf-base:amd64 (8.3.0-19cross1) ... Setting up linux-libc-dev-armhf-cross (4.19.37-5cross3) ... Setting up gcc-9-cross-base (9.1.0-8cross1) ... Setting up sensible-utils (0.0.12) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up binutils-arm-linux-gnueabihf (2.32.51.20190727-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up cpp-8-arm-linux-gnueabihf (8.3.0-19cross1) ... Setting up libgomp1-armhf-cross (9.1.0-8cross1) ... Setting up libc6-dev-armhf-cross (2.28-10cross3) ... Setting up libatomic1-armhf-cross (9.1.0-8cross1) ... Setting up libgcc1-armhf-cross (1:9.1.0-8cross1) ... Setting up ucf (3.0038+nmu1) ... Setting up cpp-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libasan5-armhf-cross (9.1.0-8cross1) ... Setting up libstdc++6-armhf-cross (9.1.0-8cross1) ... Setting up libubsan1-armhf-cross (9.1.0-8cross1) ... Setting up libgcc-8-dev-armhf-cross (8.3.0-19cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-8-dev-armhf-cross (8.3.0-19cross1) ... Setting up gcc-8-arm-linux-gnueabihf (8.3.0-19cross1) ... Setting up gcc-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up g++-8-arm-linux-gnueabihf (8.3.0-19cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armhf (12.6) ... Setting up sbuild-build-depends-core-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-L5gqZs/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-L5gqZs/apt_archive ./ InRelease Get:2 copy:/<>/resolver-L5gqZs/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-L5gqZs/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-L5gqZs/apt_archive ./ Sources [485 B] Get:5 copy:/<>/resolver-L5gqZs/apt_archive ./ Packages [570 B] Fetched 2018 B in 0s (107 kB/s) Reading package lists... Reading package lists... Install essential 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-essential-dummy:armhf 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 840 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-L5gqZs/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 840 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:armhf. (Reading database ... 15042 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-essential-dummy:armhf (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:armhf (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper-compat (= 12), cmake, libhdf5-dev, libhts-dev Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper-compat (= 12), cmake, libhdf5-dev, libhts-dev dpkg-deb: building package 'sbuild-build-depends-kallisto-dummy' in '/<>/resolver-L5gqZs/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-essential-dummy sbuild-build-depends-kallisto-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-L5gqZs/apt_archive ./ InRelease Get:2 copy:/<>/resolver-L5gqZs/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-L5gqZs/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-L5gqZs/apt_archive ./ Sources [653 B] Get:5 copy:/<>/resolver-L5gqZs/apt_archive ./ Packages [734 B] Fetched 2350 B in 0s (121 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 bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gcc-9-base:armhf gettext gettext-base groff-base hdf5-helpers:armhf intltool-debian libaec-dev:armhf libaec0:armhf libarchive-zip-perl libarchive13 libasan5:armhf libatomic1:armhf libbsd0 libbz2-1.0:armhf libc6:armhf libc6-dev:armhf libcom-err2:armhf libcroco3 libcurl3-gnutls:armhf libcurl4 libdb5.3:armhf libdeflate0:armhf libelf1 libexpat1 libffi6:armhf libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libgcrypt20:armhf libgfortran5:armhf libglib2.0-0 libgmp10:armhf libgnutls30:armhf libgomp1:armhf libgpg-error0:armhf libgssapi-krb5-2 libgssapi-krb5-2:armhf libhdf5-103:armhf libhdf5-cpp-103:armhf libhdf5-dev:armhf libhogweed4:armhf libhts-dev:armhf libhts2:armhf libidn2-0:armhf libjpeg62-turbo:armhf libjpeg62-turbo-dev:armhf libjsoncpp1 libk5crypto3 libk5crypto3:armhf libkeyutils1 libkeyutils1:armhf libkrb5-3 libkrb5-3:armhf libkrb5support0 libkrb5support0:armhf libldap-2.4-2 libldap-2.4-2:armhf libldap-common liblzma-dev:armhf liblzma5:armhf libncurses6 libnettle6:armhf libnghttp2-14 libnghttp2-14:armhf libp11-kit0:armhf libpipeline1 libprocps7 libpsl5 libpsl5:armhf librhash0 librtmp1 librtmp1:armhf libsasl2-2 libsasl2-2:armhf libsasl2-modules-db libsasl2-modules-db:armhf libsigsegv2 libssh2-1 libssh2-1:armhf libssl1.1 libssl1.1:armhf libstdc++-8-dev:armhf libstdc++6:armhf libsub-override-perl libsz2:armhf libtasn1-6:armhf libtool libubsan1:armhf libuchardet0 libunistring2:armhf libuv1 linux-libc-dev:armhf lsb-base m4 man-db po-debconf procps zlib1g:armhf zlib1g-dev:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip glibc-doc:armhf libc-l10n:armhf locales:armhf manpages-dev:armhf rng-tools:armhf gnutls-bin:armhf krb5-doc krb5-user krb5-doc:armhf krb5-user:armhf libhdf5-doc:armhf liblzma-doc:armhf libstdc++-8-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx ca-certificates:armhf ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n:armhf krb5-locales krb5-locales:armhf libgpm2 publicsuffix publicsuffix:armhf libsasl2-modules libsasl2-modules:armhf libltdl-dev libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gcc-9-base:armhf gettext gettext-base groff-base hdf5-helpers:armhf intltool-debian libaec-dev:armhf libaec0:armhf libarchive-zip-perl libarchive13 libasan5:armhf libatomic1:armhf libbsd0 libbz2-1.0:armhf libc6:armhf libc6-dev:armhf libcom-err2:armhf libcroco3 libcurl3-gnutls:armhf libcurl4 libdb5.3:armhf libdeflate0:armhf libelf1 libexpat1 libffi6:armhf libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libgcrypt20:armhf libgfortran5:armhf libglib2.0-0 libgmp10:armhf libgnutls30:armhf libgomp1:armhf libgpg-error0:armhf libgssapi-krb5-2 libgssapi-krb5-2:armhf libhdf5-103:armhf libhdf5-cpp-103:armhf libhdf5-dev:armhf libhogweed4:armhf libhts-dev:armhf libhts2:armhf libidn2-0:armhf libjpeg62-turbo:armhf libjpeg62-turbo-dev:armhf libjsoncpp1 libk5crypto3 libk5crypto3:armhf libkeyutils1 libkeyutils1:armhf libkrb5-3 libkrb5-3:armhf libkrb5support0 libkrb5support0:armhf libldap-2.4-2 libldap-2.4-2:armhf libldap-common liblzma-dev:armhf liblzma5:armhf libncurses6 libnettle6:armhf libnghttp2-14 libnghttp2-14:armhf libp11-kit0:armhf libpipeline1 libprocps7 libpsl5 libpsl5:armhf librhash0 librtmp1 librtmp1:armhf libsasl2-2 libsasl2-2:armhf libsasl2-modules-db libsasl2-modules-db:armhf libsigsegv2 libssh2-1 libssh2-1:armhf libssl1.1 libssl1.1:armhf libstdc++-8-dev:armhf libstdc++6:armhf libsub-override-perl libsz2:armhf libtasn1-6:armhf libtool libubsan1:armhf libuchardet0 libunistring2:armhf libuv1 linux-libc-dev:armhf lsb-base m4 man-db po-debconf procps sbuild-build-depends-kallisto-dummy:armhf zlib1g:armhf zlib1g-dev:armhf 0 upgraded, 112 newly installed, 0 to remove and 0 not upgraded. Need to get 44.9 MB of archives. After this operation, 152 MB of additional disk space will be used. Get:1 copy:/<>/resolver-L5gqZs/apt_archive ./ sbuild-build-depends-kallisto-dummy 0.invalid.0 [892 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.6.1-1 [1295 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main armhf gcc-9-base armhf 9.1.0-10 [190 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20190803-1 [102 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive13 amd64 3.3.3-4 [314 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5support0 amd64 1.17-6 [64.6 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libk5crypto3 amd64 1.17-6 [116 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1c-1 [1535 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5-3 amd64 1.17-6 [366 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-6 [156 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1 [69.0 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1 [106 