sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org +==============================================================================+ | jellyfish1 1.1.11-8 (amd64) Fri, 18 Aug 2023 03:35:57 +0000 | +==============================================================================+ Package: jellyfish1 Version: 1.1.11-8 Source Version: 1.1.11-8 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.bKNaZggNks... I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish1-eIzHhD/resolver-McdX1k' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [210 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [10.3 MB] Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [9449 kB] Get:4 http://mirror.einval.org/debian unstable/main amd64 Packages [9582 kB] Fetched 29.5 MB in 8s (3804 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libgpg-error0 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libpam-modules libpam-modules-bin libpam-runtime libpam0g zlib1g 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1216 kB of archives. After this operation, 101 kB disk space will be freed. Get:1 http://mirror.einval.org/debian unstable/main arm64 libpam0g arm64 1.5.2-7 [65.4 kB] Get:2 http://mirror.einval.org/debian unstable/main arm64 libpam-modules-bin arm64 1.5.2-7 [49.9 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libpam-modules arm64 1.5.2-7 [261 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libpam-runtime all 1.5.2-7 [136 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libgpg-error0 arm64 1.47-2 [73.4 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 zlib1g arm64 1:1.2.13.dfsg-3 [82.9 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-3 [123 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-3 [314 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-3 [31.7 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-3 [79.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1216 kB in 0s (27.9 MB/s) (Reading database ... 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Preparing to unpack .../libk5crypto3_1.20.1-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.20.1-3) over (1.20.1-2) ... Setting up libkrb5support0:arm64 (1.20.1-3) ... Setting up libk5crypto3:arm64 (1.20.1-3) ... Setting up libkrb5-3:arm64 (1.20.1-3) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-3) ... Processing triggers for libc-bin (2.37-7) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'jellyfish1' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/jellyfish1.git Please use: git clone https://salsa.debian.org/med-team/jellyfish1.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1076 kB of source archives. Get:1 http://mirror.einval.org/debian unstable/main jellyfish1 1.1.11-8 (dsc) [2154 B] Get:2 http://mirror.einval.org/debian unstable/main jellyfish1 1.1.11-8 (tar) [1067 kB] Get:3 http://mirror.einval.org/debian unstable/main jellyfish1 1.1.11-8 (diff) [6316 B] Fetched 1076 kB in 0s (12.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/jellyfish1-eIzHhD/jellyfish1-1.1.11' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish1-eIzHhD' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [714 B] Get:5 copy:/<>/apt_archive ./ Packages [757 B] Fetched 2080 B in 0s (113 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-base:amd64 gcc-13-cross-base gcc-13-x86-64-linux-gnu gcc-13-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfakeroot libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-13-dev:amd64 libgcc-13-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libhwasan0:amd64 libhwasan0-amd64-cross libicu72 libio-string-perl libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1 libnsl-dev:amd64 libnsl2:amd64 libpipeline1 libquadmath0:amd64 libquadmath0-amd64-cross libssl3:amd64 libstdc++-13-dev:amd64 libstdc++-13-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-13-locales cpp-13-doc cpp-doc dh-make binutils-multiarch g++-13-multilib-x86-64-linux-gnu gcc-13-doc gcc-13-multilib-x86-64-linux-gnu manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 krb5-doc:amd64 krb5-user:amd64 libstdc++-13-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:amd64 libarchive-cpio-perl krb5-locales:amd64 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-base:amd64 gcc-13-cross-base gcc-13-x86-64-linux-gnu gcc-13-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfakeroot libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-13-dev:amd64 libgcc-13-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libhwasan0:amd64 libhwasan0-amd64-cross libicu72 libio-string-perl libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1 libnsl-dev:amd64 libnsl2:amd64 libpipeline1 libquadmath0:amd64 libquadmath0-amd64-cross libssl3:amd64 libstdc++-13-dev:amd64 libstdc++-13-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:amd64 sensible-utils ucf 0 upgraded, 105 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After this operation, 421 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-5 [15.1 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.20 [19.3 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.44-3 [42.5 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.21-13 [159 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-2 [1122 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.39.1-4 [89.0 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.11.2-3 [1368 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-3 [276 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.21-13 [496 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 gcc-13-x86-64-linux-gnu-base arm64 13.2.0-2cross1 [39.6 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 cpp-13-x86-64-linux-gnu arm64 13.2.0-2cross1 [9274 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:13.2.0-1 [4116 B] Get:22 http://mirror.einval.org/debian unstable/main arm64 cross-config all 2.6.20 [16.3 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.41-4 [2384 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 gcc-13-cross-base all 13.2.0-2cross1 [35.2 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 13.2.0-2cross1 [57.7 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 13.2.0-2cross1 [128 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 13.2.0-2cross1 [25.5 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 13.2.0-2cross1 [8988 B] Get:29 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 13.2.0-2cross1 [2552 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 13.2.0-2cross1 [1101 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 13.2.0-2cross1 [2326 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.37-3cross1 [1477 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 13.2.0-2cross1 [648 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 13.2.0-2cross1 [1009 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 13.2.0-2cross1 [1153 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 13.2.0-2cross1 [145 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libgcc-13-dev-amd64-cross all 13.2.0-2cross1 [2542 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 gcc-13-x86-64-linux-gnu arm64 13.2.0-2cross1 [18.3 MB] Get:39 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:13.2.0-1 [1472 B] Get:40 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 6.3.7-1cross1 [1917 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.37-3cross1 [1897 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libstdc++-13-dev-amd64-cross all 13.2.0-2cross1 [2201 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 g++-13-x86-64-linux-gnu arm64 13.2.0-2cross1 [10.1 MB] Get:44 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:13.2.0-1 [1176 B] Get:45 http://mirror.einval.org/debian unstable/main arm64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3 [618 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1+b1 [309 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libyaml-perl all 1.30-2 [63.4 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 dpkg-cross all 2.6.20 [25.8 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.10 [3488 B] Get:61 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.11.5 [81.8 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get:66 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:68 http://mirror.einval.org/debian unstable/main arm64 libelf1 arm64 0.189-4 [173 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1 [101 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.21-13 [1248 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.11.5 [952 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.32.1-1 [27.9 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.32.1-1 [66.3 kB] Get:76 http://mirror.einval.org/debian unstable/main amd64 gcc-13-base amd64 13.2.0-2 [39.3 kB] Get:77 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 13.2.0-2 [57.7 kB] Get:78 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.37-7 [2754 kB] Get:79 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 13.2.0-2 [2559 kB] Get:80 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 13.2.0-2 [9288 B] Get:81 http://mirror.einval.org/debian unstable/main amd64 linux-libc-dev amd64 6.4.4-3 [1798 kB] Get:82 http://mirror.einval.org/debian unstable/main amd64 libcrypt1 amd64 1:4.4.36-2 [89.7 kB] Get:83 http://mirror.einval.org/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.36-2 [118 kB] Get:84 http://mirror.einval.org/debian unstable/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB] Get:85 http://mirror.einval.