Thu Jul 30 02:32:41 UTC 2020 I: starting to build rapmap/buster/arm64 on jenkins on '2020-07-30 02:32' Thu Jul 30 02:32:41 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_13/5270/console.log Thu Jul 30 02:32:41 UTC 2020 I: Downloading source for buster/rapmap=0.12.0+dfsg-3 --2020-07-30 02:32:41-- http://deb.debian.org/debian/pool/main/r/rapmap/rapmap_0.12.0+dfsg-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2299 (2.2K) Saving to: ‘rapmap_0.12.0+dfsg-3.dsc’ 0K .. 100% 27.3M=0s 2020-07-30 02:32:41 (27.3 MB/s) - ‘rapmap_0.12.0+dfsg-3.dsc’ saved [2299/2299] Thu Jul 30 02:32:41 UTC 2020 I: rapmap_0.12.0+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rapmap Binary: rapmap, rapmap-example-data, rapmap-dev Architecture: any all Version: 0.12.0+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe Homepage: https://github.com/COMBINE-lab/RapMap Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/rapmap Vcs-Git: https://salsa.debian.org/med-team/rapmap.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python-markdown Package-List: rapmap deb science optional arch=any rapmap-dev deb science optional arch=all rapmap-example-data deb science optional arch=all Checksums-Sha1: 735d1e35ddc61f82a27e2ecea6bdc0f06c087607 547544 rapmap_0.12.0+dfsg.orig.tar.xz 5905960a7b4254129a1f852c8220d8bfeca52fda 10824 rapmap_0.12.0+dfsg-3.debian.tar.xz Checksums-Sha256: 13a03f40f7a43f89a5f274c13178985285017a0e8ccc2df6e22674ae3769b447 547544 rapmap_0.12.0+dfsg.orig.tar.xz 7e8c697c7ff293c9fb40fa4861d5b389198e5e4a8b603a02a7337377f8f1afa3 10824 rapmap_0.12.0+dfsg-3.debian.tar.xz Files: 3d0c0771498411b4b6fc24532b3b58f3 547544 rapmap_0.12.0+dfsg.orig.tar.xz f1f5712a1366f611ff503cb618e978d3 10824 rapmap_0.12.0+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAlwsm3EACgkQPCZ2P2xn 5uIQaA//ZQcWdJdnfc9SZYVlCQZZNZzrH4i8xE33DSPRQws4Ttz4Rjv8i3LK0hMv N1mi8vf74oDfHdG++GypxdAspSlzICzWvCtg9PjNC9JkHx+VBYPWHfTPlBxV/HeY Du2+Mbae8dYOA7sWaLBxxwe9emkuwr1BzIYzTY2g6l+rJXvpXNyClu/WSmxDlU6X cnxMhZAOk2SkBhl3wIB2RNY0mePX15//9m0SW+pn2EOLpSdCEeC5CkjONjzLdf1v S6QdRyLPszMNh1QQw1qPFEFe7RRNknCKX0hKMFg0JtTatvNg4PLw6fKMcEcagEpr 47qBybygHK7ClOu7vB6r7yLkto0m+PWmk9ZSdk6YGn8VQAzGJM2dPvhFQJa1ETZD 97uapbXhkODsGOZ7v25is6JFRWgmJzQX1DSE9n9DjQ+Q5utTuAizO6o21/hVFxuG RyfvqZx37vX91KNmBOBfKjeqXWlAG9/17pCyHBPCHmZ0E/9D3wZt5qK63AoWiiF0 dYX9onepw7NoEAQ9pe0Kj3FrjtB20wu1JsTIDqLgnBGnPZIJ57tc2AQvzG89zO6m eL/oWeLEpScvf5b5gSVGAjrYqqNvQCDoWtN++2J1EwLsFUf+YhUM8dlW5HkkIEmu mS6CFDTqANIjb2pzXed0zI3fRVvjK8KJIClZf5L2XO8nHG9dtoU= =ouX+ -----END PGP SIGNATURE----- Thu Jul 30 02:32:41 UTC 2020 I: Checking whether the package is not for us Thu Jul 30 02:32:41 UTC 2020 I: Starting 1st build on remote node codethink-sled12-arm64.debian.net. Thu Jul 30 02:32:41 UTC 2020 I: Preparing to do remote build '1' on codethink-sled12-arm64.debian.net. Thu Jul 30 02:35:19 UTC 2020 I: Deleting $TMPDIR on codethink-sled12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 29 14:32:55 -12 2020 I: pbuilder-time-stamp: 1596076375 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [rapmap_0.12.0+dfsg-3.dsc] I: copying [./rapmap_0.12.0+dfsg.orig.tar.xz] I: copying [./rapmap_0.12.0+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Jan 1 23:07:29 2019 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rapmap_0.12.0+dfsg-3.dsc dpkg-source: info: extracting rapmap in rapmap-0.12.0+dfsg dpkg-source: info: unpacking rapmap_0.12.0+dfsg.orig.tar.xz dpkg-source: info: unpacking rapmap_0.12.0+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-libs.patch dpkg-source: info: applying use_shared_libs.patch dpkg-source: info: applying avoid_privacy_breach.patch dpkg-source: info: applying spelling dpkg-source: info: applying portable_pause dpkg-source: info: applying no_gomp_needed I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30864/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='30864' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/pbuilderrc_HvfJ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/b1 --logfile b1/build.log rapmap_0.12.0+dfsg-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled12-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 27 20:26 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/30864/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python-markdown dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libjellyfish-2.0-dev; however: Package libjellyfish-2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libspdlog-dev; however: Package libspdlog-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on python-markdown; however: Package python-markdown is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbsd0{a} libcereal-dev{a} libcroco3{a} libcurl4{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libicu63{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libjemalloc-dev{a} libjemalloc2{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps7{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsparsehash-dev{a} libspdlog-dev{a} libssh2-1{a} libssl1.1{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} lsb-base{a} m4{a} man-db{a} mime-support{a} pkg-config{a} po-debconf{a} procps{a} python{a} python-markdown{a} python-minimal{a} python-pkg-resources{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix