sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir +==============================================================================+ | bedops 2.4.40+dfsg-1 (amd64) Wed, 27 Oct 2021 02:34:33 +0000 | +==============================================================================+ Package: bedops Version: 2.4.40+dfsg-1 Source Version: 2.4.40+dfsg-1 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-c4d4a529-dec5-4995-9321-05fdacfd73fb' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-tEXlxQ/resolver-VLAyoZ' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [165 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:4 http://mirror.einval.org/debian sid/main amd64 Packages [8792 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9295 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8658 kB] Fetched 26.9 MB in 7s (3803 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'bedops' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bedops.git Please use: git clone https://salsa.debian.org/med-team/bedops.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.5 MB of source archives. Get:1 http://mirror.einval.org/debian sid/main bedops 2.4.40+dfsg-1 (dsc) [2178 B] Get:2 http://mirror.einval.org/debian sid/main bedops 2.4.40+dfsg-1 (tar) [13.4 MB] Get:3 http://mirror.einval.org/debian sid/main bedops 2.4.40+dfsg-1 (diff) [10.3 kB] Fetched 13.5 MB in 0s (39.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedops-tEXlxQ/bedops-2.4.40+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-tEXlxQ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, 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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [441 B] Get:5 copy:/<>/apt_archive ./ Packages [527 B] Fetched 1925 B in 0s (45.3 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... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-11-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-11-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-11-base:amd64 gcc-11-cross-base gcc-11-x86-64-linux-gnu gcc-11-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:amd64 libasan6-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbz2-1.0:amd64 libbz2-dev:amd64 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 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:amd64 libgcc-11-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libicu67 libio-string-perl libitm1:amd64 libitm1-amd64-cross libjansson-dev:amd64 libjansson4:amd64 libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1 libmpdec3 libncursesw6 libnsl-dev:amd64 libnsl2:amd64 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 libsigsegv2 libsqlite3-0 libssl1.1:amd64 libstdc++-11-dev:amd64 libstdc++-11-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan0:amd64 libtsan0-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 media-types po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.9 python3.9-minimal readline-common sensible-utils ucf zlib1g:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-11-locales cpp-doc dh-make binutils-multiarch g++-11-multilib-x86-64-linux-gnu gcc-11-doc gcc-11-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++-11-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx bzip2-doc:amd64 libidn2-0:amd64 libarchive-cpio-perl krb5-locales:amd64 libgpm2 ca-certificates 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-11-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-11-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-11-base:amd64 gcc-11-cross-base gcc-11-x86-64-linux-gnu gcc-11-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:amd64 libasan6-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbz2-1.0:amd64 libbz2-dev:amd64 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 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:amd64 libgcc-11-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libicu67 libio-string-perl libitm1:amd64 libitm1-amd64-cross libjansson-dev:amd64 libjansson4:amd64 libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1 libmpdec3 libncursesw6 libnsl-dev:amd64 libnsl2:amd64 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 libsigsegv2 libsqlite3-0 libssl1.1:amd64 libstdc++-11-dev:amd64 libstdc++-11-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan0:amd64 libtsan0-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 media-types po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.9 python3.9-minimal readline-common sbuild-build-depends-main-dummy:amd64 sensible-utils ucf zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 125 newly installed, 0 to remove and 0 not upgraded. Need to get 220 MB of archives. After this operation, 806 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [956 B] Get:2 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.37.2-4 [143 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-7 [883 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libpython3.9-minimal arm64 3.9.7-4 [800 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.4.1-3 [89.8 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 python3.9-minimal arm64 3.9.7-4 [1885 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 media-types all 4.0.0 [30.3 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libmpdec3 arm64 2.5.1-2 [84.4 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libncursesw6 arm64 6.2+20210905-1 [122 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 readline-common all 8.1-2 [73.8 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1-2 [160 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.36.0-2 [768 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libpython3.9-stdlib arm64 3.9.7-4 [1663 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 python3.9 arm64 3.9.7-4 [480 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get:22 http://mirror.einval.org/debian sid/main amd64 gcc-11-base amd64 11.2.0-10 [206 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.17 [21.5 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.39-3 [69.1 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-4 [173 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.5-1 [823 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-4 [510 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 gcc-11-x86-64-linux-gnu-base arm64 11.2.0-9cross1 [205 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 cpp-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [48.2 MB] Get:37 http://mirror.einval.org/debian sid/main arm64 cpp-x86-64-linux-gnu arm64 4:11.2.0-2 [17.0 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 binutils-x86-64-linux-gnu arm64 2.37-7 [2046 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 gcc-11-cross-base all 11.2.0-9cross1 [201 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-amd64-cross all 11.2.0-9cross1 [42.0 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libgomp1-amd64-cross