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-3 [32.3 kB] Get:86 http://mirror.einval.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-3 [79.1 kB] Get:87 http://mirror.einval.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:88 http://mirror.einval.org/debian unstable/main amd64 libssl3 amd64 3.0.10-1 [2014 kB] Get:89 http://mirror.einval.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-3 [333 kB] Get:90 http://mirror.einval.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-3 [134 kB] Get:91 http://mirror.einval.org/debian unstable/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:92 http://mirror.einval.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:93 http://mirror.einval.org/debian unstable/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:94 http://mirror.einval.org/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:95 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.37-7 [1903 kB] Get:96 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 13.2.0-2 [131 kB] Get:97 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 13.2.0-2 [26.1 kB] Get:98 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 13.2.0-2 [1102 kB] Get:99 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 13.2.0-2 [2334 kB] Get:100 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 13.2.0-2 [694 kB] Get:101 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 13.2.0-2 [1010 kB] Get:102 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 13.2.0-2 [1154 kB] Get:103 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 13.2.0-2 [145 kB] Get:104 http://mirror.einval.org/debian unstable/main amd64 libgcc-13-dev amd64 13.2.0-2 [2539 kB] Get:105 http://mirror.einval.org/debian unstable/main amd64 libstdc++-13-dev amd64 13.2.0-2 [2221 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 103 MB in 1s (87.2 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 10350 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-5_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.20_all.deb ... Unpacking sensible-utils (0.0.20) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../003-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-13_arm64.deb ... Unpacking gettext-base (0.21-13) ... 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Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libyaml-perl (1.30-2) ... Setting up libfakeroot:arm64 (1.32.1-1) ... Setting up fakeroot (1.32.1-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up gcc-13-base:amd64 (13.2.0-2) ... Setting up gcc-13-cross-base (13.2.0-2cross1) ... Setting up libquadmath0-amd64-cross (13.2.0-2cross1) ... Setting up autopoint (0.21-13) ... Setting up libc6-amd64-cross (2.37-3cross1) ... Setting up autoconf (2.71-3) ... Setting up gcc-13-x86-64-linux-gnu-base:arm64 (13.2.0-2cross1) ... Setting up sensible-utils (0.0.20) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libgcc-s1-amd64-cross (13.2.0-2cross1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libelf1:arm64 (0.189-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up binutils-x86-64-linux-gnu (2.41-4) ... Setting up libstdc++6-amd64-cross (13.2.0-2cross1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-13) ... Setting up libtool (2.4.7-7) ... Setting up cpp-13-x86-64-linux-gnu (13.2.0-2cross1) ... Setting up libasan8-amd64-cross (13.2.0-2cross1) ... Setting up liblsan0-amd64-cross (13.2.0-2cross1) ... Setting up libc6-dev-amd64-cross (2.37-3cross1) ... Setting up libtsan2-amd64-cross (13.2.0-2cross1) ... Setting up libgomp1-amd64-cross (13.2.0-2cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libitm1-amd64-cross (13.2.0-2cross1) ... Setting up libatomic1-amd64-cross (13.2.0-2cross1) ... Setting up libhwasan0-amd64-cross (13.2.0-2cross1) ... Setting up libubsan1-amd64-cross (13.2.0-2cross1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-2) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-13-dev-amd64-cross (13.2.0-2cross1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-13-dev-amd64-cross (13.2.0-2cross1) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-2cross1) ... Setting up debhelper (13.11.5) ... Setting up libxml-simple-perl (2.25-2) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-2cross1) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-1) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-1) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-amd64 (12.10) ... Setting up libgcc-s1:amd64 (13.2.0-2) ... Setting up libc6:amd64 (2.37-7) ... Setting up libhwasan0:amd64 (13.2.0-2) ... Setting up libasan8:amd64 (13.2.0-2) ... Setting up libtsan2:amd64 (13.2.0-2) ... Setting up libstdc++6:amd64 (13.2.0-2) ... Setting up liblsan0:amd64 (13.2.0-2) ... Setting up libitm1:amd64 (13.2.0-2) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libssl3:amd64 (3.0.10-1) ... Setting up libcrypt1:amd64 (1:4.4.36-2) ... Setting up libcom-err2:amd64 (1.47.0-2) ... Setting up libgomp1:amd64 (13.2.0-2) ... Setting up libkrb5support0:amd64 (1.20.1-3) ... Setting up libquadmath0:amd64 (13.2.0-2) ... Setting up libatomic1:amd64 (13.2.0-2) ... Setting up libk5crypto3:amd64 (1.20.1-3) ... Setting up libubsan1:amd64 (13.2.0-2) ... Setting up libgcc-13-dev:amd64 (13.2.0-2) ... Setting up libcrypt-dev:amd64 (1:4.4.36-2) ... Setting up libkrb5-3:amd64 (1.20.1-3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-3) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.37-7) ... Setting up libstdc++-13-dev:amd64 (13.2.0-2) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.37-7) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64 mips64el ppc64el hppa ia64 kfreebsd-amd64 riscv64) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-7-arm64 #1 SMP Debian 6.1.20-1 (2023-03-19) arm64 (aarch64) Toolchain package versions: binutils_2.41-4 dpkg-dev_1.21.22 g++-13_13.2.0-2 gcc-13_13.2.0-2 libc6-dev_2.37-7 libstdc++-13-dev_13.2.0-2 libstdc++-13-dev-amd64-cross_13.2.0-2cross1 libstdc++6_13.2.0-2 libstdc++6-amd64-cross_13.2.0-2cross1 linux-libc-dev_6.4.4-3 Package versions: apt_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.1 bash_5.2.15-2+b4 binutils_2.41-4 binutils-aarch64-linux-gnu_2.41-4 binutils-common_2.41-4 binutils-x86-64-linux-gnu_2.41-4 bsdextrautils_2.39.1-4 bsdutils_1:2.39.1-4 build-essential_12.10 bzip2_1.0.8-5+b1 coreutils_9.1-1 cpp_4:13.2.0-1 cpp-13_13.2.0-2 cpp-13-x86-64-linux-gnu_13.2.0-2cross1 cpp-x86-64-linux-gnu_4:13.2.0-1 cross-config_2.6.20 crossbuild-essential-amd64_12.10 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.5 debian-archive-keyring_2023.4 debianutils_5.8-1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.22 dpkg-cross_2.6.20 dpkg-dev_1.21.22 dwz_0.15-1 fakeroot_1.32.1-1 file_1:5.44-3 findutils_4.9.0-5 g++_4:13.2.0-1 g++-13_13.2.0-2 g++-13-x86-64-linux-gnu_13.2.0-2cross1 g++-x86-64-linux-gnu_4:13.2.0-1 gcc_4:13.2.0-1 gcc-13_13.2.0-2 gcc-13-base_13.2.0-2 gcc-13-cross-base_13.2.0-2cross1 gcc-13-x86-64-linux-gnu_13.2.0-2cross1 gcc-13-x86-64-linux-gnu-base_13.2.0-2cross1 gcc-x86-64-linux-gnu_4:13.2.0-1 gettext_0.21-13 gettext-base_0.21-13 gpgv_2.2.40-1.1 grep_3.11-2 groff-base_1.23.0-2 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libasan8_13.2.0-2 libasan8-amd64-cross_13.2.0-2cross1 libatomic1_13.2.0-2 libatomic1-amd64-cross_13.2.0-2cross1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-4 libblkid1_2.39.1-4 libbz2-1.0_1.0.8-5+b1 libc-bin_2.37-7 libc-dev-bin_2.37-7 libc6_2.37-7 libc6-amd64-cross_2.37-3cross1 libc6-dev_2.37-7 libc6-dev-amd64-cross_2.37-3cross1 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-4 libcc1-0_13.2.0-2 libcom-err2_1.47.0-2 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-4 libctf0_2.41-4 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270 libdebhelper-perl_13.11.5 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.21.22 libelf1_0.189-4 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-13-dev_13.2.0-2 libgcc-13-dev-amd64-cross_13.2.0-2cross1 libgcc-s1_13.2.0-2 libgcc-s1-amd64-cross_13.2.0-2cross1 libgcrypt20_1.10.2-2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-3 libgomp1_13.2.0-2 libgomp1-amd64-cross_13.2.0-2cross1 libgpg-error0_1.47-2 libgprofng0_2.41-4 libgssapi-krb5-2_1.20.1-3 libhogweed6_3.9.1-2 libhwasan0_13.2.0-2 libhwasan0-amd64-cross_13.2.0-2cross1 libicu72_72.1-3 libidn2-0_2.3.4-1 libio-string-perl_1.08-4 libisl23_0.26-3 libitm1_13.2.0-2 libitm1-amd64-cross_13.2.0-2cross1 libjansson4_2.14-2 libk5crypto3_1.20.1-3 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-3 libkrb5support0_1.20.1-3 liblocale-gettext-perl_1.07-5 liblsan0_13.2.0-2 liblsan0-amd64-cross_13.2.0-2cross1 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.1.0-1 libmount1_2.39.1-4 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libnettle8_3.9.1-2 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.0-4 libpam-modules_1.5.2-7 libpam-modules-bin_1.5.2-7 libpam-runtime_1.5.2-7 libpam0g_1.5.2-7 libpcre2-8-0_10.42-2 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libquadmath0_13.2.0-2 libquadmath0-amd64-cross_13.2.0-2cross1 libseccomp2_2.5.4-1+b3 libselinux1_3.5-1 libsframe1_2.41-4 libsmartcols1_2.39.1-4 libssl3_3.0.10-1 libstdc++-13-dev_13.2.0-2 libstdc++-13-dev-amd64-cross_13.2.0-2cross1 libstdc++6_13.2.0-2 libstdc++6-amd64-cross_13.2.0-2cross1 libsub-override-perl_0.09-4 libsystemd0_254.1-2 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20230625-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libtsan2_13.2.0-2 libtsan2-amd64-cross_13.2.0-2cross1 libubsan1_13.2.0-2 libubsan1-amd64-cross_13.2.0-2cross1 libuchardet0_0.0.7-1 libudev1_254.1-2 libunistring2_1.0-2 libuuid1_2.39.1-4 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SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: jellyfish1 Binary: jellyfish1 Architecture: amd64 arm64 mips64el ppc64el hppa ia64 kfreebsd-amd64 riscv64 Version: 1.1.11-8 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish1 Vcs-Git: https://salsa.debian.org/med-team/jellyfish1.