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-common all 2.4.48+dfsg-1 [90.8 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.48+dfsg-1 [226 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libnghttp2-14 amd64 1.37.0-1 [83.3 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libcurl4 amd64 7.65.3-1 [336 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.7-1 [106 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libuv1 amd64 1.30.1-1 [116 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.4.0-1 [21.9 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.4.0-1 [14.0 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12.20190723-1 [80.6 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.60.6-1 [1294 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.3 [1029 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main armhf gcc-8-base armhf 8.3.0-19 [192 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main armhf hdf5-helpers armhf 1.10.4+repack-10 [35.2 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main armhf libgcc1 armhf 1:9.1.0-10 [37.3 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.28-10 [2390 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main armhf libaec0 armhf 1.0.4-1 [20.4 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main armhf libsz2 armhf 1.0.4-1 [6616 B] Get:62 http://debian.oregonstate.edu/debian unstable/main armhf libaec-dev armhf 1.0.4-1 [18.3 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main armhf libasan5 armhf 9.1.0-10 [370 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 9.1.0-10 [6880 B] Get:65 http://debian.oregonstate.edu/debian unstable/main armhf libbz2-1.0 armhf 1.0.6-9.2 [43.6 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 5.2.7-1 [1211 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.28-10 [2149 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main armhf libcom-err2 armhf 1.45.3-4 [69.6 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main armhf libgmp10 armhf 2:6.1.2+dfsg-4 [205 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main armhf libnettle6 armhf 3.4.1-1 [227 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main armhf libhogweed4 armhf 3.4.1-1 [130 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main armhf libunistring2 armhf 0.9.10-2 [371 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main armhf libidn2-0 armhf 2.2.0-1 [80.3 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main armhf libffi6 armhf 3.2.1-9 [18.9 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main armhf libp11-kit0 armhf 0.23.15-2 [292 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main armhf libtasn1-6 armhf 4.14-2 [48.7 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main armhf libgnutls30 armhf 3.6.9-4 [1097 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main armhf libkrb5support0 armhf 1.17-6 [61.3 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main armhf libk5crypto3 armhf 1.17-6 [114 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main armhf libssl1.1 armhf 1.1.1c-1 [1294 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main armhf libkrb5-3 armhf 1.17-6 [322 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main armhf libgssapi-krb5-2 armhf 1.17-6 [135 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main armhf libdb5.3 armhf 5.3.28+dfsg1-0.6 [597 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1 [67.3 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main armhf libsasl2-2 armhf 2.1.27+dfsg-1 [98.7 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main armhf libldap-2.4-2 armhf 2.4.48+dfsg-1 [203 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main armhf libnghttp2-14 armhf 1.37.0-1 [72.9 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g armhf 1:1.2.11.dfsg-1+b1 [85.1 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main armhf libgpg-error0 armhf 1.36-7 [63.1 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main armhf libgcrypt20 armhf 1.8.4-5 [501 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main armhf libcurl3-gnutls armhf 7.65.3-1 [302 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main armhf libdeflate0 armhf 1.2-1 [46.4 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 9.1.0-10 [75.1 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 9.1.0-10 [431 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 9.1.0-10 [113 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-8-dev armhf 8.3.0-19 [612 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main armhf libgfortran5 armhf 9.1.0-10 [238 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main armhf libhdf5-103 armhf 1.10.4+repack-10 [1285 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-10 [123 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1+b1 [204 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [112 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [182 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armhf libhdf5-dev armhf 1.10.4+repack-10 [2515 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armhf liblzma5 armhf 5.2.4-1 [145 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armhf libhts2 armhf 1.9-11 [261 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main armhf liblzma-dev armhf 5.2.4-1 [204 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main armhf libhts-dev armhf 1.9-11 [4289 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-8-dev armhf 8.3.0-19 [1561 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.9 MB in 1s (45.1 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15042 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.6.1-1_amd64.deb ... Unpacking man-db (2.8.6.1-1) ... 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Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up hdf5-helpers:armhf (1.10.4+repack-10) ... Setting up libarchive13:amd64 (3.3.3-4) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.60.6-1) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1c-1) ... Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up libnghttp2-14:amd64 (1.37.0-1) ... Setting up linux-libc-dev:armhf (5.2.7-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libldap-common (2.4.48+dfsg-1) ... Setting up libkrb5support0:amd64 (1.17-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:amd64 (1.30.1-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20190803-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up gcc-8-base:armhf (8.3.0-19) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libk5crypto3:amd64 (1.17-6) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1) ... Setting up librhash0:amd64 (1.3.8-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up cmake-data (3.13.4-1) ... Setting up libkrb5-3:amd64 (1.17-6) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up gcc-9-base:armhf (9.1.0-10) ... Setting up libfile-stripnondeterminism-perl (1.4.0-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up libldap-2.4-2:amd64 (2.4.48+dfsg-1) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-6) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12.20190723-1) ... Setting up groff-base (1.22.4-3) ... Setting up libcurl4:amd64 (7.65.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21) ... Setting up man-db (2.8.6.