all 11.2.0-9cross1 [104 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libitm1-amd64-cross all 11.2.0-9cross1 [25.5 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libatomic1-amd64-cross all 11.2.0-9cross1 [8764 B] Get:45 http://mirror.einval.org/debian sid/main arm64 libasan6-amd64-cross all 11.2.0-9cross1 [2044 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 liblsan0-amd64-cross all 11.2.0-9cross1 [885 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libtsan0-amd64-cross all 11.2.0-9cross1 [2010 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libc6-amd64-cross all 2.32-1cross4 [1570 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libstdc++6-amd64-cross all 11.2.0-9cross1 [535 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libubsan1-amd64-cross all 11.2.0-9cross1 [834 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libquadmath0-amd64-cross all 11.2.0-9cross1 [145 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libgcc-11-dev-amd64-cross all 11.2.0-9cross1 [2357 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 gcc-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [54.7 MB] Get:54 http://mirror.einval.org/debian sid/main arm64 gcc-x86-64-linux-gnu arm64 4:11.2.0-2 [1460 B] Get:55 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-amd64-cross all 5.10.46-4cross4 [1468 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libc6-dev-amd64-cross all 2.32-1cross4 [2248 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libstdc++-11-dev-amd64-cross all 11.2.0-9cross1 [1952 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 g++-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [52.2 MB] Get:59 http://mirror.einval.org/debian sid/main arm64 g++-x86-64-linux-gnu arm64 4:11.2.0-2 [1176 B] Get:60 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.12+dfsg-5 [632 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-amd64 all 12.9 [6708 B] Get:76 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.5.2 [192 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.6-15 [513 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.12.0-2 [15.5 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.185-2 [171 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-4 [1261 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.5.2 [1056 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 help2man arm64 1.48.5 [143 kB] Get:90 http://mirror.einval.org/debian sid/main amd64 libgcc-s1 amd64 11.2.0-10 [42.0 kB] Get:91 http://mirror.einval.org/debian sid/main amd64 libc6 amd64 2.32-4 [2820 kB] Get:92 http://mirror.einval.org/debian sid/main amd64 libasan6 amd64 11.2.0-10 [2050 kB] Get:93 http://mirror.einval.org/debian sid/main amd64 libatomic1 amd64 11.2.0-10 [9052 B] Get:94 http://mirror.einval.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-4 [45.8 kB] Get:95 http://mirror.einval.org/debian sid/main amd64 linux-libc-dev amd64 5.14.12-1 [1434 kB] Get:96 http://mirror.einval.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.25-2 [89.2 kB] Get:97 http://mirror.einval.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.25-2 [104 kB] Get:98 http://mirror.einval.org/debian sid/main amd64 libcom-err2 amd64 1.46.4-1 [75.2 kB] Get:99 http://mirror.einval.org/debian sid/main amd64 libkrb5support0 amd64 1.18.3-7 [65.4 kB] Get:100 http://mirror.einval.org/debian sid/main amd64 libk5crypto3 amd64 1.18.3-7 [113 kB] Get:101 http://mirror.einval.org/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:102 http://mirror.einval.org/debian sid/main amd64 libssl1.1 amd64 1.1.1l-1 [1555 kB] Get:103 http://mirror.einval.org/debian sid/main amd64 libkrb5-3 amd64 1.18.3-7 [363 kB] Get:104 http://mirror.einval.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.18.3-7 [165 kB] Get:105 http://mirror.einval.org/debian sid/main amd64 libtirpc3 amd64 1.3.2-2 [83.9 kB] Get:106 http://mirror.einval.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:107 http://mirror.einval.org/debian sid/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB] Get:108 http://mirror.einval.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:109 http://mirror.einval.org/debian sid/main amd64 libc6-dev amd64 2.32-4 [2251 kB] Get:110 http://mirror.einval.org/debian sid/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get:111 http://mirror.einval.org/debian sid/main amd64 libgomp1 amd64 11.2.0-10 [106 kB] Get:112 http://mirror.einval.org/debian sid/main amd64 libitm1 amd64 11.2.0-10 [26.0 kB] Get:113 http://mirror.einval.org/debian sid/main amd64 liblsan0 amd64 11.2.0-10 [886 kB] Get:114 http://mirror.einval.org/debian sid/main amd64 libtsan0 amd64 11.2.0-10 [2019 kB] Get:115 http://mirror.einval.org/debian sid/main amd64 libstdc++6 amd64 11.2.0-10 [577 kB] Get:116 http://mirror.einval.org/debian sid/main amd64 libubsan1 amd64 11.2.0-10 [835 kB] Get:117 http://mirror.einval.org/debian sid/main amd64 libquadmath0 amd64 11.2.0-10 [145 kB] Get:118 http://mirror.einval.org/debian sid/main amd64 libgcc-11-dev amd64 11.2.0-10 [2357 kB] Get:119 http://mirror.einval.org/debian sid/main amd64 libjansson4 amd64 2.13.1-1.1 [39.7 kB] Get:120 http://mirror.einval.org/debian sid/main amd64 libjansson-dev amd64 2.13.1-1.1 [42.9 kB] Get:121 http://mirror.einval.org/debian sid/main amd64 libstdc++-11-dev amd64 11.2.0-10 [1952 kB] Get:122 http://mirror.einval.org/debian sid/main arm64 python3-lib2to3 all 3.9.7-1 [79.4 kB] Get:123 http://mirror.einval.org/debian sid/main arm64 python3-distutils all 3.9.7-1 [146 kB] Get:124 http://mirror.einval.org/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] Get:125 http://mirror.einval.org/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 220 MB in 3s (79.3 MB/s) Selecting previously unselected package bsdextrautils. 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Preparing to unpack .../105-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up gcc-11-base:amd64 (11.2.0-10) ... Setting up libfile-which-perl (1.23-1) ... Setting up linux-libc-dev-amd64-cross (5.10.46-4cross4) ... Setting up bsdextrautils (2.37.2-4) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.5.2) ... Setting up libsqlite3-0:arm64 (3.36.0-2) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up linux-libc-dev:amd64 (5.14.12-1) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up gettext-base (0.21-4) ... Setting up gcc-11-x86-64-linux-gnu-base:arm64 (11.2.0-9cross1) ... Setting up file (1:5.39-3) ... Setting up libyaml-perl (1.30-1) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libc6-amd64-cross (2.32-1cross4) ... Setting up libncursesw6:arm64 (6.2+20210905-1) ... Setting up gcc-11-cross-base (11.2.0-9cross1) ... Setting up sensible-utils (0.0.17) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-2) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgcc-s1-amd64-cross (11.2.0-9cross1) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up libelf1:arm64 (0.185-2) ... Setting up readline-common (8.1-2) ... Setting up libxml2:arm64 (2.9.12+dfsg-5) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libasan6-amd64-cross (11.2.0-9cross1) ... Setting up binutils-x86-64-linux-gnu (2.37-7) ... Setting up libstdc++6-amd64-cross (11.2.0-9cross1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up liblsan0-amd64-cross (11.2.0-9cross1) ... Setting up libc6-dev-amd64-cross (2.32-1cross4) ... Setting up libreadline8:arm64 (8.1-2) ... Setting up libtsan0-amd64-cross (11.2.0-9cross1) ... Setting up cpp-11-x86-64-linux-gnu (11.2.0-9cross1) ... Setting up m4 (1.4.18-5) ... Setting up libgomp1-amd64-cross (11.2.0-9cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.5) ... Setting up libitm1-amd64-cross (11.2.0-9cross1) ... Setting up libatomic1-amd64-cross (11.2.0-9cross1) ... Setting up libquadmath0-amd64-cross (11.2.0-9cross1) ... Setting up libubsan1-amd64-cross (11.2.0-9cross1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up libpython3.9-stdlib:arm64 (3.9.7-4) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up cpp-x86-64-linux-gnu (4:11.2.0-2) ... Setting up automake (1:1.16.5-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgcc-11-dev-amd64-cross (11.2.0-9cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... 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 dh-autoreconf (20) ... Setting up gcc-11-x86-64-linux-gnu (11.2.0-9cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+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++-11-dev-amd64-cross (11.2.0-9cross1) ... Setting up python3.9 (3.9.7-4) ... Setting up g++-11-x86-64-linux-gnu (11.2.0-9cross1) ... Setting up gcc-x86-64-linux-gnu (4:11.2.0-2) ... Setting up debhelper (13.5.2) ... Setting up python3 (3.9.2-3) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-x86-64-linux-gnu (4:11.2.0-2) ... Setting up python3-lib2to3 (3.9.7-1) ... Setting up python3-distutils (3.9.7-1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-amd64 (12.9) ... Setting up libgcc-s1:amd64 (11.2.0-10) ... Setting up libc6:amd64 (2.32-4) ... Setting up libbz2-1.0:amd64 (1.0.8-4) ... Setting up libstdc++6:amd64 (11.2.0-10) ... Setting up liblsan0:amd64 (11.2.0-10) ... Setting up libitm1:amd64 (11.2.0-10) ... Setting up libtsan0:amd64 (11.2.0-10) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up libssl1.1:amd64 (1.1.1l-1) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ... Setting up libcrypt1:amd64 (1:4.4.25-2) ... Setting up libcom-err2:amd64 (1.46.4-1) ... Setting up libgomp1:amd64 (11.2.0-10) ... Setting up libasan6:amd64 (11.2.0-10) ... Setting up libjansson4:amd64 (2.13.1-1.1) ... Setting up libkrb5support0:amd64 (1.18.3-7) ... Setting up libquadmath0:amd64 (11.2.0-10) ... Setting up libatomic1:amd64 (11.2.0-10) ... Setting up libk5crypto3:amd64 (1.18.3-7) ... Setting up libubsan1:amd64 (11.2.0-10) ... Setting up libgcc-11-dev:amd64 (11.2.0-10) ... Setting up libcrypt-dev:amd64 (1:4.4.25-2) ... Setting up libkrb5-3:amd64 (1.18.3-7) ... Setting up libjansson-dev:amd64 (2.13.1-1.1) ... Setting up libgssapi-krb5-2:amd64 (1.18.3-7) ... Setting up libtirpc3:amd64 (1.3.2-2) ... Setting up libtirpc-dev:amd64 (1.3.2-2) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.32-4) ... Setting up libbz2-dev:amd64 (1.0.8-4) ... Setting up libstdc++-11-dev:amd64 (11.2.0-10) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.32-4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64) Toolchain package versions: binutils_2.37-7 dpkg-dev_1.20.9 g++-11_11.2.0-10 gcc-11_11.2.0-10 libc6-dev_2.32-4 libstdc++-11-dev_11.2.0-10 libstdc++-11-dev-amd64-cross_11.2.0-9cross1 libstdc++6_11.2.0-10 libstdc++6-amd64-cross_11.2.0-9cross1 linux-libc-dev_5.14.12-1 Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-3+b2 binutils_2.37-7 binutils-aarch64-linux-gnu_2.37-7 binutils-common_2.37-7 binutils-x86-64-linux-gnu_2.37-7 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:11.2.0-2 cpp-11_11.2.0-10 cpp-11-x86-64-linux-gnu_11.2.0-9cross1 cpp-x86-64-linux-gnu_4:11.2.0-2 cross-config_2.6.18+nmu2 crossbuild-essential-amd64_12.9 dash_0.5.11+git20210120+802ebd4-2 debconf_1.5.78 debhelper_13.5.2 debian-archive-keyring_2021.1.1 debianutils_5.5-1 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dpkg_1.20.9 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.20.9 dwz_0.14-1 fakeroot_1.26-1 file_1:5.39-3 findutils_4.8.0-1 g++_4:11.2.0-2 g++-11_11.2.0-10 g++-11-x86-64-linux-gnu_11.2.0-9cross1 g++-x86-64-linux-gnu_4:11.2.0-2 gcc_4:11.2.0-2 gcc-10-base_10.3.0-11 gcc-11_11.2.0-10 gcc-11-base_11.2.0-10 gcc-11-cross-base_11.2.0-9cross1 gcc-11-x86-64-linux-gnu_11.2.0-9cross1 gcc-11-x86-64-linux-gnu-base_11.2.0-9cross1 gcc-x86-64-linux-gnu_4:11.2.0-2 gettext_0.21-4 gettext-base_0.21-4 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 help2man_1.48.5 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10 libasan6-amd64-cross_11.2.0-9cross1 libatomic1_11.2.0-10 libatomic1-amd64-cross_11.2.0-9cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-7 libblkid1_2.37.2-4 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.32-4 libc-dev-bin_2.32-4 libc6_2.32-4 libc6-amd64-cross_2.32-1cross4 libc6-dev_2.32-4 libc6-dev-amd64-cross_2.32-1cross4 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10 libcom-err2_1.46.4-1 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-7 libctf0_2.37-7 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdebian-dpkgcross-perl_2.6.18+nmu2 libdpkg-perl_1.20.9 libelf1_0.185-2 libexpat1_2.4.1-3 libfakeroot_1.26-1 libffi8_3.4.2-3 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.12.0-2 libfile-which-perl_1.23-1 libgcc-11-dev_11.2.0-10 libgcc-11-dev-amd64-cross_11.2.0-9cross1 libgcc-s1_11.2.0-10 libgcc-s1-amd64-cross_11.2.0-9cross1 libgcrypt20_1.9.4-3+b1 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10 libgomp1-amd64-cross_11.2.0-9cross1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhwasan0_11.2.0-10 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl23_0.24-2 libitm1_11.2.0-10 libitm1-amd64-cross_11.2.0-9cross1 libjansson-dev_2.13.1-1.1 libjansson4_2.13.1-1.1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 liblocale-gettext-perl_1.07-4+b1 liblsan0_11.2.0-10 liblsan0-amd64-cross_11.2.0-9cross1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncursesw6_6.2+20210905-1 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.3-1 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4 libpython3.9-stdlib_3.9.7-4 libquadmath0_11.2.0-10 libquadmath0-amd64-cross_11.2.0-9cross1 libreadline8_8.1-2 libseccomp2_2.5.2-2 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10 libstdc++-11-dev-amd64-cross_11.2.0-9cross1 libstdc++6_11.2.0-10 libstdc++6-amd64-cross_11.2.0-9cross1 libsub-override-perl_0.09-2 libsystemd0_249.5-1 libtasn1-6_4.17.0-2 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtsan0_11.2.0-10 libtsan0-amd64-cross_11.2.0-9cross1 libubsan1_11.2.0-10 libubsan1-amd64-cross_11.2.0-9cross1 libuchardet0_0.0.7-1 libudev1_249.5-1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml-libxml-perl_2.0134+dfsg-2+b1 libxml-namespacesupport-perl_1.12-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2 libyaml-perl_1.30-1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.14.12-1 linux-libc-dev-amd64-cross_5.10.46-4cross4 login_1:4.8.1-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-4 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-distutils_3.9.7-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3.9_3.9.7-4 python3.9-minimal_3.9.7-4 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 ucf_3.0043 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bedops Binary: bedops, bedops-doc Architecture: any all Version: 2.4.40+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Homepage: https://github.com/bedops/bedops Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/bedops Vcs-Git: https://salsa.debian.org/med-team/bedops.