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: jellyfish1 deb science optional arch=amd64,arm64,mips64el,ppc64el,hppa,ia64,kfreebsd-amd64,riscv64 Checksums-Sha1: 8bd6a7b382e94d37adfddd916dec2b0e36f840fd 1067138 jellyfish1_1.1.11.orig.tar.gz ed77ac76ebddcdeb9fc84cbfe03256a0fbfaef09 6316 jellyfish1_1.1.11-8.debian.tar.xz Checksums-Sha256: 496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2 1067138 jellyfish1_1.1.11.orig.tar.gz fd5f8b9a5fe8ef5e1b48cf2fb9ce2b65514f5cb92c4af967d51876b40d80370c 6316 jellyfish1_1.1.11-8.debian.tar.xz Files: dc994ea8b0896156500ea8c648f24846 1067138 jellyfish1_1.1.11.orig.tar.gz da972f42f1facc2cd6e8ccfffcc9041f 6316 jellyfish1_1.1.11-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmLeOvwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGNdQ/8CtwmBvcu/pNmjX8Nn7TFSw578RtLmrtg u4CS8h8YSY26P57vx+c7xZa8V/t9CaFnPnG5VKGq8SQPrWjeciGKFv/Ibavy5eEK AB8X4sHmVxZ/YhFaG8iNHg1/XSjbuTk9Vwwj+ZQknpeAJw/LpDLMHDTMP96gSV8y gI4LVhZ0uSORhuQ9CWXF1qF/9Dust2g4H3zUwTjkOrjCoPwkbkcP9FcFhE8lxNNf Marh4wG5KRHBhpWwswNqHvI2sPIOtSB9K3G9vwYCOJIcL/C5/xGLlkMrD4TqxOyI hMQIq+sX6bUmzHzzhrsnz4S2T4x22ygtIj2iXPHJH3zWqFcI5n5EevBUdg1ukFGz Z5eAdKWU4LPHisS90oyJSKCWcVscRywW84EuWDi4Dc3d/bJ6IebxivQM31/XKU17 J+sx8n3wwDAumUooNZSRcJsbihAZQ3ZXnXRZU6b9y2ODfFkPzgFYZ/NX1+x0Nn2A oqr7WIBWHkh3VVy7zXnBGHjvSkQizLFZcQz1HXgYgydYAEkIwAyOIWGkUKBb1GxF EbgZ3sf1TCustftShm5l7ts3oO2jlM4LKmIi9lwSlV/T97Y8YxcjqTEtJI46bs27 plpwOMiyMxS4KvWzdjrOTFg/mVufcFccTb3DX2OjKNc2iktHdYMOXJTbR5nsFJiI 5piuOJHYZQc= =m7iO -----END PGP SIGNATURE----- gpgv: Signature made Mon Jul 25 06:41:00 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./jellyfish1_1.1.11-8.dsc: no acceptable signature found dpkg-source: info: extracting jellyfish1 in /<> dpkg-source: info: unpacking jellyfish1_1.1.11.orig.tar.gz dpkg-source: info: unpacking jellyfish1_1.1.11-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying man dpkg-source: info: applying arm64.patch dpkg-source: info: applying mips.patch dpkg-source: info: applying autoconf.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/var/lib/sbuild LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package jellyfish1 dpkg-buildpackage: info: source version 1.1.11-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:8: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:8: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:61: the top level configure.ac:8: installing './compile' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure -a ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=x86_64-linux-gnu configure: loading site script /etc/dpkg-cross/cross-config.amd64 checking build system type... aarch64-unknown-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for x86_64-linux-gnu-strip... x86_64-linux-gnu-strip checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for x86_64-linux-gnu-gcc... x86_64-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C11 features... none needed checking whether x86_64-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-linux-gnu-gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by x86_64-linux-gnu-gcc... /usr/x86_64-linux-gnu/bin/ld checking if the linker (/usr/x86_64-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-linux-gnu-nm -B checking the name lister (/usr/bin/x86_64-linux-gnu-nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-linux-gnu-file... no checking for file... file configure: WARNING: using cross tools not prefixed with host triplet checking for x86_64-linux-gnu-objdump... x86_64-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-linux-gnu-ar... x86_64-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-linux-gnu-strip... (cached) x86_64-linux-gnu-strip checking for x86_64-linux-gnu-ranlib... x86_64-linux-gnu-ranlib checking command to parse /usr/bin/x86_64-linux-gnu-nm -B output from x86_64-linux-gnu-gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for x86_64-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-linux-gnu-gcc static flag -static works... yes checking if x86_64-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-linux-gnu-gcc linker (/usr/x86_64-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for x86_64-linux-gnu-g++... x86_64-linux-gnu-g++ checking whether the compiler supports GNU C++... yes checking whether x86_64-linux-gnu-g++ accepts -g... yes checking for x86_64-linux-gnu-g++ option to enable C++11 features... none needed checking dependency style of x86_64-linux-gnu-g++... none checking how to run the C++ preprocessor... x86_64-linux-gnu-g++ -E checking for ld used by x86_64-linux-gnu-g++... /usr/x86_64-linux-gnu/bin/ld -m elf_x86_64 checking if the linker (/usr/x86_64-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-linux-gnu-g++ linker (/usr/x86_64-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-linux-gnu-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-linux-gnu-g++ static flag -static works... yes checking if x86_64-linux-gnu-g++ supports -c -o file.o... yes checking if x86_64-linux-gnu-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-linux-gnu-g++ linker (/usr/x86_64-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for md5sum... md5sum checking for __int128... yes checking for x86_64-linux-gnu-g++ options needed to detect all undeclared functions... none needed checking whether strerror_r is declared... yes checking whether strerror_r returns char *... yes checking for execinfo.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating tests/compat.sh config.status: creating jellyfish-1.1.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all make -j1 all bin/generate_sequence bin/test_all make[2]: Entering directory '/<>' make all-am make[3]: Entering directory '/<>' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/jellyfish.o jellyfish/jellyfish.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/stats_main.o jellyfish/stats_main.cc In file included from jellyfish/stats_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/stats_main.cc:83:34: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/stats_main.cc:26: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’ at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/stats_main.cc:25: ./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’ at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_merge.o jellyfish/hash_merge.cc In file included from jellyfish/hash_merge.cc:32: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/mer_counting.hpp:31, from jellyfish/hash_merge.cc:34: ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::compacted_hash::reader; std::ostream = std::basic_ostream]’: jellyfish/hash_merge.cc:189:38: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here 36 | struct header { | ^~~~~~ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘SquareBinaryMatrix jellyfish::compacted_hash::reader::get_hash_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]’ at ./jellyfish/compacted_hash.hpp:245:59, inlined from ‘int merge_main(int, char**)’ at jellyfish/hash_merge.cc:138:69: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp: In function ‘int merge_main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘SquareBinaryMatrix jellyfish::compacted_hash::reader::get_hash_inverse_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]’ at ./jellyfish/compacted_hash.hpp:246:67, inlined from ‘int merge_main(int, char**)’ at jellyfish/hash_merge.cc:140:35: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function ‘int merge_main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘SquareBinaryMatrix jellyfish::compacted_hash::reader::get_hash_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]’ at ./jellyfish/compacted_hash.hpp:245:59, inlined from ‘int merge_main(int, char**)’ at jellyfish/hash_merge.cc:135:45: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function ‘int merge_main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘SquareBinaryMatrix jellyfish::compacted_hash::reader::get_hash_inverse_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]’ at ./jellyfish/compacted_hash.hpp:246:67, inlined from ‘int merge_main(int, char**)’ at jellyfish/hash_merge.cc:136:61: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function ‘int merge_main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mer_counter.o jellyfish/mer_counter.cc In file included from jellyfish/mer_counter.cc:33: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]’: ./jellyfish/invertible_hash_array.hpp:116:11: required from ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]’ jellyfish/mer_counter.cc:142:66: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::InvalidMatrix]’: ./jellyfish/invertible_hash_array.hpp:185:11: required from ‘void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ jellyfish/mer_counter.cc:149:22: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::sequence_parser::sequence_t]’ ./jellyfish/parse_dna.hpp:178:75: required from ‘jellyfish::parse_dna::parse_dna(T, T, uint_t, unsigned int, size_t) [with T = __gnu_cxx::__normal_iterator >; uint_t = long unsigned int; size_t = long unsigned int]’ jellyfish/mer_counter.cc:138:60: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/mer_counting.hpp:31, from jellyfish/mer_counter.cc:38: ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; std::ostream = std::basic_ostream]’: ./jellyfish/direct_sorted_dumper.hpp:101:39: required from ‘void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]’ ./jellyfish/direct_sorted_dumper.hpp:91:8: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here 36 | struct header { | ^~~~~~ ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::invertible_hash::array; std::ostream = std::basic_ostream]’: ./jellyfish/sorted_dumper.hpp:116:39: required from ‘void jellyfish::sorted_dumper::_dump() [with storage_t = jellyfish::invertible_hash::array; atomic_t = atomic::gcc]’ ./jellyfish/sorted_dumper.hpp:105:8: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here 36 | struct header { | ^~~~~~ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:17: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_quake; hash_t = jellyfish::hash, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::capped_integer; ary_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:17: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash, jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = long unsigned int; ary_t = jellyfish::invertible_hash::array; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:17: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘void jellyfish::direct_indexing::array::write_ary_header(std::ostream*) const [with key_t = long unsigned int; val_t = jellyfish::capped_integer; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/direct_indexing_array.hpp:52:28, inlined from ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>]’ at ./jellyfish/compacted_hash.hpp:121:30, inlined from ‘void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]’ at ./jellyfish/direct_sorted_dumper.hpp:101:39: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/mer_counter.cc:36: ./jellyfish/misc.hpp: In member function ‘void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:187:21, inlined from ‘void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:183:12: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:112:9: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In constructor ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_main.o jellyfish/histo_main.cc In file included from jellyfish/histo_main.cc:25: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/histo_main.cc:111:34: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’ at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’ at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘SquareBinaryMatrix jellyfish::compacted_hash::query::get_hash_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]’ at ./jellyfish/compacted_hash.hpp:370:59, inlined from ‘int histo_main(int, char**)’ at jellyfish/histo_main.cc:121:60: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function ‘int histo_main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘SquareBinaryMatrix jellyfish::compacted_hash::query::get_hash_inverse_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]’ at ./jellyfish/compacted_hash.hpp:371:67, inlined from ‘int histo_main(int, char**)’ at jellyfish/histo_main.cc:122:68: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function ‘int histo_main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_main.o jellyfish/dump_main.cc jellyfish/dump_main.cc: In function ‘int dump_main(int, char**)’: jellyfish/dump_main.cc:86:24: warning: catching polymorphic type ‘class mapped_file::ErrorMMap’ by value [-Wcatch-value=] 86 | } catch(mapped_file::ErrorMMap) { | ^~~~~~~~~ In file included from jellyfish/dump_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/dump_main.cc:65:44: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_main.cc:26: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’ at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/dump_main.cc:25: ./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’ at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/query_main.o jellyfish/query_main.cc In file included from ./jellyfish/mapped_file.hpp:29, from ./jellyfish/hash.hpp:27, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/query_main.cc:63:34: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’ at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/query_main.cc:23: ./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’ at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_fastq_main.o jellyfish/dump_fastq_main.cc In file included from jellyfish/dump_fastq_main.cc:25: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_fastq_main.cc:27: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/aligned_values_array.hpp:49:9, inlined from ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’ at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/dump_fastq_main.cc:26: ./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/aligned_values_array.hpp:49:9, inlined from ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’ at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_fastq_main.o jellyfish/histo_fastq_main.cc In file included from jellyfish/histo_fastq_main.cc:26: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_fastq_main.cc:28: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/aligned_values_array.hpp:49:9, inlined from ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’ at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/histo_fastq_main.cc:27: ./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/aligned_values_array.hpp:49:9, inlined from ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’ at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/cite.o jellyfish/cite.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_fastq_merge.o jellyfish/hash_fastq_merge.cc In file included from jellyfish/hash_fastq_merge.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array; atomic = atomic::gcc]’ jellyfish/hash_fastq_merge.cc:49:12: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]’: ./jellyfish/invertible_hash_array.hpp:116:11: required from ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]’ ./jellyfish/aligned_values_array.hpp:41:9: required from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(size_t, uint_t, uint_t, size_t*) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]’ jellyfish/hash_fastq_merge.cc:28:79: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_fastq_merge.cc:19: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/aligned_values_array.hpp:49:9, inlined from ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’ at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/aligned_values_array.hpp:49:9, inlined from ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’ at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ at ./jellyfish/invertible_hash_array.hpp:112:9: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In constructor ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/yaggo.o jellyfish/yaggo.cpp /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/square_binary_matrix.lo jellyfish/square_binary_matrix.