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up cmake (3.13.4-1) ... Setting up dh-autoreconf (19) ... Setting up libc6:armhf (2.28-10) ... Setting up dh-strip-nondeterminism (1.4.0-1) ... Setting up libtasn1-6:armhf (4.14-2) ... Setting up libc6-dev:armhf (2.28-10) ... Setting up libbz2-1.0:armhf (1.0.6-9.2) ... Setting up libdb5.3:armhf (5.3.28+dfsg1-0.6) ... Setting up libkeyutils1:armhf (1.6-6) ... Setting up liblzma5:armhf (5.2.4-1) ... Setting up libgpg-error0:armhf (1.36-7) ... Setting up libgcc1:armhf (1:9.1.0-10) ... Setting up libssl1.1:armhf (1.1.1c-1) ... Setting up libnghttp2-14:armhf (1.37.0-1) ... Setting up libunistring2:armhf (0.9.10-2) ... Setting up libdeflate0:armhf (1.2-1) ... Setting up libgcrypt20:armhf (1.8.4-5) ... Setting up debhelper (12.3) ... Setting up zlib1g:armhf (1:1.2.11.dfsg-1+b1) ... Setting up libffi6:armhf (3.2.1-9) ... Setting up libidn2-0:armhf (2.2.0-1) ... Setting up libcom-err2:armhf (1.45.3-4) ... Setting up libgomp1:armhf (9.1.0-10) ... Setting up libaec0:armhf (1.0.4-1) ... Setting up libkrb5support0:armhf (1.17-6) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1) ... Setting up libasan5:armhf (9.1.0-10) ... Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ... Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ... Setting up libgmp10:armhf (2:6.1.2+dfsg-4) ... Setting up libp11-kit0:armhf (0.23.15-2) ... Setting up libatomic1:armhf (9.1.0-10) ... Setting up libk5crypto3:armhf (1.17-6) ... Setting up libnettle6:armhf (3.4.1-1) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1) ... Setting up libgfortran5:armhf (9.1.0-10) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1+b1) ... Setting up libssh2-1:armhf (1.8.0-2.1) ... Setting up libkrb5-3:armhf (1.17-6) ... Setting up libstdc++6:armhf (9.1.0-10) ... Setting up libsz2:armhf (1.0.4-1) ... Setting up libpsl5:armhf (0.20.2-2) ... Setting up libhogweed4:armhf (3.4.1-1) ... Setting up libaec-dev:armhf (1.0.4-1) ... Setting up libgnutls30:armhf (3.6.9-4) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up libhdf5-103:armhf (1.10.4+repack-10) ... Setting up libgssapi-krb5-2:armhf (1.17-6) ... Setting up libubsan1:armhf (9.1.0-10) ... Setting up libhdf5-cpp-103:armhf (1.10.4+repack-10) ... Setting up libldap-2.4-2:armhf (2.4.48+dfsg-1) ... Setting up libcurl3-gnutls:armhf (7.65.3-1) ... Setting up libhdf5-dev:armhf (1.10.4+repack-10) ... 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 libgcc-8-dev:armhf (8.3.0-19) ... Setting up libstdc++-8-dev:armhf (8.3.0-19) ... Setting up libhts2:armhf (1.9-11) ... Setting up libhts-dev:armhf (1.9-11) ... Setting up sbuild-build-depends-kallisto-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.32.51.20190727-1 dpkg-dev_1.19.7 g++-8_8.3.0-19 gcc-8_8.3.0-19 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-19 libstdc++-8-dev-armhf-cross_8.3.0-19cross1 libstdc++6_9.1.0-10 libstdc++6-armhf-cross_9.1.0-8cross1 linux-libc-dev_5.2.7-1 Package versions: adduser_3.118 apt_1.8.3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.32.51.20190727-1 binutils-arm-linux-gnueabihf_2.32.51.20190727-1 binutils-common_2.32.51.20190727-1 binutils-x86-64-linux-gnu_2.32.51.20190727-1 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.6 bzip2_1.0.6-9.2 cmake_3.13.4-1 cmake-data_3.13.4-1 coreutils_8.30-3+b1 cpp_4:8.3.0-1 cpp-8_8.3.0-19 cpp-8-arm-linux-gnueabihf_8.3.0-19cross1 cpp-arm-linux-gnueabihf_4:8.3.0-1 cross-config_2.6.15-3 crossbuild-essential-armhf_12.6 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.3 debian-archive-keyring_2019.1 debianutils_4.8.6.3 dh-autoreconf_19 dh-strip-nondeterminism_1.4.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.12.20190723-1 e2fsprogs_1.45.3-4 fakeroot_1.23-1 fdisk_2.34-0.1 file_1:5.37-5 findutils_4.6.0+git+20190510-2 g++_4:8.3.0-1 g++-8_8.3.0-19 g++-8-arm-linux-gnueabihf_8.3.0-19cross1 g++-arm-linux-gnueabihf_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-19 gcc-8-arm-linux-gnueabihf_8.3.0-19cross1 gcc-8-arm-linux-gnueabihf-base_8.3.0-19cross1 gcc-8-base_8.3.0-19 gcc-8-cross-base_8.3.0-19cross1 gcc-9-base_9.1.0-10 gcc-9-cross-base_9.1.0-8cross1 gcc-arm-linux-gnueabihf_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hdf5-helpers_1.10.4+repack-10 hostname_3.21 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg5.0_1.8.3 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-4 libasan5_9.1.0-10 libasan5-armhf-cross_9.1.0-8cross1 libatomic1_9.1.0-10 libatomic1-armhf-cross_9.1.0-8cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.32.51.20190727-1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.2 libc-bin_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-armhf-cross_2.28-10cross3 libc6-dev_2.28-10 libc6-dev-armhf-cross_2.28-10cross3 libcap-ng0_0.7.9-2 libcc1-0_9.1.0-10 libcom-err2_1.45.3-4 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libcurl3-gnutls_7.65.3-1 libcurl4_7.65.3-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-3 libdeflate0_1.2-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.7-1 libext2fs2_1.45.3-4 libfakeroot_1.23-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.4.0-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-19 libgcc-8-dev-armhf-cross_8.3.0-19cross1 libgcc1_1:9.1.0-10 libgcc1-armhf-cross_1:9.1.0-8cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4+b1 libgdbm6_1.18.1-4+b1 libgfortran5_9.1.0-10 libglib2.0-0_2.60.6-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-4 libgomp1_9.1.0-10 libgomp1-armhf-cross_9.1.0-8cross1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6 libhdf5-103_1.10.4+repack-10 libhdf5-cpp-103_1.10.4+repack-10 libhdf5-dev_1.10.4+repack-10 libhogweed4_3.4.1-1 libhts-dev_1.9-11 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.2.0-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_9.1.0-10 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjsoncpp1_1.7.4-3 libk5crypto3_1.17-6 libkeyutils1_1.6-6 libkrb5-3_1.17-6 libkrb5support0_1.17-6 libldap-2.4-2_2.4.48+dfsg-1 libldap-common_2.4.48+dfsg-1 liblocale-gettext-perl_1.07-3+b4 liblsan0_9.1.0-10 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-19 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.4.1-1 libnghttp2-14_1.37.0-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.32-5+b1 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libquadmath0_9.1.0-10 librhash0_1.3.8-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.4.1-2 libselinux1_2.9-2+b2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2+b2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.3-4 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-19 libstdc++-8-dev-armhf-cross_8.3.0-19cross1 libstdc++6_9.1.0-10 libstdc++6-armhf-cross_9.1.0-8cross1 libsub-override-perl_0.09-2 libsystemd0_241-7 libsz2_1.0.4-1 libtasn1-6_4.14-2 libtinfo6_6.1+20190803-1 libtool_2.4.6-10 libtsan0_9.1.0-10 libubsan1_9.1.0-10 libubsan1-armhf-cross_9.1.0-8cross1 libuchardet0_0.0.6-3 libudev1_241-7 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.30.1-1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.29-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_5.2.7-1 linux-libc-dev-armhf-cross_4.19.37-5cross3 login_1:4.7-2 logsave_1.45.3-4 lsb-base_10.2019051400 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.6.1-1 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20190803-1 ncurses-bin_6.1+20190803-1 passwd_1:4.7-2 patch_2.7.6-6 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 po-debconf_1.0.21 procps_2:3.3.15-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-kallisto-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.95-4 tar_1.30+dfsg-6+b1 tzdata_2019b-1 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1+b1 zlib1g-dev_1:1.2.11.dfsg-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Aug 7 11:04:42 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kallisto_0.46.0+dfsg-1.dsc dpkg-source: info: extracting kallisto in /<>/kallisto-0.46.0+dfsg dpkg-source: info: unpacking kallisto_0.46.0+dfsg.orig.tar.xz dpkg-source: info: unpacking kallisto_0.46.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_htslib.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-80681b51-07df-48b9-9434-fde1a6fc6dd3 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package kallisto dpkg-buildpackage: info: source version 0.46.