python-pygments python-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 33.5 MB of archives. After unpacking 130 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libprocps7 arm64 2:3.3.15-2 [58.0 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 lsb-base all 10.2019051400 [28.4 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 procps arm64 2:3.3.15-2 [245 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 cmake-data all 3.13.4-1 [1476 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libarchive13 arm64 3.3.3-4+deb10u1 [291 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u2 [216 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 libcurl4 arm64 7.64.0-4+deb10u1 [312 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libjsoncpp1 arm64 1.7.4-3 [71.0 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 librhash0 arm64 1.3.8-1 [121 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 libuv1 arm64 1.24.1-1 [105 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 cmake arm64 3.13.4-1 [3046 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 72 http://deb.debian.org/debian buster/main arm64 libcereal-dev arm64 1.2.2-3 [258 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 libdivsufsort3 arm64 2.0.1-4 [38.9 kB] Get: 74 http://deb.debian.org/debian buster/main arm64 libdivsufsort-dev arm64 2.0.1-4 [27.4 kB] Get: 75 http://deb.debian.org/debian buster/main arm64 libjellyfish-2.0-2 arm64 2.2.10-2 [60.1 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 libjellyfish-2.0-dev arm64 2.2.10-2 [132 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 libjemalloc2 arm64 5.1.0-3 [178 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 libjemalloc-dev arm64 5.1.0-3 [315 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 libsparsehash-dev all 2.0.2-1 [76.9 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 libspdlog-dev arm64 1:1.3.1-1 [176 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 libtclap-dev arm64 1.2.2-1 [139 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 pkg-config arm64 0.29-6 [62.2 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 python-markdown all 3.0.1-3 [60.6 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 33.5 MB in 8s (4263 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... 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Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Unpacking libprocps7:arm64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../03-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../04-procps_2%3a3.3.15-2_arm64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... 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Unpacking debhelper (12.1.1) ... Selecting previously unselected package libcereal-dev. Preparing to unpack .../51-libcereal-dev_1.2.2-3_arm64.deb ... Unpacking libcereal-dev (1.2.2-3) ... Selecting previously unselected package libdivsufsort3:arm64. Preparing to unpack .../52-libdivsufsort3_2.0.1-4_arm64.deb ... Unpacking libdivsufsort3:arm64 (2.0.1-4) ... Selecting previously unselected package libdivsufsort-dev:arm64. Preparing to unpack .../53-libdivsufsort-dev_2.0.1-4_arm64.deb ... Unpacking libdivsufsort-dev:arm64 (2.0.1-4) ... Selecting previously unselected package libjellyfish-2.0-2:arm64. Preparing to unpack .../54-libjellyfish-2.0-2_2.2.10-2_arm64.deb ... Unpacking libjellyfish-2.0-2:arm64 (2.2.10-2) ... Selecting previously unselected package libjellyfish-2.0-dev:arm64. Preparing to unpack .../55-libjellyfish-2.0-dev_2.2.10-2_arm64.deb ... Unpacking libjellyfish-2.0-dev:arm64 (2.2.10-2) ... Selecting previously unselected package libjemalloc2:arm64. 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/rapmap-0.12.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package rapmap dpkg-buildpackage: info: source version 0.12.0+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/rapmap-0.12.0+dfsg' dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam make[1]: Leaving directory '/build/rapmap-0.12.0+dfsg' debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/rapmap-0.12.0+dfsg' dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true cd obj-aarch64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true .. -- 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/cc -- Check for working C compiler: /usr/bin/cc -- 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/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- DISABLING NATIVE ARCH. -- 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 Making Default build type -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11") -- Found Cereal: /usr/include (Required is at least version "1.2.2") -- Cereal