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -fPIC -DPIC -o jellyfish/.libs/square_binary_matrix.o In file included from ./jellyfish/square_binary_matrix.hpp:27, from jellyfish/square_binary_matrix.cc:21: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::SingularMatrix]’: jellyfish/square_binary_matrix.cc:93:2: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘SquareBinaryMatrix SquareBinaryMatrix::transpose() const’ at jellyfish/square_binary_matrix.cc:52:30: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/square_binary_matrix.cc:20: ./jellyfish/misc.hpp: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::transpose() const’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘void SquareBinaryMatrix::alloc_columns()’ at ./jellyfish/square_binary_matrix.hpp:55:26, inlined from ‘void SquareBinaryMatrix::load(std::istream*)’ at jellyfish/square_binary_matrix.cc:143:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘void SquareBinaryMatrix::load(std::istream*)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘void SquareBinaryMatrix::alloc_columns()’ at ./jellyfish/square_binary_matrix.hpp:55:26, inlined from ‘size_t SquareBinaryMatrix::read(const char*)’ at jellyfish/square_binary_matrix.cc:154:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘size_t SquareBinaryMatrix::read(const char*)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘SquareBinaryMatrix SquareBinaryMatrix::operator*(const SquareBinaryMatrix&) const’ at jellyfish/square_binary_matrix.cc:65:30: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::operator*(const SquareBinaryMatrix&) const’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘SquareBinaryMatrix SquareBinaryMatrix::inverse() const’ at jellyfish/square_binary_matrix.cc:80:33: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::inverse() const’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘SquareBinaryMatrix SquareBinaryMatrix::inverse() const’ at jellyfish/square_binary_matrix.cc:81:30: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::inverse() const’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -o jellyfish/square_binary_matrix.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/err.lo jellyfish/err.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -fPIC -DPIC -o jellyfish/.libs/err.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -o jellyfish/err.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/misc.lo jellyfish/misc.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -fPIC -DPIC -o jellyfish/.libs/misc.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -o jellyfish/misc.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/storage.lo jellyfish/storage.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -fPIC -DPIC -o jellyfish/.libs/storage.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -o jellyfish/storage.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/thread_exec.lo jellyfish/thread_exec.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -fPIC -DPIC -o jellyfish/.libs/thread_exec.o In file included from jellyfish/thread_exec.hpp:26, from jellyfish/thread_exec.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = thread_exec::Error]’: jellyfish/thread_exec.cc:28:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -o jellyfish/thread_exec.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/time.lo jellyfish/time.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -fPIC -DPIC -o jellyfish/.libs/time.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -o jellyfish/time.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/file_parser.lo jellyfish/file_parser.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -fPIC -DPIC -o jellyfish/.libs/file_parser.o In file included from jellyfish/file_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/file_parser.cc:33:5: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -o jellyfish/file_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/read_parser.lo jellyfish/read_parser.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -fPIC -DPIC -o jellyfish/.libs/read_parser.o In file included from ./jellyfish/file_parser.hpp:24, from ./jellyfish/read_parser.hpp:20, from jellyfish/read_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/read_parser.cc:30:5: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -o jellyfish/read_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_read.lo jellyfish/parse_read.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -fPIC -DPIC -o jellyfish/.libs/parse_read.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -o jellyfish/parse_read.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/half.lo jellyfish/half.cpp libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -fPIC -DPIC -o jellyfish/.libs/half.o In file included from jellyfish/half.cpp:48: ./jellyfish/half.h: In constructor ‘half::half(float)’: ./jellyfish/half.h:471:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 471 | register int e = (x.i >> 23) & 0x000001ff; | ^ ./jellyfish/half.h:482:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 482 | register int m = x.i & 0x007fffff; | ^ jellyfish/half.cpp: In static member function ‘static short int half::convert(int)’: jellyfish/half.cpp:98:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 98 | register int s = (i >> 16) & 0x00008000; | ^ jellyfish/half.cpp:99:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 99 | register int e = ((i >> 23) & 0x000000ff) - (127 - 15); | ^ jellyfish/half.cpp:100:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 100 | register int m = i & 0x007fffff; | ^ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -o jellyfish/half.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mapped_file.lo jellyfish/mapped_file.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -fPIC -DPIC -o jellyfish/.libs/mapped_file.o In file included from ./jellyfish/mapped_file.hpp:29, from jellyfish/mapped_file.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -o jellyfish/mapped_file.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_dna.lo jellyfish/parse_dna.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_dna.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -o jellyfish/parse_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_quake.lo jellyfish/parse_quake.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -fPIC -DPIC -o jellyfish/.libs/parse_quake.o In file included from ./jellyfish/double_fifo_input.hpp:23, from ./jellyfish/parse_quake.hpp:22, from jellyfish/parse_quake.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]’ jellyfish/parse_quake.cc:27:40: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -o jellyfish/parse_quake.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_qual_dna.lo jellyfish/parse_qual_dna.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_qual_dna.o In file included from ./jellyfish/double_fifo_input.hpp:23, from ./jellyfish/parse_qual_dna.hpp:22, from jellyfish/parse_qual_dna.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]’ jellyfish/parse_qual_dna.cc:27:55: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -o jellyfish/parse_qual_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/sequence_parser.lo jellyfish/sequence_parser.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -fPIC -DPIC -o jellyfish/.libs/sequence_parser.o In file included from ./jellyfish/sequence_parser.hpp:21, from jellyfish/sequence_parser.cc:18: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/sequence_parser.cc:32:5: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -o jellyfish/sequence_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/seq_qual_parser.lo jellyfish/seq_qual_parser.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -fPIC -DPIC -o jellyfish/.libs/seq_qual_parser.o In file included from ./jellyfish/seq_qual_parser.hpp:21, from jellyfish/seq_qual_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/seq_qual_parser.cc:31:5: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_seq_qual_parser::FastqSeqQualParserError]’: jellyfish/seq_qual_parser.cc:47:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -o jellyfish/seq_qual_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/backtrace.lo jellyfish/backtrace.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -fPIC -DPIC -o jellyfish/.libs/backtrace.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -o jellyfish/backtrace.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/floats.lo jellyfish/floats.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -fPIC -DPIC -o jellyfish/.libs/floats.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -o jellyfish/floats.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dbg.lo jellyfish/dbg.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -fPIC -DPIC -o jellyfish/.libs/dbg.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -o jellyfish/dbg.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/allocators_mmap.lo jellyfish/allocators_mmap.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -fPIC -DPIC -o jellyfish/.libs/allocators_mmap.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -o jellyfish/allocators_mmap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dna_codes.lo jellyfish/dna_codes.cc libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -fPIC -DPIC -o jellyfish/.libs/dna_codes.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -o jellyfish/dna_codes.