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/kallisto-0.46.0+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_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=arm -DCMAKE_C_COMPILER=arm-linux-gnueabihf-gcc -DCMAKE_CXX_COMPILER=arm-linux-gnueabihf-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-qmake -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DDEBIAN_BUILD=1 -DLINK=shared .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/arm-linux-gnueabihf-gcc -- Check for working C compiler: /usr/bin/arm-linux-gnueabihf-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/arm-linux-gnueabihf-g++ -- Check for working CXX compiler: /usr/bin/arm-linux-gnueabihf-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- 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 -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib/arm-linux-gnueabihf/hdf5/serial/libhdf5.so;/usr/lib/arm-linux-gnueabihf/libpthread.so;/usr/lib/arm-linux-gnueabihf/libsz.so;/usr/lib/arm-linux-gnueabihf/libz.so;/usr/lib/arm-linux-gnueabihf/libdl.so;/usr/lib/arm-linux-gnueabihf/libm.so (found version "1.10.4") -- 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 PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE QMAKE_EXECUTABLE -- Build files have been written to: /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf make[1]: Leaving directory '/<>/kallisto-0.46.0+dfsg' dh_auto_build -a cd obj-arm-linux-gnueabihf && make -j1 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<>/kallisto-0.46.0+dfsg -B/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/kallisto-0.46.0+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-0.46.0+dfsg/obj-arm-linux-gnueabihf' cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/kallisto-0.46.0+dfsg /<>/kallisto-0.46.0+dfsg/src /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake --color= Scanning dependencies of target kallisto_core make[3]: Leaving directory '/<>/kallisto-0.46.0+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-0.46.0+dfsg/obj-arm-linux-gnueabihf' [ 4%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/BUSData.cpp [ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/BUSTools.cpp [ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/Bootstrap.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.h:7, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/PlaintextWriter.h:13, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.h:7, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.h:12, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.cpp:1: /<>/kallisto-0.46.0+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:66:107: warning: left shift count >= width of type [-Wshift-count-overflow] return std::hash()(x.first) ^ (std::hash()(x.second)<<32); ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.h:7, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.h:7, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.h:7, from /<>/kallisto-0.46.0+dfsg/src/Bootstrap.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = int]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/GeneModel.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:10, from /<>/kallisto-0.46.0+dfsg/src/GeneModel.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/GeneModel.cpp:1: /<>/kallisto-0.46.0+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:66:107: warning: left shift count >= width of type [-Wshift-count-overflow] return std::hash()(x.first) ^ (std::hash()(x.second)<<32); ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:10, from /<>/kallisto-0.46.0+dfsg/src/GeneModel.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ [ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/H5Writer.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/EMAlgorithm.h:5, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.h:4, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/PlaintextWriter.h:13, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.h:7, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.cpp:1: /<>/kallisto-0.46.0+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:66:107: warning: left shift count >= width of type [-Wshift-count-overflow] return std::hash()(x.first) ^ (std::hash()(x.second)<<32); ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/EMAlgorithm.h:5, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.h:4, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/common.h:7, from /<>/kallisto-0.46.0+dfsg/src/EMAlgorithm.h:4, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.h:4, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/common.h:7, from /<>/kallisto-0.46.0+dfsg/src/EMAlgorithm.h:4, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.h:4, from /<>/kallisto-0.46.0+dfsg/src/H5Writer.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In constructor 'H5Converter::H5Converter(const string&, const string&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/Kmer.cpp [ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/KmerIndex.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:218:13: required from 'void KmerHashTable::reserve(size_t, bool) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.cpp:848:32: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void KmerIndex::BuildDeBruijnGraph(const ProgramOptions&, const std::vector >&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/KmerIterator.cpp [ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/Merge.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/Merge.cpp:11: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/Merge.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/Merge.cpp:5: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'bool MergeBatchDirectories(const ProgramOptions&, int&, int64_t&, int64_t&, int64_t&, int&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/MinCollector.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/MinCollector.h:11, from /<>/kallisto-0.46.0+dfsg/src/MinCollector.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ [ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/PlaintextWriter.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/PlaintextWriter.h:12, from /<>/kallisto-0.46.0+dfsg/src/PlaintextWriter.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/PlaintextWriter.h:13, from /<>/kallisto-0.46.0+dfsg/src/PlaintextWriter.cpp:1: /<>/kallisto-0.46.0+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:66:107: warning: left shift count >= width of type [-Wshift-count-overflow] return std::hash()(x.first) ^ (std::hash()(x.second)<<32); ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/PlaintextWriter.h:12, from /<>/kallisto-0.46.0+dfsg/src/PlaintextWriter.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ [ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/ProcessReads.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/MinCollector.h:11, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.h:13, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:21, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /<>/kallisto-0.46.0+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:66:107: warning: left shift count >= width of type [-Wshift-count-overflow] return std::hash()(x.first) ^ (std::hash()(x.second)<<32); ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/MinCollector.h:11, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:9, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:9, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = bam1_t; _Alloc = std::allocator]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void BUSProcessor::processBuffer()': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void MasterProcessor::processAln(const EMAlgorithm&, bool)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/algorithm:62, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:9, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:7, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.cpp:22: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void AlnProcessor::processBufferTrans()': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void AlnProcessor::processBufferGenome()': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/PseudoBam.