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev Build-Depends-Indep: sphinx-common, libjs-mathjax, python3-sphinx Package-List: bedops deb science optional arch=any bedops-doc deb doc optional arch=all Checksums-Sha1: d2819342382ce8a8d9519971bd5f6f09b46e53f6 13444448 bedops_2.4.40+dfsg.orig.tar.xz b87353f93d1ef742f06ad98e360a6dfa65d2f4ef 10264 bedops_2.4.40+dfsg-1.debian.tar.xz Checksums-Sha256: 014839e322e14715da2b8b6d879ed9600ef6b558c0bf860c04c64d49328dfc71 13444448 bedops_2.4.40+dfsg.orig.tar.xz 81af8570785380e094f2aaaef9f742f3404b70f01980a1d990de2be391633c1c 10264 bedops_2.4.40+dfsg-1.debian.tar.xz Files: e811a862f0a3c82ee3c4285ebec8393a 13444448 bedops_2.4.40+dfsg.orig.tar.xz 6cf3c54a2b54a622c50c2e42bdb0fe6f 10264 bedops_2.4.40+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmF1G4oSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxXgcQAJ4ugqYcEIJUI28KOfybiurOgzRjrR8u aq/V8bdyuKIVylcZTPfhttXBSANEZX00gYIOgLFd1l7yUuOzwdBBoh+HTBjn5GIi otGGxkGbkLSrV+AoAsXskEaAGtC4tU6yGTmP5Q9ChMH/38SEnG3iTdm4YS5v4bKz DSoxDBqNA8QNssnU1haJkSSDN3dnhFJR4W6XOzyeO3tiQ5XneyLhDAqH82JEAXs4 iWGTJwipFqJWcTgfZlVrSWgbuBDF3n0koygY0leqeM/6WQbSaNTeysYRVO+Mvpo3 OFQzC+e/25GY1aUB5DadthKSrOOSB0QA1eZP/nw2M9P9MAEXMWuXQabDSJt7umdz BQXJXzmeFTjOB2q/+7LsUkCce85nuq2vOyBi9Yk58vIqpRyeF9+JrvqmjKG2i8dR PvCf7GR1m3ocNDHgyNefyiVAedk3+f8tQBmu2SnmQUS2mW/cgkeRIko58JFyLs0A Ju8lH6gh22dovqAQMHKF3QveNZD8fXvIfqKOCi6EXnp8g/XYWpG/bD9sLzRTaAxM E7l0yNk4Y5tZqu3lzzxfqNR5WSr3bcNnNSsfaTuIs4SjRdQueq9yAS+9sn6/ziYF R7NmGCX20ZcdjoDmywzdBCBrejlxCNgx7ILDoIeeJVRsI4ylN5aETuv+daNv2Zzo I6vLn9aOWkUw =Qup3 -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.a5TMBDaO/trustedkeys.kbx': General error gpgv: Signature made Sun Oct 24 08:38:34 2021 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedops_2.4.40+dfsg-1.dsc dpkg-source: info: extracting bedops in /<> dpkg-source: info: unpacking bedops_2.4.40+dfsg.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.40+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests_use_installed_binaries.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying use_debian_libs dpkg-source: info: applying parallel.patch dpkg-source: info: applying adapt_to_new_sphinx.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ ulimit -c --------- 0 I: Finished running 'ulimit -c'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmutg PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=crossqa-sid SCHROOT_CHROOT_NAME=crossqa-sid SCHROOT_COMMAND=env SCHROOT_GID=1002 SCHROOT_GROUP=helmutg SCHROOT_SESSION_ID=crossqa-sid-c4d4a529-dec5-4995-9321-05fdacfd73fb SCHROOT_UID=1002 SCHROOT_USER=helmutg SHELL=/bin/sh USER=helmutg dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.40+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j1 clean make[2]: Entering directory '/<>' make clean -f system.mk/Makefile.linux make[3]: Entering directory '/<>' rm -rf bin rm -rf bin rm -rf bin rm -rf modules make -C applications/bed/bedextract/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedextract/src' rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedextract/src' make -C applications/bed/bedmap/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedmap/src' rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedmap/src' make -C applications/bed/bedops/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedops/src' rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedops/src' make -C applications/bed/closestfeats/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/closestfeats/src' rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/closestfeats/src' make -C applications/bed/conversion/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/conversion/src' rm -rf ../bin rm -rf objects rm -rf *.so *~ make[4]: Leaving directory '/<>/applications/bed/conversion/src' make -C applications/bed/sort-bed/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/sort-bed/src' rm -rf objects-typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/sort-bed/src' make -C applications/bed/starch/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/starch/src' rm -rf ../lib rm -f ../lib/libstarch_debug.a rm -f ../lib/libstarch_gprof.a rm -rf objects rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/starch/src' rm -rf third-party/bzip2-1.0.6 rm -f third-party/bzip2 rm -rf third-party/jansson-2.6 rm -f third-party/jansson rm -rf third-party/zlib-1.2.7 rm -f third-party/zlib rm -rf bin make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' rm -rf docs/_build/ make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc make[1]: Entering directory '/<>' make -f system.mk/Makefile.linux make[2]: Entering directory '/<>' #bzcat | tar -x -C third-party #cd third-party/jansson-2.6 && ./configure --prefix=/<>/third-party/jansson-2.6 && make && make install && cd /<> && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #bzcat | tar -x -C third-party #cd third-party/bzip2-1.0.6 && make libbz2.a && cd /<> && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2 #bzcat | tar -x -C third-party #cd third-party/zlib-1.2.7 && ./configure --static && make && cd /<> && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib make build -f /<>/system.mk/Makefile.linux make[3]: Entering directory '/<>' make -C applications/bed/bedextract/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedextract/src' mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && x86_64-linux-gnu-g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ExtractRows.cpp In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedextract/src' make -C applications/bed/bedmap/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedmap/src' mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && x86_64-linux-gnu-g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedmap.cpp In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedmap/src' make -C