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link x86_64-linux-gnu-g++ -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:1:0 -Wl,-z,relro -Wl,-z,now -o libjellyfish-1.1.la -rpath /usr/lib/x86_64-linux-gnu jellyfish/square_binary_matrix.lo jellyfish/err.lo jellyfish/misc.lo jellyfish/storage.lo jellyfish/thread_exec.lo jellyfish/time.lo jellyfish/file_parser.lo jellyfish/read_parser.lo jellyfish/parse_read.lo jellyfish/half.lo jellyfish/mapped_file.lo jellyfish/parse_dna.lo jellyfish/parse_quake.lo jellyfish/parse_qual_dna.lo jellyfish/sequence_parser.lo jellyfish/seq_qual_parser.lo jellyfish/backtrace.lo jellyfish/floats.lo jellyfish/dbg.lo jellyfish/allocators_mmap.lo jellyfish/dna_codes.lo libtool: link: x86_64-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc-cross/x86_64-linux-gnu/13/../../../../x86_64-linux-gnu/lib/../lib/crti.o /usr/lib/gcc-cross/x86_64-linux-gnu/13/crtbeginS.o jellyfish/.libs/square_binary_matrix.o jellyfish/.libs/err.o jellyfish/.libs/misc.o jellyfish/.libs/storage.o jellyfish/.libs/thread_exec.o jellyfish/.libs/time.o jellyfish/.libs/file_parser.o jellyfish/.libs/read_parser.o jellyfish/.libs/parse_read.o jellyfish/.libs/half.o jellyfish/.libs/mapped_file.o jellyfish/.libs/parse_dna.o jellyfish/.libs/parse_quake.o jellyfish/.libs/parse_qual_dna.o jellyfish/.libs/sequence_parser.o jellyfish/.libs/seq_qual_parser.o jellyfish/.libs/backtrace.o jellyfish/.libs/floats.o jellyfish/.libs/dbg.o jellyfish/.libs/allocators_mmap.o jellyfish/.libs/dna_codes.o -L/usr/lib/gcc-cross/x86_64-linux-gnu/13 -L/usr/lib/gcc-cross/x86_64-linux-gnu/13/../../../../x86_64-linux-gnu/lib/../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc-cross/x86_64-linux-gnu/13/../../../../x86_64-linux-gnu/lib -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc-cross/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc-cross/x86_64-linux-gnu/13/../../../../x86_64-linux-gnu/lib/../lib/crtn.o -g -O3 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libjellyfish-1.1.so.1 -o .libs/libjellyfish-1.1.so.1.0.1 libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so.1" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so.1") libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so") libtool: link: x86_64-linux-gnu-ar cr .libs/libjellyfish-1.1.a jellyfish/square_binary_matrix.o jellyfish/err.o jellyfish/misc.o jellyfish/storage.o jellyfish/thread_exec.o jellyfish/time.o jellyfish/file_parser.o jellyfish/read_parser.o jellyfish/parse_read.o jellyfish/half.o jellyfish/mapped_file.o jellyfish/parse_dna.o jellyfish/parse_quake.o jellyfish/parse_qual_dna.o jellyfish/sequence_parser.o jellyfish/seq_qual_parser.o jellyfish/backtrace.o jellyfish/floats.o jellyfish/dbg.o jellyfish/allocators_mmap.o jellyfish/dna_codes.o libtool: link: x86_64-linux-gnu-ranlib .libs/libjellyfish-1.1.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-1.1.la" && ln -s "../libjellyfish-1.1.la" "libjellyfish-1.1.la" ) /bin/bash ./libtool --tag=CXX --mode=link x86_64-linux-gnu-g++ -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,--as-needed -latomic -Wl,-z,relro -Wl,-z,now -o bin/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o libjellyfish-1.1.la libtool: link: x86_64-linux-gnu-g++ -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o -lpthread -latomic ./.libs/libjellyfish-1.1.so make[3]: Leaving directory '/<>' x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc In file included from jellyfish/generate_sequence.cc:22: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from jellyfish/generate_sequence.cc:24: In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘int main(int, char**)’ at jellyfish/generate_sequence.cc:76:39: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/generate_sequence.cc:23: ./jellyfish/misc.hpp: In function ‘int main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘int main(int, char**)’ at jellyfish/generate_sequence.cc:76:57: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function ‘int main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const uint64_t*, int)’ at ./jellyfish/square_binary_matrix.hpp:71:80, inlined from ‘int main(int, char**)’ at jellyfish/generate_sequence.cc:80:13: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function ‘int main(int, char**)’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp /bin/bash ./libtool --tag=CXX --mode=link x86_64-linux-gnu-g++ -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -Wl,-z,now -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o libjellyfish-1.1.la libtool: link: x86_64-linux-gnu-g++ -g -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o -lpthread ./.libs/libjellyfish-1.1.so x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_square_binary_matrix.o `test -f 'unit_tests/test_square_binary_matrix.cc' || echo './'`unit_tests/test_square_binary_matrix.cc unit_tests/test_square_binary_matrix.cc: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: unit_tests/test_square_binary_matrix.cc:81:48: warning: catching polymorphic type ‘class SquareBinaryMatrix::SingularMatrix’ by value [-Wcatch-value=] 81 | } catch(SquareBinaryMatrix::SingularMatrix e) { | ^ In file included from ./jellyfish/square_binary_matrix.hpp:27, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’ at unit_tests/test_square_binary_matrix.cc:32:34: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from ./jellyfish/square_binary_matrix.hpp:28: ./jellyfish/misc.hpp: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’ at unit_tests/test_square_binary_matrix.cc:37:33: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’ at unit_tests/test_square_binary_matrix.cc:38:35: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’ at unit_tests/test_square_binary_matrix.cc:47:31: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’ at unit_tests/test_square_binary_matrix.cc:48:13: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’ at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’ at unit_tests/test_square_binary_matrix.cc:52:32: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In member function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’, inlined from ‘SquareBinaryMatrix::SquareBinaryMatrix(int)’ at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’ at unit_tests/test_square_binary_matrix.cc:73:32: ./jellyfish/square_binary_matrix.hpp:44:5: warning: ‘*&ptr’ may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_main_a-gtest_main.o `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_a-gtest-all.o `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc In file included from ./unit_tests/gtest/include/gtest/internal/gtest-internal.h:40, from ./unit_tests/gtest/include/gtest/gtest.h:57, from unit_tests/gtest/src/gtest-all.cc:39: ./unit_tests/gtest/include/gtest/internal/gtest-port.h: In static member function ‘static const char* testing::internal::String::CloneCString(const char*)’: ./unit_tests/gtest/include/gtest/internal/gtest-port.h:1615:17: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 1615 | return strncpy(dest, src, n); | ^ In file included from unit_tests/gtest/src/gtest-all.cc:42: ./unit_tests/gtest/src/gtest.cc:851:39: note: length computed here 851 | NULL : CloneString(c_str, strlen(c_str)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ rm -f libgtest.a x86_64-linux-gnu-ar cru libgtest.a unit_tests/gtest/src/libgtest_a-gtest-all.o x86_64-linux-gnu-ar: `u' modifier ignored since `D' is the default (see `U') x86_64-linux-gnu-ranlib libgtest.a rm -f libgtest_main.a x86_64-linux-gnu-ar cru libgtest_main.a unit_tests/gtest/src/libgtest_main_a-gtest_main.o libgtest.a x86_64-linux-gnu-ar: `u' modifier ignored since `D' is the default (see `U') x86_64-linux-gnu-ranlib libgtest_main.a /bin/bash ./libtool --tag=CXX --mode=link x86_64-linux-gnu-g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -Wl,-z,now -o bin/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o libgtest_main.a libgtest.a libjellyfish-1.1.la libtool: link: x86_64-linux-gnu-g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o -lpthread libgtest_main.a libgtest.a ./.libs/libjellyfish-1.1.so make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install --destdir=debian/tmp make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-1.1.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.so.1.0.1 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1 || { rm -f libjellyfish-1.1.so.1 && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so || { rm -f libjellyfish-1.1.so && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.lai /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.la libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: install: x86_64-linux-gnu-ranlib /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<>/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-1.1.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /<>/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/install -c -m 644 jellyfish/allocators_malloc.hpp jellyfish/allocators_mmap.hpp jellyfish/allocators_shm.hpp jellyfish/atomic_gcc.hpp jellyfish/compacted_dumper.hpp jellyfish/compacted_hash.hpp jellyfish/concurrent_queues.hpp jellyfish/direct_indexing_array.hpp jellyfish/direct_sorted_dumper.hpp jellyfish/divisor.hpp jellyfish/dumper.hpp jellyfish/hash_function.hpp jellyfish/hash.hpp jellyfish/heap.hpp jellyfish/invertible_hash_array.hpp jellyfish/locking_hash_counters.hpp jellyfish/locks_pthread.hpp jellyfish/mapped_file.hpp jellyfish/mer_counting.hpp jellyfish/err.hpp jellyfish/misc.hpp jellyfish/offsets_key_value.hpp jellyfish/reversible_hash_function.hpp jellyfish/sorted_dumper.hpp jellyfish/square_binary_matrix.hpp jellyfish/storage.hpp jellyfish/thread_exec.hpp jellyfish/time.hpp jellyfish/token_ring.hpp jellyfish/raw_dumper.hpp jellyfish/capped_integer.hpp jellyfish/aligned_values_array.hpp jellyfish/fastq_dumper.hpp jellyfish/floats.hpp jellyfish/circular_buffer.hpp jellyfish/counter.hpp jellyfish/parse_quake.hpp jellyfish/parse_dna.hpp jellyfish/parse_qual_dna.hpp jellyfish/file_parser.hpp '/<>/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/install -c -m 644 jellyfish/sequence_parser.hpp jellyfish/seq_qual_parser.hpp jellyfish/double_fifo_input.hpp jellyfish/read_parser.hpp jellyfish/parse_read.hpp jellyfish/simple_growing_array.hpp jellyfish/toFloat.h jellyfish/eLut.h jellyfish/dbg.hpp jellyfish/half.h jellyfish/backtrace.hpp jellyfish/dna_codes.hpp jellyfish/simple_circular_buffer.hpp '/<>/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-1.1.