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.h:12, from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.cpp:3: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.h:13, from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.cpp:3: /<>/kallisto-0.46.0+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:66:107: warning: left shift count >= width of type [-Wshift-count-overflow] return std::hash()(x.first) ^ (std::hash()(x.second)<<32); ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.h:12, from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.cpp:3: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ [ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/common.cpp [ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/h5utils.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/h5utils.h:9, from /<>/kallisto-0.46.0+dfsg/src/h5utils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/h5utils.h:9, from /<>/kallisto-0.46.0+dfsg/src/h5utils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'void read_vector(hid_t, hid_t, hid_t, std::vector&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/hash.cpp [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/main.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/MinCollector.h:11, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:17: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.h:13, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:21, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:17: /<>/kallisto-0.46.0+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:66:107: warning: left shift count >= width of type [-Wshift-count-overflow] return std::hash()(x.first) ^ (std::hash()(x.second)<<32); ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/MinCollector.h:11, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:17: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/arm-linux-gnueabihf/include/c++/8/bits/random.h:34, from /usr/arm-linux-gnueabihf/include/c++/8/random:49, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:3: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/arm-linux-gnueabihf/include/c++/8/bits/random.h:34, from /usr/arm-linux-gnueabihf/include/c++/8/random:49, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:3: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = int]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/<>/kallisto-0.46.0+dfsg/src -I/usr/include/hdf5/serial -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/weights.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/weights.h:4, from /<>/kallisto-0.46.0+dfsg/src/weights.cpp:1: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/weights.h:4, from /<>/kallisto-0.46.0+dfsg/src/weights.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/weights.h:4, from /<>/kallisto-0.46.0+dfsg/src/weights.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'std::vector calc_eff_lens(const std::vector&, double)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'std::vector calc_eff_lens(const std::vector&, const std::vector&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'std::vector get_frag_len_means(const std::vector&, const std::vector&)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/weights.h:4, from /<>/kallisto-0.46.0+dfsg/src/weights.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:7, from /<>/kallisto-0.46.0+dfsg/src/weights.h:4, from /<>/kallisto-0.46.0+dfsg/src/weights.cpp:1: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 90%] Linking CXX static library libkallisto_core.a cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto_core.dir/link.txt --verbose=1 /usr/bin/arm-linux-gnueabihf-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/arm-linux-gnueabihf-ranlib libkallisto_core.a make[3]: Leaving directory '/<>/kallisto-0.46.0+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-0.46.0+dfsg/obj-arm-linux-gnueabihf' cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/kallisto-0.46.0+dfsg /<>/kallisto-0.46.0+dfsg/src /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto.dir/DependInfo.cmake --color= Scanning dependencies of target kallisto make[3]: Leaving directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build make[3]: Entering directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' [ 95%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -I/usr/include/hdf5/serial -I/<>/kallisto-0.46.0+dfsg/src -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+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-0.46.0+dfsg/src/main.cpp In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/MinCollector.h:11, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:17: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:15: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/PseudoBam.h:13, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:21, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:17: /<>/kallisto-0.46.0+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /<>/kallisto-0.46.0+dfsg/src/GeneModel.h:66:107: warning: left shift count >= width of type [-Wshift-count-overflow] return std::hash()(x.first) ^ (std::hash()(x.second)<<32); ^~ In file included from /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:18, from /<>/kallisto-0.46.0+dfsg/src/MinCollector.h:11, from /<>/kallisto-0.46.0+dfsg/src/ProcessReads.h:18, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:17: /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /<>/kallisto-0.46.0+dfsg/src/KmerIndex.h:96:106: required from here /<>/kallisto-0.46.0+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] v |= v >> 32; ~~^~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:69, from /usr/arm-linux-gnueabihf/include/c++/8/bits/random.h:34, from /usr/arm-linux-gnueabihf/include/c++/8/random:49, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:3: /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/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/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/8/vector:64, from /usr/arm-linux-gnueabihf/include/c++/8/bits/random.h:34, from /usr/arm-linux-gnueabihf/include/c++/8/random:49, from /<>/kallisto-0.46.0+dfsg/src/main.cpp:3: /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In member function 'void std::discrete_distribution<_IntType>::param_type::_M_initialize() [with _IntType = int]': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)': /usr/arm-linux-gnueabihf/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [100%] Linking CXX executable kallisto cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto.dir/link.txt --verbose=1 /usr/bin/arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>/kallisto-0.46.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kallisto.dir/main.cpp.o -o kallisto -Wl,-rpath,/usr/lib/arm-linux-gnueabihf/hdf5/serial: libkallisto_core.a -lpthread -lhts /usr/lib/arm-linux-gnueabihf/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm -lrt make[3]: Leaving directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' [100%] Built target kallisto make[2]: Leaving directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a cd obj-arm-linux-gnueabihf && make -j1 install DESTDIR=/<>/kallisto-0.46.