found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29") -- Found Jemalloc: /usr/lib/aarch64-linux-gnu/libjemalloc.so (found version "5.1.0-0-g61efbda7098de6fe64c362d309824864308c36d4") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = .git/ -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR JELLYFISH_ROOT -- Build files have been written to: /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/rapmap-0.12.0+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/rapmap-0.12.0+dfsg' dh_auto_build cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/rapmap-0.12.0+dfsg -B/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/depend make[4]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rapmap-0.12.0+dfsg /build/rapmap-0.12.0+dfsg/src /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/rapmap.dir/DependInfo.cmake --color= Scanning dependencies of target rapmap make[4]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/build make[4]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' [ 15%] Building CXX object src/CMakeFiles/rapmap.dir/RapMap.cpp.o [ 15%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMap.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMap.cpp cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type 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/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/HitManager.cpp.o -c /build/rapmap-0.12.0+dfsg/src/HitManager.cpp cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /build/rapmap-0.12.0+dfsg/src/FastxParser.cpp [ 61%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o [ 53%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapFileSystem.cpp cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp [ 69%] Building CXX object src/CMakeFiles/rapmap.dir/rank9b.cpp.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/rank9b.cpp.o -c /build/rapmap-0.12.0+dfsg/src/rank9b.cpp [ 76%] Building CXX object src/CMakeFiles/rapmap.dir/stringpiece.cc.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/stringpiece.cc.o -c /build/rapmap-0.12.0+dfsg/src/stringpiece.cc [ 84%] Building C object src/CMakeFiles/rapmap.dir/xxhash.c.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/rapmap.dir/xxhash.c.o -c /build/rapmap-0.12.0+dfsg/src/xxhash.c [ 92%] Building C object src/CMakeFiles/rapmap.dir/bit_array.c.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cc -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/rapmap.dir/bit_array.c.o -c /build/rapmap-0.12.0+dfsg/src/bit_array.c In file included from /build/rapmap-0.12.0+dfsg/include/zstr/zstr.hpp:16, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:62: /build/rapmap-0.12.0+dfsg/include/zstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*, const string&, std::ios_base::openmode)': /build/rapmap-0.12.0+dfsg/include/zstr/strict_fstream.hpp:128:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] catch (std::ios_base::failure e) {} ^ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:5, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:23: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair >; Alloc = spp::libc_allocator > >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2382:9: required from 'bool spp::sparsetable::read_metadata(INPUT*) [with INPUT = std::basic_ifstream; T = std::pair >; Alloc = spp::libc_allocator > >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2435:13: required from 'bool spp::sparsetable::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer >; INPUT = std::basic_ifstream; T = std::pair >; Alloc = spp::libc_allocator > >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3455:20: required from 'bool spp::sparse_hashtable::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer >; INPUT = std::basic_ifstream; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3918:46: required from 'bool spp::sparse_hash_map::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer >; INPUT = std::basic_ifstream; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:73:7: required from 'bool loadHashFromIndex(const string&, RegHashT, rapmap::utils::KmerKeyHasher>&) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; RegHashT, rapmap::utils::KmerKeyHasher> = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:113:26: required from 'bool RapMapSAIndex::load(const string&) [with IndexT = int; HashT = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >; std::__cxx11::string = std::__cxx11::basic_string]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:178:16: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:5, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:23: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:5, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:23: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair >; Alloc = spp::libc_allocator > >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2382:9: required from 'bool spp::sparsetable::read_metadata(INPUT*) [with INPUT = std::basic_ifstream; T = std::pair >; Alloc = spp::libc_allocator > >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2435:13: required from 'bool spp::sparsetable::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer >; INPUT = std::basic_ifstream; T = std::pair >; Alloc = spp::libc_allocator > >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3455:20: required from 'bool spp::sparse_hashtable::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer >; INPUT = std::basic_ifstream; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3918:46: required from 'bool spp::sparse_hash_map::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer >; INPUT = std::basic_ifstream; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:73:7: required from 'bool loadHashFromIndex(const string&, RegHashT, rapmap::utils::KmerKeyHasher>&) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; RegHashT, rapmap::utils::KmerKeyHasher> = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:113:26: required from 'bool RapMapSAIndex::load(const string&) [with IndexT = long int; HashT = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >; std::__cxx11::string = std::__cxx11::basic_string]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:181:16: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:5, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:23: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:5, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:23: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2382:9: required from 'bool spp::sparsetable::read_metadata(INPUT*) [with INPUT = std::basic_ifstream; T = std::pair; Alloc = spp::libc_allocator >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2435:13: required from 'bool spp::sparsetable::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer; INPUT = std::basic_ifstream; T = std::pair; Alloc = spp::libc_allocator >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3455:20: required from 'bool spp::sparse_hashtable::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer; INPUT = std::basic_ifstream; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3918:46: required from 'bool spp::sparse_hash_map::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer; INPUT = std::basic_ifstream; Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >]' /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:244:17: required from 'void FrugalBooMap::load(const string&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; std::__cxx11::string = std::__cxx11::basic_string]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:82:5: required from 'bool loadHashFromIndex(const string&, PerfectHashT >&) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; PerfectHashT > = FrugalBooMap >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:113:26: required from 'bool RapMapSAIndex::load(const string&) [with IndexT = int; HashT = FrugalBooMap >; std::__cxx11::string = std::__cxx11::basic_string]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:184:16: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:5, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:23: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:5, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:23: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2382:9: required from 'bool spp::sparsetable::read_metadata(INPUT*) [with INPUT = std::basic_ifstream; T = std::pair; Alloc = spp::libc_allocator >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2435:13: required from 'bool spp::sparsetable::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer; INPUT = std::basic_ifstream; T = std::pair; Alloc = spp::libc_allocator >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3455:20: required from 'bool spp::sparse_hashtable::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer; INPUT = std::basic_ifstream; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3918:46: required from 'bool spp::sparse_hash_map::unserialize(ValueSerializer, INPUT*) [with ValueSerializer = spp_utils::pod_hash_serializer; INPUT = std::basic_ifstream; Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >]' /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:244:17: required from 'void FrugalBooMap::load(const string&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; std::__cxx11::string = std::__cxx11::basic_string]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:82:5: required from 'bool loadHashFromIndex(const string&, PerfectHashT >&) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; PerfectHashT > = FrugalBooMap >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:113:26: required from 'bool RapMapSAIndex::load(const string&) [with IndexT = long int; HashT = FrugalBooMap >; std::__cxx11::string = std::__cxx11::basic_string]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:185:16: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:5, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp:23: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hashtable::value_type = std::pair > >; spp::sparse_hashtable::key_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; spp::sparse_hash_map::mapped_type = std::vector >; spp::sparse_hash_map::key_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:603:33: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable > >, spp::libc_allocator > > > >::group_type' {aka 'class spp::sparsegroup > >, spp::libc_allocator > > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable > >, spp::libc_allocator > > > >::group_type' {aka 'class spp::sparsegroup > >, spp::libc_allocator > > > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair >; Alloc = spp::libc_allocator > >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::value_type = std::pair >; spp::sparse_hashtable::key_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hash_map::mapped_type = rapmap::utils::SAInterval; spp::sparse_hash_map::key_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:759:34: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair >; Alloc = spp::libc_allocator > >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hashtable::value_type = std::pair >; spp::sparse_hashtable::key_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; spp::sparse_hash_map::mapped_type = rapmap::utils::SAInterval; spp::sparse_hash_map::key_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:780:34: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable >, spp::libc_allocator > > >::group_type' {aka 'class spp::sparsegroup >, spp::libc_allocator > > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = long int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = long int; spp::sparse_hash_map::key_type = long int]' /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:756:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:777:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2241:17: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::reference = std::pair&; spp::sparsetable::value_type = std::pair; spp::sparsetable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3171:34: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::reference = std::pair&; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3280:81: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = long int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = long int; spp::sparse_hash_map::key_type = long int]' /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:756:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1384:19: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(_group + i, _group + i-1, sizeof(*_group)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/utility:70, from /usr/include/c++/8/algorithm:60, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:22: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here struct pair ^~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2241:17: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::reference = std::pair&; spp::sparsetable::value_type = std::pair; spp::sparsetable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3171:34: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::reference = std::pair&; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3280:81: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:777:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1384:19: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(_group + i, _group + i-1, sizeof(*_group)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/utility:70, from /usr/include/c++/8/algorithm:60, from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:22: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here struct pair ^~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = long int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = long int; spp::sparse_hash_map::key_type = long int]' /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; FrugalBooMap::IteratorT = KVProxy<__gnu_cxx::__normal_iterator > >, rapmap::utils::SAInterval >; typename std::vector::iterator = __gnu_cxx::__normal_iterator > >]' /build/rapmap-0.12.0+dfsg/include/SACollector.hpp:196:13: required from 'bool SACollector::operator()(std::__cxx11::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::__cxx11::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = long int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:303:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:392:17: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:493:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:691:53: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; FrugalBooMap::IteratorT = KVProxy<__gnu_cxx::__normal_iterator >, rapmap::utils::SAInterval >; typename std::vector::iterator = __gnu_cxx::__normal_iterator >]' /build/rapmap-0.12.0+dfsg/include/SACollector.hpp:196:13: required from 'bool