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' mkdir -p debian/tmp/usr/lib/jellyfish1 mv debian/tmp/usr/bin/* debian/tmp/usr/lib/jellyfish1 dh_install find debian -name "*.a" -delete find debian -name "*.la" -delete find debian -name "*.so" -delete find debian -name "pkgconfig" -type d | xargs rm -rf # there is no development package for this version any more - remove header files to keep dh_missing happy rm -rf debian/tmp/usr/include/jellyfish* make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman mv debian/jellyfish1/usr/share/man/man1/jellyfish.1 debian/jellyfish1/usr/share/man/man1/jellyfish1.1 make[1]: Leaving directory '/<>' dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-8_amd64.deb'. dpkg-deb: building package 'jellyfish1-dbgsym' in '../jellyfish1-dbgsym_1.1.11-8_amd64.deb'. dpkg-genbuildinfo --build=any -O../jellyfish1_1.1.11-8_amd64.buildinfo dpkg-genchanges --build=any -O../jellyfish1_1.1.11-8_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-08-18T03:42:50Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ jellyfish1_1.1.11-8_amd64.changes: ---------------------------------- Format: 1.8 Date: Tue, 05 Apr 2022 15:32:32 +0200 Source: jellyfish1 Binary: jellyfish1 jellyfish1-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 1.1.11-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: jellyfish1 - count k-mers in DNA sequences Closes: 1008944 Changes: jellyfish1 (1.1.11-8) unstable; urgency=medium . * Restrict architectures to 64bit Closes: #1008944 Checksums-Sha1: 08a18b9f065a33911993f68eb3c9111da7a36fc4 1190704 jellyfish1-dbgsym_1.1.11-8_amd64.deb fd6adfdb6ba8ed945d033cd5895b20c9ce50e470 5116 jellyfish1_1.1.11-8_amd64.buildinfo 22d4c4e3bb51401366c5b8ee8ed51ccdbca8b5a9 135512 jellyfish1_1.1.11-8_amd64.deb Checksums-Sha256: d16b804470de1df757ccfd6413e84878f3d014f076a7dcc46c6c87a9de6ed7cd 1190704 jellyfish1-dbgsym_1.1.11-8_amd64.deb afa286da0527bdd2a0dd8e20336b9afe00e7c6262d852dda781f53716332e66e 5116 jellyfish1_1.1.11-8_amd64.buildinfo 1c1ffa0a5dcfc0f43600f47f14832f2f3648ea311f3be6905ef746c9f952aa24 135512 jellyfish1_1.1.11-8_amd64.deb Files: 4c3e0b2d3700ef147298ef27854aa461 1190704 debug optional jellyfish1-dbgsym_1.1.11-8_amd64.deb e9ac1c744cddbfc5ad9d5166bb4de1ed 5116 science optional jellyfish1_1.1.11-8_amd64.buildinfo 09bd05685c4630865fc04af8d9e82f80 135512 science optional jellyfish1_1.1.11-8_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: jellyfish1 Binary: jellyfish1 jellyfish1-dbgsym Architecture: amd64 Version: 1.1.11-8 Checksums-Md5: 4c3e0b2d3700ef147298ef27854aa461 1190704 jellyfish1-dbgsym_1.1.11-8_amd64.deb 09bd05685c4630865fc04af8d9e82f80 135512 jellyfish1_1.1.11-8_amd64.deb Checksums-Sha1: 08a18b9f065a33911993f68eb3c9111da7a36fc4 1190704 jellyfish1-dbgsym_1.1.11-8_amd64.deb 22d4c4e3bb51401366c5b8ee8ed51ccdbca8b5a9 135512 jellyfish1_1.1.11-8_amd64.deb Checksums-Sha256: d16b804470de1df757ccfd6413e84878f3d014f076a7dcc46c6c87a9de6ed7cd 1190704 jellyfish1-dbgsym_1.1.11-8_amd64.deb 1c1ffa0a5dcfc0f43600f47f14832f2f3648ea311f3be6905ef746c9f952aa24 135512 jellyfish1_1.1.11-8_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Fri, 18 Aug 2023 03:42:49 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-13), autotools-dev (= 20220109.1), base-files (= 13), base-passwd (= 3.6.1), bash (= 5.2.15-2+b4), binutils (= 2.41-4), binutils-aarch64-linux-gnu (= 2.41-4), binutils-common (= 2.41-4), bsdextrautils (= 2.39.1-4), bsdutils (= 1:2.39.1-4), build-essential (= 12.10), bzip2 (= 1.0.8-5+b1), coreutils (= 9.1-1), cpp (= 4:13.2.0-1), cpp-13 (= 13.2.0-2), dash (= 0.5.12-6), debconf (= 1.5.82), debhelper (= 13.11.5), debianutils (= 5.8-1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.21.22), dpkg-dev (= 1.21.22), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-5), g++ (= 4:13.2.0-1), g++-13 (= 13.2.0-2), gcc (= 4:13.2.0-1), gcc-13 (= 13.2.0-2), gcc-13-base (= 13.2.0-2), gettext (= 0.21-13), gettext-base (= 0.21-13), grep (= 3.11-2), groff-base (= 1.23.0-2), gzip (= 1.12-1), hostname (= 3.23+nmu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.2.0-2), libatomic1 (= 13.2.0-2), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1), libaudit1 (= 1:3.1.1-1), libbinutils (= 2.41-4), libblkid1 (= 2.39.1-4), libbz2-1.0 (= 1.0.8-5+b1), libc-bin (= 2.37-7), libc-dev-bin (= 2.37-7), libc6 (= 2.37-7), libc6-dev (= 2.37-7), libcap-ng0 (= 0.8.3-1+b3), libcap2 (= 1:2.66-4), libcc1-0 (= 13.2.0-2), libcom-err2 (= 1.47.0-2), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41-4), libctf0 (= 2.41-4), libdb5.3 (= 5.3.28+dfsg2-2), libdebconfclient0 (= 0.270), libdebhelper-perl (= 13.11.5), libdpkg-perl (= 1.21.22), libelf1 (= 0.189-4), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-2), libgcc-s1 (= 13.2.0-2), libgcrypt20 (= 1.10.2-2), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.3.0+dfsg-2), libgomp1 (= 13.2.0-2), libgpg-error0 (= 1.47-2), libgprofng0 (= 2.41-4), libgssapi-krb5-2 (= 1.20.1-3), libhwasan0 (= 13.2.0-2), libicu72 (= 72.1-3), libisl23 (= 0.26-3), libitm1 (= 13.2.0-2), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-3), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-3), libkrb5support0 (= 1.20.1-3), liblsan0 (= 13.2.0-2), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.1.0-1), libmount1 (= 2.39.1-4), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libnumber-compare-perl (= 0.03-3), libpam-modules (= 1.5.2-7), libpam-modules-bin (= 1.5.2-7), libpam-runtime (= 1.5.2-7), libpam0g (= 1.5.2-7), libpcre2-8-0 (= 10.42-2), libperl5.36 (= 5.36.0-7), libpipeline1 (= 1.5.7-1), libquadmath0 (= 13.2.0-2), libseccomp2 (= 2.5.4-1+b3), libselinux1 (= 3.5-1), libsframe1 (= 2.41-4), libsmartcols1 (= 2.39.1-4), libssl3 (= 3.0.10-1), libstdc++-13-dev (= 13.2.0-2), libstdc++6 (= 13.2.0-2), libsub-override-perl (= 0.09-4), libsystemd0 (= 254.1-2), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.4+20230625-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-7), libtsan2 (= 13.2.0-2), libubsan1 (= 13.2.0-2), libuchardet0 (= 0.0.7-1), libudev1 (= 254.1-2), libunistring2 (= 1.0-2), libuuid1 (= 2.39.1-4), libxml2 (= 2.9.14+dfsg-1.3), libzstd1 (= 1.5.5+dfsg2-1), linux-libc-dev (= 6.4.4-3), login (= 1:4.13+dfsg1-1+b1), m4 (= 1.4.19-3), make (= 4.3-4.1), man-db (= 2.11.2-3), mawk (= 1.3.4.20230730-1), ncurses-base (= 6.4+20230625-2), ncurses-bin (= 6.4+20230625-2), patch (= 2.7.6-7), perl (= 5.36.0-7), perl-base (= 5.36.0-7), perl-modules-5.36 (= 5.36.0-7), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.07-1), tar (= 1.34+dfsg-1.2), usrmerge (= 35), util-linux (= 2.39.1-4), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-3) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649165552" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ jellyfish1-dbgsym_1.1.11-8_amd64.deb ------------------------------------ new Debian package, version 2.0. size 1190704 bytes: control archive=648 bytes. 426 bytes, 12 lines control 299 bytes, 3 lines md5sums Package: jellyfish1-dbgsym Source: jellyfish1 Version: 1.1.11-8 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1261 Depends: jellyfish1 (= 1.1.11-8) Section: debug Priority: optional Description: debug symbols for jellyfish1 Build-Ids: 0dc06d595c7ee19f99abf21fbc2db0c919935f32 c75152e34cf85b7a79c03a395b9ade1f7da37b1a drwxr-xr-x root/root 0 2022-04-05 13:32 ./ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/debug/.build-id/0d/ -rw-r--r-- root/root 254168 2022-04-05 13:32 ./usr/lib/debug/.build-id/0d/c06d595c7ee19f99abf21fbc2db0c919935f32.debug drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/debug/.build-id/c7/ -rw-r--r-- root/root 994328 2022-04-05 13:32 ./usr/lib/debug/.build-id/c7/5152e34cf85b7a79c03a395b9ade1f7da37b1a.debug drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 27240 2022-04-05 13:32 ./usr/lib/debug/.dwz/x86_64-linux-gnu/jellyfish1.debug drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-04-05 13:32 ./usr/share/doc/jellyfish1-dbgsym -> jellyfish1 jellyfish1_1.1.11-8_amd64.deb ----------------------------- new Debian package, version 2.0. size 135512 bytes: control archive=1352 bytes. 