applications/bed/bedops/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedops/src' mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && x86_64-linux-gnu-g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedops.cpp In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator& Bed::bed_check_iterator::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:261:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:140:11, inlined from ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*>, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’ at Bedops.cpp:1411:39: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*>, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator& Bed::bed_check_iterator::operator++() [with BedType = Bed::BasicCoords; long unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:261:36, inlined from ‘BedOperations::BedPadReader::BedType* BedOperations::BedPadReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:140:11, inlined from ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*, std::allocator*> >, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’ at Bedops.cpp:1411:39: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘void BedOperations::nextPartitionGroup(BedFiles&, PQueue&) [with BedFiles = std::vector*, 512> >*, std::allocator*, 512> >*> >; PQueue = std::priority_queue*, std::vector*, std::allocator*> >, Bed::InvertGenomicAddressCompare, Bed::BasicCoords > >]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedops/src' make -C applications/bed/closestfeats/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/closestfeats/src' mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && x86_64-linux-gnu-g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ClosestFeature.cpp In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/closestfeats/src' make -C applications/bed/conversion/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/conversion/src' mkdir -p ../bin && x86_64-linux-gnu-gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -iquote"/<>/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread convert2bed.c: In function ‘c2b_line_convert_rmsk_to_bed_unsorted’: convert2bed.c:3783:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3783 | fprintf(stderr, "Error: Invalid query coordinates at line [%llu]\n", c2b_globals.rmsk->line); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu rm -rf objects make[4]: Leaving directory '/<>/applications/bed/conversion/src' make -C applications/bed/sort-bed/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/sort-bed/src' mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘void starch::UNSTARCH_printMetadataSignature(const unsigned char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2278 | static_cast( mdSha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers SortDetails.cpp: In function ‘ChromBedData* initializeChromBedData(char*, double*)’: SortDetails.cpp:250:12: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ SortDetails.cpp: In function ‘void lexSortBedData(BedData*)’: SortDetails.cpp:1343:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1343 | strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:1342:33: note: length computed here 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘ChromBedData* initializeChromBedData(char*, double*)’, inlined from ‘int processData(const char**, unsigned int, double, char*, bool, bool)’ at SortDetails.cpp:909:59: SortDetails.cpp:250:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function ‘int processData(const char**, unsigned int, double, char*, bool, bool)’: SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 1 | ~~~~~~^~~~~~~~~~ mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && x86_64-linux-gnu-g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::listJSONMetadata(FILE*, FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1226:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1226 | static_cast( getArchiveType() ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1230 | static_cast( getArchiveHeaderFlag() ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1231:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1231 | static_cast( getArchiveShowNewlineFlag() )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractAllData(const string&, FILE*)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:2003:51: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2003 | static_cast( getArchiveHeaderFlag() )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:2014:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2014 | static_cast( getArchiveHeaderFlag() )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of ‘Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’: CheckSort.cpp:51:28: required from here ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:268:12: warning: implicitly-declared ‘Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)’ is deprecated [-Wdeprecated-copy] 268 | auto __tmp = *this; | ^~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because ‘Bed::bed_check_iterator*, 16>’ has user-provided ‘bool Bed::bed_check_iterator::operator=(const Bed::bed_check_iterator&) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ 308 | bool operator=(const bed_check_iterator& b); | ^~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:295:14: warning: implicitly-declared ‘Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)’ is deprecated [-Wdeprecated-copy] 295 | return __tmp; | ^~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because ‘Bed::bed_check_iterator*, 16>’ has user-provided ‘bool Bed::bed_check_iterator::operator=(const Bed::bed_check_iterator&) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ 308 | bool operator=(const bed_check_iterator& b); | ^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’, inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52, inlined from ‘static bool starch::Starch::isStarch(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56, inlined from ‘static bool starch::Starch::isStarch(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:678:25, inlined from ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:92:90: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ In member function ‘void starch::Starch::setCurrentChromosome(char*)’, inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from ‘Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, inlined from ‘Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:267:24, inlined from ‘int checkSort(const char**, unsigned int)’ at CheckSort.cpp:51:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘int checkSort(const char**, unsigned int)’: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ mkdir -p ../bin && x86_64-linux-gnu-g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical rm -rf objects-typical make[4]: Leaving directory '/<>/applications/bed/sort-bed/src' make -C applications/bed/starch/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/starch/src' mkdir -p objects x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘void starch::UNSTARCH_printMetadataSignature(const unsigned char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2278 | static_cast( mdSha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’: ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’: ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’: ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ mkdir -p objects x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here 311 | strncpy(iter->filename, fn, strlen(fn) + 1); | ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ mkdir -p objects x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p ../lib ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o mkdir -p ../bin x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../.. starch.c: In function ‘int main(int, char**)’: starch.c:106:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 106 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:121:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 121 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:123:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 123 | static_cast( kStarchFinalizeTransformTrue ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:146:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 146 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:161:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 161 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:163:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 163 | static_cast( kStarchFinalizeTransformTrue ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:191:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 191 | static_cast( type ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:194:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 194 | static_cast( bedGeneratePerChrSignatureFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:195:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 195 | static_cast( bedHeaderFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:196:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 196 | static_cast( bedReportProgressFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starch.c:197:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 197 | static_cast( bedReportProgressN )) != STARCH_EXIT_SUCCESS) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 mkdir -p ../bin x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. unstarch.c: In function ‘int main(int, char**)’: unstarch.c:401:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 401 | static_cast( metadataOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:402:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 402 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:422:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 422 | static_cast( metadataOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:423:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 423 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:452:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 452 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:453:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 453 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:473:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 473 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:474:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 474 | static_cast( headerFlag )) != 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:567:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 567 | UNSTARCH_printCompressionType(static_cast( type )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:798:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 798 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:809:82: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 809 | static_cast( sizeof(starchRevision2HeaderBytes) ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c: In function ‘void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)’: unstarch.c:1334:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1334 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unstarch.c:1336:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1336 | static_cast( sha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 mkdir -p ../bin x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. In file included from /usr/x86_64-linux-gnu/include/c++/11/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int main(int, char**)’: starchcat.c:136:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 136 | assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:137:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 137 | assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:138:87: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:138:133: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:139:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 139 | assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:140:145: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 140 | assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, &numChromosomes, reinterpret_cast( mdRecords ), static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:141:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 141 | assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:142:124: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:142:213: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:143:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 143 | assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:144:127: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 144 | assert( STARCHCAT_buildChromosomeSummaries ( &summaries, reinterpret_cast( summary ), static_cast( numChromosomes ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:164:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 164 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:178:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 178 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:223:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 223 | assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:233:68: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 233 | assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast( numRecords ) ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: starchcat.c:1338:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1338 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:1806:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1806 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*)’: starchcat.c:2450:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2450 | static_cast( inRec->mdOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2451:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2451 | static_cast( inRec->hFlag )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2471:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2471 | static_cast( inRec->mdOffset ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2472:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2472 | static_cast( inRec->hFlag )) != 0 ) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2509:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2509 | static_cast( outType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2511:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2511 | static_cast( kStarchFinalizeTransformFalse ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’: starchcat.c:3152:54: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast( inRecIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3316:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3316 | static_cast( summary->numRecords ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3455:77: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3455 | static_cast( flushZStreamFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_mergeInputRecordsToOutput(starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*)’: starchcat.c:4265:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4265 | static_cast( outType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4267:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4267 | static_cast( kStarchFinalizeTransformFalse ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*)’: starchcat.c:4402:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4402 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4420:63: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4420 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4447:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4447 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4479:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4479 | static_cast( hFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT_freeChromosomeSummaries(starch::ChromosomeSummaries**)’: starchcat.c:4541:62: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 4541 | STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), static_cast( (*chrSums)->numChromosomes )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/cassert:44, from starchcat.c:33: starchcat.c: In function ‘int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: starchcat.c:5902:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5902 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5929:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5929 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5952:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5952 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:5990:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 5990 | static_cast( outputType ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6025:38: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6025 | static_cast( hFlag ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6053:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6053 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:6055:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6055 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(starch::Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, starch::TransformState*)’: starchcat.c:6719:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 6719 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_fillExtractionBufferFromGzipStream(starch::Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, starch::TransformState*)’: starchcat.c:7060:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 7060 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’: starchcat.c:3123:16: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:3123:78: note: length computed here 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); | ~~~~~~^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 mkdir -p ../bin cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical mkdir -p ../bin cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical mkdir -p ../bin cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical mkdir -p ../bin cp starch-diff.py ../bin/starch-diff-typical mkdir -p ../bin x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. starchstrip.c: In function ‘void starch::STARCHSTRIP_write_updated_metadata(FILE*)’: starchstrip.c:124:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 124 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchstrip.c:126:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 126 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 rm -rf objects make[4]: Leaving directory '/<>/applications/bed/starch/src' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/bedops-2.4.40\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' mkdir -p bin cp applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/wig2starch bin cp applications/bed/starch/bin/starchcluster_sge-typical bin/starchcluster_sge cp applications/bed/starch/bin/starchcluster_gnuParallel-typical bin/starchcluster_gnuParallel cp applications/bed/starch/bin/starchcluster_slurm-typical bin/starchcluster_slurm cp applications/bed/starch/bin/starch-diff-typical bin/starch-diff cp applications/bed/sort-bed/bin/sort-bed-typical bin/sort-bed cp applications/bed/sort-bed/bin/update-sort-bed-slurm-typical bin/update-sort-bed-slurm cp applications/bed/sort-bed/bin/update-sort-bed-starch-slurm-typical bin/update-sort-bed-starch-slurm cp applications/bed/sort-bed/bin/update-sort-bed-migrate-candidates-typical bin/update-sort-bed-migrate-candidates cp applications/bed/bedops/bin/bedops-typical bin/bedops cp applications/bed/closestfeats/bin/closest-features-typical bin/closest-features cp applications/bed/bedmap/bin/bedmap-typical bin/bedmap cp applications/bed/bedextract/bin/bedextract-typical bin/bedextract cp applications/bed/starch/bin/starch-typical bin/starch cp applications/bed/starch/bin/unstarch-typical bin/unstarch cp applications/bed/starch/bin/starchcat-typical bin/starchcat cp applications/bed/starch/bin/starchstrip-typical bin/starchstrip cp applications/bed/conversion/bin/convert2bed-typical bin/convert2bed make[1]: Leaving directory '/<>' debian/rules override_dh_install-arch make[1]: Entering directory '/<>' dh_install -a mv bin/starch bin/bedops-starch mkdir -p debian/bedops/usr/bin/ cp bin/* debian/bedops/usr/bin/ make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman-arch make[1]: Entering directory '/<>' cd bin && for f in * ; do help2man --no-discard-stderr --version-string="2.4.40+dfsg" -o $f.1 ./$f; done help2man: can't get `--help' info from ./bam2bed_gnuParallel help2man: can't get `--help' info from ./bam2bed_sge help2man: can't get `--help' info from ./bam2bed_slurm help2man: can't get `--help' info