SACollector::operator()(std::__cxx11::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::__cxx11::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:303:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:392:17: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:493:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:706:55: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2241:17: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::reference = std::pair&; spp::sparsetable::value_type = std::pair; spp::sparsetable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3171:34: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::reference = std::pair&; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3280:81: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; FrugalBooMap::IteratorT = KVProxy<__gnu_cxx::__normal_iterator > >, rapmap::utils::SAInterval >; typename std::vector::iterator = __gnu_cxx::__normal_iterator > >]' /build/rapmap-0.12.0+dfsg/include/SACollector.hpp:196:13: required from 'bool SACollector::operator()(std::__cxx11::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::__cxx11::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = long int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:303:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:392:17: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:493:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:691:53: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1384:19: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(_group + i, _group + i-1, sizeof(*_group)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:22: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here struct pair ^~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2241:17: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::reference = std::pair&; spp::sparsetable::value_type = std::pair; spp::sparsetable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3171:34: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::reference = std::pair&; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::size_type = long unsigned int]' /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3280:81: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; FrugalBooMap::IteratorT = KVProxy<__gnu_cxx::__normal_iterator >, rapmap::utils::SAInterval >; typename std::vector::iterator = __gnu_cxx::__normal_iterator >]' /build/rapmap-0.12.0+dfsg/include/SACollector.hpp:196:13: required from 'bool SACollector::operator()(std::__cxx11::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::__cxx11::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = int]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:303:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:392:17: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:493:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:706:55: required from here /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1384:19: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] memcpy(_group + i, _group + i-1, sizeof(*_group)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:22: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here struct pair ^~~~ cc1plus: warning: unrecognized command line option '-Wno-unused-local-typedef' cc1plus: warning: unrecognized command line option '-Wno-unused-local-typedef' At global scope: cc1plus: warning: unrecognized command line option '-Wno-unused-local-typedef' [100%] Linking CXX executable rapmap cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/rapmap.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rapmap.dir/RapMap.cpp.o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o CMakeFiles/rapmap.dir/HitManager.cpp.o CMakeFiles/rapmap.dir/FastxParser.cpp.o CMakeFiles/rapmap.dir/rank9b.cpp.o CMakeFiles/rapmap.dir/stringpiece.cc.o CMakeFiles/rapmap.dir/xxhash.c.o CMakeFiles/rapmap.dir/bit_array.c.o -o rapmap -L/build/rapmap-0.12.0+dfsg/lib -L/build/rapmap-0.12.0+dfsg/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" -lz -ldivsufsort -ldivsufsort64 -lm -lz -ljemalloc -lpthread make[4]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' [100%] Built target rapmap make[3]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' markdown_py -f README.html README.md make[1]: Leaving directory '/build/rapmap-0.12.0+dfsg' dh_auto_test cd obj-aarch64-linux-gnu && make -j8 test ARGS\+=-j8 make[1]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process -j8 Test project /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu Start 1: quasi_map_test Start 2: quasi_map_test_ph 1/2 Test #1: quasi_map_test ................... Passed 0.23 sec 2/2 Test #2: quasi_map_test_ph ................ Passed 0.25 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.25 sec make[1]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/rapmap-0.12.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/rapmap-0.12.0+dfsg -B/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/depend make[3]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rapmap-0.12.0+dfsg /build/rapmap-0.12.0+dfsg/src /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/rapmap.