1312 bytes, 28 lines control 504 bytes, 7 lines md5sums 42 bytes, 1 lines shlibs 68 bytes, 2 lines triggers Package: jellyfish1 Version: 1.1.11-8 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 647 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1) Enhances: kraken Section: science Priority: optional Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Description: count k-mers in DNA sequences JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This is the latest version of the 1.x series of jellyfish which is used by some other applications that are not compatible with version 2.x which is provided inside the jellyfish package. drwxr-xr-x root/root 0 2022-04-05 13:32 ./ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/bin/ lrwxrwxrwx root/root 0 2022-04-05 13:32 ./usr/bin/jellyfish1 -> ../lib/jellyfish1/jellyfish drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/jellyfish1/ -rwxr-xr-x root/root 260736 2022-04-05 13:32 ./usr/lib/jellyfish1/jellyfish drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2022-04-05 13:32 ./usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1 -> libjellyfish-1.1.so.1.0.1 -rw-r--r-- root/root 368848 2022-04-05 13:32 ./usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/doc/jellyfish1/ -rw-r--r-- root/root 2333 2013-05-29 19:45 ./usr/share/doc/jellyfish1/README -rw-r--r-- root/root 613 2022-04-05 13:32 ./usr/share/doc/jellyfish1/changelog.Debian.gz -rw-r--r-- root/root 2337 2022-04-05 13:32 ./usr/share/doc/jellyfish1/copyright drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 66 2022-04-05 13:32 ./usr/share/lintian/overrides/jellyfish1 drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/man/ drwxr-xr-x root/root 0 2022-04-05 13:32 ./usr/share/man/man1/ -rw-r--r-- root/root 4556 2022-04-05 13:32 ./usr/share/man/man1/jellyfish1.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1296 B] Get:5 copy:/<>/apt_archive ./ Packages [1375 B] Fetched 3286 B in 0s (186 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl libio-compress-brotli-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:amd64 t1utils unzip 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 13.5 MB of archives. After this operation, 53.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.0.10-1 [1382 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20230311 [153 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.65-1 [31.2 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libassuan0 arm64 2.5.6-1 [47.3 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.2.40-1.1 [557 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.42.0-1 [803 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.2.40-1.1 [903 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.15.0-1 [2906 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.40+b2 [66.1 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b1 [10.4 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.008-2 [15.9 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b1 [22.9 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:23 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.63-1+b1 [42.8 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.64-2+b1 [121 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.19-2 [91.0 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.81-1 [98.6 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.57-1 [221 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:32 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b1 [35.3 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.46-1 [13.5 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.29-1 [16.5 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-2+b1 [24.2 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:41 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.37-1 [129 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.58-2 [43.6 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-1+b1 [34.0 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b1 [98.8 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.83-2+b1 [24.2 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b1 [28.3 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 6.44-2 [81.8 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B] Get:73 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.92-2+b1 [308 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.083-1 [218 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.22-1 [25.3 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.11-1 [10.5 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.72-1 [187 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.023-2 [11.0 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.13-6 [39.0 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB] Get:90 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:96 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.5.10-1+b3 [167 kB] Get:97 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-3 [10.9 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.27-1 [12.3 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:101 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b1 [17.1 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1 [11.2 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.636-1 [42.3 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.004+ds-1 [95.4 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.004+ds-1 [97.2 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:109 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.38-1 [58.7 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.29-1 [28.5 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b1 [24.1 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b1 [8396 B] Get:113 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.16-1 [13.0 kB] Get:114 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-1+b2 [196 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.44-2+b1 [72.2 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.62-2 [19.9 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.17-1 [116 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.86+ds-1 [32.8 kB] Get:121 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.10-6 [58.0 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get:126 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.5 MB in 0s (51.8 MB/s) Selecting previously unselected package netbase. (Reading database ... 16728 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.10-1_arm64.deb ... Unpacking openssl (3.0.10-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.65-1_arm64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../005-libassuan0_2.5.6-1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.6-1) ... Selecting previously unselected package libreadline8:arm64. 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Setting up plzip (1.10-6) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-2) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:arm64 (0.46-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:arm64 (4.37-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-28) ... Setting up libsqlite3-0:arm64 (3.42.0-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.86+ds-1) ... Setting up libio-interactive-perl (1.023-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:arm64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:arm64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:arm64 (2.5.6-1) ... Setting up libconfig-tiny-perl (2.29-1) ... Setting up libsereal-encoder-perl (5.004+ds-1) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004005-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.38-1) ... Setting up libipc-system-simple-perl (1.30-2) ... 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Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.10-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up readline-common (8.2-1.3) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1) ... Setting up libmarkdown2:arm64 (2.2.7-2) ... Setting up liburi-perl (5.19-2) ... Setting up iso-codes (4.15.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:arm64 (1.92-2+b1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libnet-http-perl (6.22-1) ... Setting up libtext-markdown-discount-perl (0.16-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:arm64 (0.008-2) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:arm64 (3.81-1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up libio-socket-ssl-perl (2.083-1) ... Setting up gpg (2.2.40-1.1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.44-2) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:arm64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.57-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.58-2) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.72-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.17-1) ... Setting up liblwp-protocol-https-perl (6.11-1) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.37-7) ... Processing triggers for man-db (2.11.2-3) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 58004 Build-Time: 325 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 50 Job: jellyfish1_1.1.11-8 Lintian: pass Machine Architecture: arm64 Package: jellyfish1 Package-Time: 413 Source-Version: 1.1.11-8 Space: 58004 Status: successful Version: 1.1.11-8 -------------------------------------------------------------------------------- Finished at 2023-08-18T03:42:50Z Build needed 00:06:53, 58004k disk space