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<>/kallisto-0.46.0+dfsg -B/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/kallisto-0.46.0+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-0.46.0+dfsg/obj-arm-linux-gnueabihf' cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/kallisto-0.46.0+dfsg /<>/kallisto-0.46.0+dfsg/src /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/kallisto-0.46.0+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-0.46.0+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/CMakeFiles/kallisto_core.dir/build'. make[3]: Leaving directory '/<>/kallisto-0.46.0+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-0.46.0+dfsg/obj-arm-linux-gnueabihf' cd /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/kallisto-0.46.0+dfsg /<>/kallisto-0.46.0+dfsg/src /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/kallisto.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build make[3]: Entering directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'src/CMakeFiles/kallisto.dir/build'. make[3]: Leaving directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' [100%] Built target kallisto make[2]: Leaving directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/kallisto-0.46.0+dfsg/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/kallisto-0.46.0+dfsg/debian/tmp/usr/bin/kallisto -- Set runtime path of "/<>/kallisto-0.46.0+dfsg/debian/tmp/usr/bin/kallisto" to "" make[1]: Leaving directory '/<>/kallisto-0.46.0+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 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 dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/kallisto/usr/bin/kallisto was not linked against libdl.so.2 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/kallisto/usr/bin/kallisto was not linked against librt.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/kallisto/usr/bin/kallisto was not linked against libsz.so.2 (it uses none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'kallisto' in '../kallisto_0.46.0+dfsg-1_armhf.deb'. dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_0.46.0+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../kallisto_0.46.0+dfsg-1_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 2019-08-10T20:14:01Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/resolver-L5gqZs/apt_archive/sbuild-build-depends-lintian-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-kallisto-dummy sbuild-build-depends-lintian-dummy dpkg-scanpackages: info: Wrote 4 entries to output Packages file. Ign:1 copy:/<>/resolver-L5gqZs/apt_archive ./ InRelease Get:2 copy:/<>/resolver-L5gqZs/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-L5gqZs/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-L5gqZs/apt_archive ./ Sources [771 B] Get:5 copy:/<>/resolver-L5gqZs/apt_archive ./ Packages [847 B] Fetched 2581 B in 0s (139 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libclass-xsaccessor-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armhf t1utils 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 7000 kB of archives. After this operation, 19.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-L5gqZs/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-2 [72.4 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-2 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1+b1 [33.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.17-3 [524 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.29.0-1 [645 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.17-3 [881 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b1 [71.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b1 [11.4 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.44-1 [223 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1 [15.7 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.88-1 [320 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.066-1 [210 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.20-1 [367 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.10-1 [8362 B] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.41-1 [79.0 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b1 [25.5 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.74-1 [268 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.016-1+b1 [17.0 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.000006-1 [19.4 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006003-1 [19.7 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003004-2 [57.4 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.79+repack-2 [34.0 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.17.0 [1273 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7000 kB in 0s (24.6 MB/s) Selecting previously unselected package readline-common. (Reading database ... 20992 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-2_all.deb ... Unpacking readline-common (8.0-2) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-2_amd64.deb ... Unpacking libreadline8:amd64 (8.0-2) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.62-1+b1_amd64.deb ... Unpacking diffstat (1.62-1+b1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.17-3_amd64.deb ... Unpacking gpgconf (2.2.17-3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../06-libsqlite3-0_3.29.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.29.0-1) ... Selecting previously unselected package gpg. Preparing to unpack .../07-gpg_2.2.17-3_amd64.deb ... Unpacking gpg (2.2.17-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../08-libapt-pkg-perl_0.1.36+b1_amd64.deb ... Unpacking libapt-pkg-perl (0.1.36+b1) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../09-libb-hooks-op-check-perl_0.22-1+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../10-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../11-libhtml-tagset-perl_3.20-3_all.deb ... Unpacking libhtml-tagset-perl (3.20-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../12-liburi-perl_1.76-1_all.deb ... Unpacking liburi-perl (1.76-1) ... Selecting previously unselected package libhtml-parser-perl. Preparing to unpack .../13-libhtml-parser-perl_3.72-3+b3_amd64.deb ... Unpacking libhtml-parser-perl (3.72-3+b3) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../14-libcgi-pm-perl_4.44-1_all.deb ... Unpacking libcgi-pm-perl (4.44-1) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../15-libsub-name-perl_0.21-1+b3_amd64.deb ... Unpacking libsub-name-perl (0.21-1+b3) ... Selecting previously unselected package libclass-accessor-perl. Preparing to unpack .../16-libclass-accessor-perl_0.51-1_all.deb ... Unpacking libclass-accessor-perl (0.51-1) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../17-libclass-method-modifiers-perl_2.12-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.12-1) ... Selecting previously unselected package libclone-perl. Preparing to unpack .../18-libclone-perl_0.41-1+b1_amd64.deb ... Unpacking libclone-perl (0.41-1+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../19-libdynaloader-functions-perl_0.003-1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../20-libdevel-callchecker-perl_0.008-1_amd64.deb ... Unpacking libdevel-callchecker-perl (0.008-1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../21-libsub-exporter-progressive-perl_0.001013-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-1) ... Selecting previously unselected package libdevel-globaldestruction-perl. Preparing to unpack .../22-libdevel-globaldestruction-perl_0.14-1_all.deb ... Unpacking libdevel-globaldestruction-perl (0.14-1) ... Selecting previously unselected package libdigest-hmac-perl. Preparing to unpack .../23-libdigest-hmac-perl_1.03+dfsg-2_all.deb ... Unpacking libdigest-hmac-perl (1.03+dfsg-2) ... Selecting previously unselected package perl-openssl-defaults:amd64. Preparing to unpack .../24-perl-openssl-defaults_3_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (3) ... Selecting previously unselected package libnet-ssleay-perl. Preparing to unpack .../25-libnet-ssleay-perl_1.88-1_amd64.deb ... Unpacking libnet-ssleay-perl (1.88-1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../26-libio-socket-ssl-perl_2.066-1_all.deb ... Unpacking libio-socket-ssl-perl (2.066-1) ... Selecting previously unselected package libnet-smtp-ssl-perl. Preparing to unpack .../27-libnet-smtp-ssl-perl_1.04-1_all.deb ... Unpacking libnet-smtp-ssl-perl (1.04-1) ... Selecting previously unselected package libtimedate-perl. 