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/build make[3]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/rapmap.dir/build'. make[3]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' [100%] Built target rapmap make[2]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/rapmap-0.12.0+dfsg/debian/tmp/usr/bin/rapmap -- Installing: /build/rapmap-0.12.0+dfsg/debian/tmp/usr/bin/RunRapMap.sh make[1]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' dh_install dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rapmap' in '../rapmap_0.12.0+dfsg-3_arm64.deb'. dpkg-deb: building package 'rapmap-dbgsym' in '../rapmap-dbgsym_0.12.0+dfsg-3_arm64.deb'. dpkg-deb: building package 'rapmap-example-data' in '../rapmap-example-data_0.12.0+dfsg-3_all.deb'. dpkg-deb: building package 'rapmap-dev' in '../rapmap-dev_0.12.0+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rapmap_0.12.0+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/30864 and its subdirectories I: Current time: Wed Jul 29 14:35:16 -12 2020 I: pbuilder-time-stamp: 1596076516 Thu Jul 30 02:35:20 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled9-arm64.debian.net. Thu Jul 30 02:35:20 UTC 2020 I: Preparing to do remote build '2' on codethink-sled9-arm64.debian.net. Thu Jul 30 02:40:42 UTC 2020 I: Deleting $TMPDIR on codethink-sled9-arm64.debian.net. Thu Jul 30 02:40:44 UTC 2020 I: rapmap_0.12.0+dfsg-3_arm64.changes: Format: 1.8 Date: Wed, 02 Jan 2019 03:07:04 -0800 Source: rapmap Binary: rapmap rapmap-dbgsym rapmap-dev rapmap-example-data Architecture: arm64 all Version: 0.12.0+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: rapmap - rapid sensitive and accurate DNA read mapping via quasi-mapping rapmap-dev - rapmap - rapid sensitive and accurate DNA read mapping (some head rapmap-example-data - example data for rapmap - rapid sensitive and accurate DNA read m Changes: rapmap (0.12.0+dfsg-3) unstable; urgency=medium . * debian/patches/portable_pause: add ppc64el and arm64 alternatives to asm("pause"). * debian/patches/no_gomp_needed: Avoid unnecessary linkage to gomp. Checksums-Sha1: 24328693cb7eab55211df77c4aa9211caacfe11f 7348184 rapmap-dbgsym_0.12.0+dfsg-3_arm64.deb face653af802e8f7c22e372b86be37338489a6bc 190792 rapmap-dev_0.12.0+dfsg-3_all.deb c1a3df3a58b879ce788fdcc04308ca12a62a7ef6 411804 rapmap-example-data_0.12.0+dfsg-3_all.deb c8e049065fc719dd9707dad97479ba64b917e0e5 7035 rapmap_0.12.0+dfsg-3_arm64.buildinfo 0b81ea73bf73ca8aea8ef2e0f22f15b3b8530b4f 678568 rapmap_0.12.0+dfsg-3_arm64.deb Checksums-Sha256: 0216643f2338779ac2f088b61e2ef83420a228bab4cb9334f26f0979a22809da 7348184 rapmap-dbgsym_0.12.0+dfsg-3_arm64.deb 1ffa3a5259759ece4f22254b7db2e355fa7cdf7f4e61ccdb796b1a677a381566 190792 rapmap-dev_0.12.0+dfsg-3_all.deb 79a482a783cb9252f042ade5e58de9539f8dc503855e89d5031e12a447c668ac 411804 rapmap-example-data_0.12.0+dfsg-3_all.deb aa38354278b0b1a55205eb77ee460a67424ab1dce53d0c4d091c0a1f152983c1 7035 rapmap_0.12.0+dfsg-3_arm64.buildinfo 49f03177ed220530394df2ef329da9f8f8a34aeaac5ab8c751f42b5c7f183bdb 678568 rapmap_0.12.0+dfsg-3_arm64.deb Files: 75c8dfdaf7e150cafd18b5d79bc6294a 7348184 debug optional rapmap-dbgsym_0.12.0+dfsg-3_arm64.deb e49ffcb4598801edc63d102ea71b113b 190792 science optional rapmap-dev_0.12.0+dfsg-3_all.deb 46c2cfdf049d3241f355c327b1485c4e 411804 science optional rapmap-example-data_0.12.0+dfsg-3_all.deb ce6808ae9bf4e839668c22840b59c18b 7035 science optional rapmap_0.12.0+dfsg-3_arm64.buildinfo 769ff0e02a5a7e12389a8dc170c29e28 678568 science optional rapmap_0.12.0+dfsg-3_arm64.deb Thu Jul 30 02:40:46 UTC 2020 I: diffoscope 153 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/rapmap_0.12.0+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/rapmap_0.12.0+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/rapmap_0.12.0+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/b1/rapmap_0.12.0+dfsg-3_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/b2/rapmap_0.12.0+dfsg-3_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.357s) 0.357s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.114s) 0.113s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Jul 30 02:43:11 UTC 2020 I: diffoscope 153 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 30 02:43:11 UTC 2020 I: rapmap from buster built successfully and reproducibly on arm64. Thu Jul 30 02:43:13 UTC 2020 I: Submitting .buildinfo files to external archives: Thu Jul 30 02:43:13 UTC 2020 I: Submitting 8.0K b1/rapmap_0.12.0+dfsg-3_arm64.buildinfo.asc Thu Jul 30 02:43:15 UTC 2020 I: Submitting 8.0K b2/rapmap_0.12.0+dfsg-3_arm64.buildinfo.asc Thu Jul 30 02:43:16 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jul 30 02:43:16 UTC 2020 I: Done submitting .buildinfo files. Thu Jul 30 02:43:16 UTC 2020 I: Removing signed rapmap_0.12.0+dfsg-3_arm64.buildinfo.asc files: removed './b1/rapmap_0.12.0+dfsg-3_arm64.buildinfo.asc' removed './b2/rapmap_0.12.0+dfsg-3_arm64.buildinfo.asc'