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Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package libfuture-perl. Preparing to unpack .../40-libfuture-perl_0.41-1_all.deb ... Unpacking libfuture-perl (0.41-1) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../41-libparams-classify-perl_0.015-1+b1_amd64.deb ... Unpacking libparams-classify-perl (0.015-1+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../42-libmodule-runtime-perl_0.016-1_all.deb ... Unpacking libmodule-runtime-perl (0.016-1) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../43-libimport-into-perl_1.002005-1_all.deb ... Unpacking libimport-into-perl (1.002005-1) ... Selecting previously unselected package libstruct-dumb-perl. Preparing to unpack .../44-libstruct-dumb-perl_0.09-1_all.deb ... Unpacking libstruct-dumb-perl (0.09-1) ... Selecting previously unselected package libio-async-perl. Preparing to unpack .../45-libio-async-perl_0.74-1_all.deb ... Unpacking libio-async-perl (0.74-1) ... Selecting previously unselected package liblinux-epoll-perl. Preparing to unpack .../46-liblinux-epoll-perl_0.016-1+b1_amd64.deb ... Unpacking liblinux-epoll-perl (0.016-1+b1) ... Selecting previously unselected package libio-async-loop-epoll-perl. Preparing to unpack .../47-libio-async-loop-epoll-perl_0.20-1_all.deb ... Unpacking libio-async-loop-epoll-perl (0.20-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../48-libio-pty-perl_1%3a1.08-1.1+b5_amd64.deb ... Unpacking libio-pty-perl (1:1.08-1.1+b5) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../49-libipc-run-perl_20180523.0-1_all.deb ... Unpacking libipc-run-perl (20180523.0-1) ... Selecting previously unselected package liblist-compare-perl. Preparing to unpack .../50-liblist-compare-perl_0.53-1_all.deb ... Unpacking liblist-compare-perl (0.53-1) ... Selecting previously unselected package liblist-moreutils-perl. Preparing to unpack .../51-liblist-moreutils-perl_0.416-1+b4_amd64.deb ... Unpacking liblist-moreutils-perl (0.416-1+b4) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../52-librole-tiny-perl_2.000006-1_all.deb ... Unpacking librole-tiny-perl (2.000006-1) ... Selecting previously unselected package libstrictures-perl. Preparing to unpack .../53-libstrictures-perl_2.000006-1_all.deb ... Unpacking libstrictures-perl (2.000006-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../54-libsub-quote-perl_2.006003-1_all.deb ... Unpacking libsub-quote-perl (2.006003-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../55-libmoo-perl_2.003004-2_all.deb ... Unpacking libmoo-perl (2.003004-2) ... Selecting previously unselected package libpath-tiny-perl. Preparing to unpack .../56-libpath-tiny-perl_0.108-1_all.deb ... 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Preparing to unpack .../62-patchutils_0.3.4-2+b1_amd64.deb ... Unpacking patchutils (0.3.4-2+b1) ... Selecting previously unselected package t1utils. Preparing to unpack .../63-t1utils_1.41-3_amd64.deb ... Unpacking t1utils (1.41-3) ... Selecting previously unselected package lintian. Preparing to unpack .../64-lintian_2.17.0_all.deb ... Unpacking lintian (2.17.0) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:armhf. Preparing to unpack .../65-sbuild-build-depends-lintian-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.36+b1) ... Setting up libstruct-dumb-perl (0.09-1) ... Setting up libdynaloader-functions-perl (0.003-1) ... Setting up libtext-glob-perl (0.10-1) ... Setting up libclass-method-modifiers-perl (2.12-1) ... Setting up liblist-compare-perl (0.53-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libclone-perl (0.41-1+b1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libsqlite3-0:amd64 (3.29.0-1) ... Setting up libfuture-perl (0.41-1) ... Setting up libyaml-libyaml-perl (0.79+repack-2) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libtext-levenshtein-perl (0.13-1) ... Setting up libassuan0:amd64 (2.5.3-7) ... Setting up libnumber-compare-perl (0.03-1) ... Setting up libio-async-perl (0.74-1) ... Setting up patchutils (0.3.4-2+b1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.25-4) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up t1utils (1.41-3) ... Setting up liblinux-epoll-perl (0.016-1+b1) ... Setting up diffstat (1.62-1+b1) ... Setting up libb-hooks-op-check-perl (0.22-1+b1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsub-name-perl (0.21-1+b3) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up librole-tiny-perl (2.000006-1) ... Setting up libdevel-globaldestruction-perl (0.14-1) ... Setting up netbase (5.6) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006003-1) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (8.0-2) ... Setting up liburi-perl (1.76-1) ... Setting up libnet-ssleay-perl (1.88-1) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b4) ... Setting up libreadline8:amd64 (8.0-2) ... Setting up libtype-tiny-perl (1.004004-1) ... Setting up libnet-dns-perl (1.20-1) ... Setting up libdevel-callchecker-perl (0.008-1) ... Setting up libio-async-loop-epoll-perl (0.20-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.17-3) ... Setting up libio-socket-ssl-perl (2.066-1) ... Setting up gpg (2.2.17-3) ... Setting up libparams-classify-perl (0.015-1+b1) ... Setting up libcgi-pm-perl (4.44-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libmailtools-perl (2.21-1) ... Setting up libemail-valid-perl (1.202-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.003004-2) ... Setting up lintian (2.17.0) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for man-db (2.8.6.1-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.28-10) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kallisto_0.46.0+dfsg-1_armhf.changes: ------------------------------------- Format: 1.8 Date: Wed, 07 Aug 2019 13:01:05 +0200 Source: kallisto Binary: kallisto kallisto-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 0.46.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: kallisto - near-optimal RNA-Seq quantification Changes: kallisto (0.46.0+dfsg-1) unstable; urgency=medium . * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.0 Checksums-Sha1: e20254c83c6cc1927a7e61652e1cfdab83c9f718 3497792 kallisto-dbgsym_0.46.0+dfsg-1_armhf.deb 5b10eb0609a0b08c4d06f20b690324536159fd2d 6023 kallisto_0.46.0+dfsg-1_armhf.buildinfo 61891618f28c23e58e4c43fe0f03f01f028316a9 205836 kallisto_0.46.0+dfsg-1_armhf.deb Checksums-Sha256: 29d193d087dc54ccf1d0e315255aa6a2bbbf04788e48b2c62f3007f05a1fda8a 3497792 kallisto-dbgsym_0.46.0+dfsg-1_armhf.deb af4986549282d5a866994ee42a61028ec5bf47466a064bf93ca51b0eb3823a62 6023 kallisto_0.46.0+dfsg-1_armhf.buildinfo 46ee76785a3300946d061c8c68394a827848eeec976924d1e89ed52ba751c266 205836 kallisto_0.46.0+dfsg-1_armhf.deb Files: b0a04db3d699cd2e12d6a420286f221b 3497792 debug optional kallisto-dbgsym_0.46.0+dfsg-1_armhf.deb 7b295433765249fab25ec7f16622bb9d 6023 science optional kallisto_0.46.0+dfsg-1_armhf.buildinfo 77a77dca4d6eb160c320dab6ff6b1f2b 205836 science optional kallisto_0.46.0+dfsg-1_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kallisto Binary: kallisto kallisto-examples Architecture: armhf Version: 0.46.0+dfsg-1 Checksums-Md5: b0a04db3d699cd2e12d6a420286f221b 3497792 kallisto-dbgsym_0.46.0+dfsg-1_armhf.deb 77a77dca4d6eb160c320dab6ff6b1f2b 205836 kallisto_0.46.0+dfsg-1_armhf.deb Checksums-Sha1: e20254c83c6cc1927a7e61652e1cfdab83c9f718 3497792 kallisto-dbgsym_0.46.0+dfsg-1_armhf.deb 61891618f28c23e58e4c43fe0f03f01f028316a9 205836 kallisto_0.46.0+dfsg-1_armhf.deb Checksums-Sha256: 29d193d087dc54ccf1d0e315255aa6a2bbbf04788e48b2c62f3007f05a1fda8a 3497792 kallisto-dbgsym_0.46.0+dfsg-1_armhf.deb 46ee76785a3300946d061c8c68394a827848eeec976924d1e89ed52ba751c266 205836 kallisto_0.46.0+dfsg-1_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 10 Aug 2019 20:14:01 +0000 Build-Path: /<>/kallisto-0.46.0+dfsg Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.32.51.20190727-1), binutils-common (= 2.32.51.20190727-1), binutils-x86-64-linux-gnu (= 2.32.51.20190727-1), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.6), bzip2 (= 1.0.6-9.2), cmake (= 3.13.4-1), cmake-data (= 3.13.4-1), coreutils (= 8.30-3+b1), cpp (= 4:8.3.0-1), cpp-8 (= 8.3.0-19), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.3), debianutils (= 4.8.6.3), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.4.0-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.12.20190723-1), fdisk (= 2.34-0.1), file (= 1:5.37-5), findutils (= 4.6.0+git+20190510-2), g++ (= 4:8.3.0-1), g++-8 (= 8.3.0-19), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-19), gcc-8-base (= 8.3.0-19), gcc-9-base (= 9.1.0-10), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3), hdf5-helpers (= 1.10.4+repack-10), hostname (= 3.21), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-4), libaec-dev (= 1.0.4-1), libaec0 (= 1.0.4-1), libarchive-zip-perl (= 1.64-1), libarchive13 (= 3.3.3-4), libasan5 (= 9.1.0-10), libatomic1 (= 9.1.0-10), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.32.51.20190727-1), libblkid1 (= 2.34-0.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.6-9.2), libc-bin (= 2.28-10), libc-dev-bin (= 2.28-10), libc6 (= 2.28-10), libc6-dev (= 2.28-10), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 9.1.0-10), libcom-err2 (= 1.45.3-4), libcroco3 (= 0.6.12-3), libcurl3-gnutls (= 7.65.3-1), libcurl4 (= 7.65.3-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.249), libdeflate0 (= 1.2-1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libexpat1 (= 2.2.7-1), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.4.0-1), libgcc-8-dev (= 8.3.0-19), libgcc1 (= 1:9.1.0-10), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-4+b1), libgdbm6 (= 1.18.1-4+b1), libgfortran5 (= 9.1.0-10), libglib2.0-0 (= 2.60.6-1), libgmp10 (= 2:6.1.2+dfsg-4), libgnutls30 (= 3.6.9-4), libgomp1 (= 9.1.0-10), libgpg-error0 (= 1.36-7), libgssapi-krb5-2 (= 1.17-6), libhdf5-103 (= 1.10.4+repack-10), libhdf5-cpp-103 (= 1.10.4+repack-10), libhdf5-dev (= 1.10.4+repack-10), libhogweed4 (= 3.4.1-1), libhts-dev (= 1.9-11), libhts2 (= 1.9-11), libicu63 (= 63.2-2), libidn2-0 (= 2.2.0-1), libisl19 (= 0.20-2), libitm1 (= 9.1.0-10), libjpeg62-turbo (= 1:1.5.2-2+b1), libjpeg62-turbo-dev (= 1:1.5.2-2+b1), libjsoncpp1 (= 1.7.4-3), libk5crypto3 (= 1.17-6), libkeyutils1 (= 1.6-6), libkrb5-3 (= 1.17-6), libkrb5support0 (= 1.17-6), libldap-2.4-2 (= 2.4.48+dfsg-1), libldap-common (= 2.4.48+dfsg-1), liblsan0 (= 9.1.0-10), liblz4-1 (= 1.8.3-1), liblzma-dev (= 5.2.4-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.37-5), libmagic1 (= 1:5.37-5), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-19), libncurses6 (= 6.1+20190803-1), libncursesw6 (= 6.1+20190803-1), libnettle6 (= 3.4.1-1), libnghttp2-14 (= 1.37.0-1), libp11-kit0 (= 0.23.15-2), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.32-5+b1), libpcre3 (= 2:8.39-12+b1), libperl5.28 (= 5.28.1-6), libpipeline1 (= 1.5.1-2), libprocps7 (= 2:3.3.15-2), libpsl5 (= 0.20.2-2), libquadmath0 (= 9.1.0-10), librhash0 (= 1.3.8-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2), libsasl2-2 (= 2.1.27+dfsg-1), libsasl2-modules-db (= 2.1.27+dfsg-1), libseccomp2 (= 2.4.1-2), libselinux1 (= 2.9-2+b2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libssh2-1 (= 1.8.0-2.1), libssl1.1 (= 1.1.1c-1), libstdc++-8-dev (= 8.3.0-19), libstdc++6 (= 9.1.0-10), libsub-override-perl (= 0.09-2), libsystemd0 (= 241-7), libsz2 (= 1.0.4-1), libtasn1-6 (= 4.14-2), libtinfo6 (= 6.1+20190803-1), libtool (= 2.4.6-10), libtsan0 (= 9.1.0-10), libubsan1 (= 9.1.0-10), libuchardet0 (= 0.0.6-3), libudev1 (= 241-7), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libuv1 (= 1.30.1-1), libxml2 (= 2.9.4+dfsg1-7+b3), libzstd1 (= 1.3.8+dfsg-3), linux-libc-dev (= 5.2.7-1), login (= 1:4.7-2), lsb-base (= 10.2019051400), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.6.1-1), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20190803-1), ncurses-bin (= 6.1+20190803-1), patch (= 2.7.6-6), perl (= 5.28.1-6), perl-base (= 5.28.1-6), perl-modules-5.28 (= 5.28.1-6), po-debconf (= 1.0.21), procps (= 2:3.3.15-2), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.95-4), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-1+b1), zlib1g-dev (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="POSIX" SOURCE_DATE_EPOCH="1565175665" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ kallisto-dbgsym_0.46.0+dfsg-1_armhf.deb --------------------------------------- new Debian package, version 2.0. size 3497792 bytes: control archive=540 bytes. 387 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: kallisto-dbgsym Source: kallisto Version: 0.46.0+dfsg-1 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 3548 Depends: kallisto (= 0.46.0+dfsg-1) Section: debug Priority: optional Description: debug symbols for kallisto Build-Ids: 77a6a29e70f65b1d7de649a2b2fbb6ee2d144d5e drwxr-xr-x root/root 0 2019-08-07 11:01 ./ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/lib/ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/lib/debug/.build-id/77/ -rw-r--r-- root/root 3622188 2019-08-07 11:01 ./usr/lib/debug/.build-id/77/a6a29e70f65b1d7de649a2b2fbb6ee2d144d5e.debug drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/share/ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-08-07 11:01 ./usr/share/doc/kallisto-dbgsym -> kallisto kallisto_0.46.0+dfsg-1_armhf.deb -------------------------------- new Debian package, version 2.0. size 205836 bytes: control archive=1128 bytes. 1327 bytes, 23 lines control 264 bytes, 4 lines md5sums Package: kallisto Version: 0.46.0+dfsg-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 433 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-103, libhts2 (>= 1.4.1), libstdc++6 (>= 6), libsz2 (>= 1.0.4), 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 2019-08-07 11:01 ./ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/bin/ -rwxr-xr-x root/root 429148 2019-08-07 11:01 ./usr/bin/kallisto drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/share/ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-08-07 11:01 ./usr/share/doc/kallisto/ -rw-r--r-- root/root 323 2019-08-07 11:01 ./usr/share/doc/kallisto/README.test -rw-r--r-- root/root 243 2019-08-07 11:01 ./usr/share/doc/kallisto/changelog.Debian.gz -rw-r--r-- root/root 4059 2019-08-07 11:01 ./usr/share/doc/kallisto/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 84192 Build-Time: 83 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 31 Job: kallisto_0.46.0+dfsg-1 Lintian: pass Machine Architecture: amd64 Package: kallisto Package-Time: 125 Source-Version: 0.46.0+dfsg-1 Space: 84192 Status: successful Version: 0.46.0+dfsg-1 -------------------------------------------------------------------------------- Finished at 2019-08-10T20:14:01Z Build needed 00:02:05, 84192k disk space