from ./bam2starch_gnuParallel help2man: can't get `--help' info from ./bam2starch_sge help2man: can't get `--help' info from ./bam2starch_slurm help2man: can't get `--help' info from ./starchcluster_gnuParallel help2man: can't get `--help' info from ./starchcluster_sge help2man: can't get `--help' info from ./starchcluster_slurm dh_installman -a make[1]: Leaving directory '/<>' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a debian/rules override_dh_dwz make[1]: Entering directory '/<>' # Work around: dwz: Too few files for multifile optimization echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/<>' 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 'bedops' in '../bedops_2.4.40+dfsg-1_amd64.deb'. dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.40+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bedops_2.4.40+dfsg-1_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 2021-10-27T03:04:12Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedops_2.4.40+dfsg-1_amd64.changes: ----------------------------------- Format: 1.8 Date: Sun, 24 Oct 2021 13:20:15 +0530 Source: bedops Binary: bedops bedops-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 2.4.40+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: bedops - high-performance genomic feature operations Closes: 997157 Changes: bedops (2.4.40+dfsg-1) unstable; urgency=medium . * Team Upload. [ Steffen Möller ] * Update metadata - indent plus ref to guix . [ Nilesh Patra ] * Add patch to fix FTBFS with new sphinx (Closes: #997157) Checksums-Sha1: 0349bf103fc548532f40a3a830028b065cc62d13 85580 bedops-dbgsym_2.4.40+dfsg-1_amd64.deb 689a3516d2a7a65a6e2cc740bb85f99ec26f74d1 5555 bedops_2.4.40+dfsg-1_amd64.buildinfo 249ae91842ba8135a223263ec29c8e9a04e1da5c 1574084 bedops_2.4.40+dfsg-1_amd64.deb Checksums-Sha256: 8dbd61264a7544ca7494d65cf1147f2b2a10c94aa57bcee1c995d0373cfbe27c 85580 bedops-dbgsym_2.4.40+dfsg-1_amd64.deb 4feaf7c326558bb4ad084895a5b76402bc4ed71dc4118ca856fe0cd3c7a95810 5555 bedops_2.4.40+dfsg-1_amd64.buildinfo bbbbe68aa8dbfeb718f62c77708cc048fc52da413e75ca5c4d5ea8bc9793ef46 1574084 bedops_2.4.40+dfsg-1_amd64.deb Files: be86fc1b3c9646b6d996ac112f581260 85580 debug optional bedops-dbgsym_2.4.40+dfsg-1_amd64.deb 9e1b5221ef7c5c010138be33105c4103 5555 science optional bedops_2.4.40+dfsg-1_amd64.buildinfo 120517f947d689428b6bda23b40cf10e 1574084 science optional bedops_2.4.40+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bedops Binary: bedops bedops-dbgsym Architecture: amd64 Version: 2.4.40+dfsg-1 Checksums-Md5: be86fc1b3c9646b6d996ac112f581260 85580 bedops-dbgsym_2.4.40+dfsg-1_amd64.deb 120517f947d689428b6bda23b40cf10e 1574084 bedops_2.4.40+dfsg-1_amd64.deb Checksums-Sha1: 0349bf103fc548532f40a3a830028b065cc62d13 85580 bedops-dbgsym_2.4.40+dfsg-1_amd64.deb 249ae91842ba8135a223263ec29c8e9a04e1da5c 1574084 bedops_2.4.40+dfsg-1_amd64.deb Checksums-Sha256: 8dbd61264a7544ca7494d65cf1147f2b2a10c94aa57bcee1c995d0373cfbe27c 85580 bedops-dbgsym_2.4.40+dfsg-1_amd64.deb bbbbe68aa8dbfeb718f62c77708cc048fc52da413e75ca5c4d5ea8bc9793ef46 1574084 bedops_2.4.40+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Wed, 27 Oct 2021 03:04:11 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1), autopoint (= 0.21-4), autotools-dev (= 20180224.1+nmu1), base-files (= 12), base-passwd (= 3.5.52), bash (= 5.1-3+b2), binutils (= 2.37-7), binutils-aarch64-linux-gnu (= 2.37-7), binutils-common (= 2.37-7), bsdextrautils (= 2.37.2-4), bsdutils (= 1:2.37.2-4), build-essential (= 12.9), bzip2 (= 1.0.8-4), coreutils (= 8.32-4), cpp (= 4:11.2.0-2), cpp-11 (= 11.2.0-10), dash (= 0.5.11+git20210120+802ebd4-2), debconf (= 1.5.78), debhelper (= 13.5.2), debianutils (= 5.5-1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.12.0-2), diffutils (= 1:3.7-5), dpkg (= 1.20.9), dpkg-dev (= 1.20.9), dwz (= 0.14-1), file (= 1:5.39-3), findutils (= 4.8.0-1), g++ (= 4:11.2.0-2), g++-11 (= 11.2.0-10), gcc (= 4:11.2.0-2), gcc-11 (= 11.2.0-10), gcc-11-base (= 11.2.0-10), gettext (= 0.21-4), gettext-base (= 0.21-4), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4), help2man (= 1.48.5), hostname (= 3.23), init-system-helpers (= 1.60), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-10), libatomic1 (= 11.2.0-10), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.6-1), libaudit1 (= 1:3.0.6-1), libbinutils (= 2.37-7), libblkid1 (= 2.37.2-4), libbz2-1.0 (= 1.0.8-4), libbz2-dev (= 1.0.8-4), libc-bin (= 2.32-4), libc-dev-bin (= 2.32-4), libc6 (= 2.32-4), libc6-dev (= 2.32-4), libcap-ng0 (= 0.7.9-2.2+b1), libcap2 (= 1:2.44-1), libcc1-0 (= 11.2.0-10), libcom-err2 (= 1.46.4-1), libcrypt-dev (= 1:4.4.25-2), libcrypt1 (= 1:4.4.25-2), libctf-nobfd0 (= 2.37-7), libctf0 (= 2.37-7), libdb5.3 (= 5.3.28+dfsg1-0.8), libdebconfclient0 (= 0.260), libdebhelper-perl (= 13.5.2), libdpkg-perl (= 1.20.9), libelf1 (= 0.185-2), libexpat1 (= 2.4.1-3), libffi8 (= 3.4.2-3), libfile-stripnondeterminism-perl (= 1.12.0-2), libgcc-11-dev (= 11.2.0-10), libgcc-s1 (= 11.2.0-10), libgcrypt20 (= 1.9.4-3+b1), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgmp10 (= 2:6.2.1+dfsg-2), libgomp1 (= 11.2.0-10), libgpg-error0 (= 1.42-3), libgssapi-krb5-2 (= 1.18.3-7), libicu67 (= 67.1-7), libisl23 (= 0.24-2), libitm1 (= 11.2.0-10), libjansson-dev (= 2.13.1-1.1), libjansson4 (= 2.13.1-1.1), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), liblocale-gettext-perl (= 1.07-4+b1), liblsan0 (= 11.2.0-10), liblz4-1 (= 1.9.3-2), liblzma5 (= 5.2.5-2), libmagic-mgc (= 1:5.39-3), libmagic1 (= 1:5.39-3), libmount1 (= 2.37.2-4), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2), libmpfr6 (= 4.1.0-3), libncursesw6 (= 6.2+20210905-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libpam-modules (= 1.4.0-10), libpam-modules-bin (= 1.4.0-10), libpam-runtime (= 1.4.0-10), libpam0g (= 1.4.0-10), libpcre2-8-0 (= 10.36-2), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.1-6), libpipeline1 (= 1.5.3-1), libpython3-stdlib (= 3.9.2-3), libpython3.9-minimal (= 3.9.7-4), libpython3.9-stdlib (= 3.9.7-4), libquadmath0 (= 11.2.0-10), libreadline8 (= 8.1-2), libseccomp2 (= 2.5.2-2), libselinux1 (= 3.1-3), libsigsegv2 (= 2.13-1), libsmartcols1 (= 2.37.2-4), libsqlite3-0 (= 3.36.0-2), libssl1.1 (= 1.1.1l-1), libstdc++-11-dev (= 11.2.0-10), libstdc++6 (= 11.2.0-10), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.5-1), libtinfo6 (= 6.2+20210905-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15), libtsan0 (= 11.2.0-10), libubsan1 (= 11.2.0-10), libuchardet0 (= 0.0.7-1), libudev1 (= 249.5-1), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4), libxml2 (= 2.9.12+dfsg-5), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.14.12-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-5), make (= 4.3-4.1), man-db (= 2.9.4-2), mawk (= 1.3.4.20200120-2), media-types (= 4.0.0), ncurses-base (= 6.2+20210905-1), ncurses-bin (= 6.2+20210905-1), patch (= 2.7.6-7), perl (= 5.32.1-6), perl-base (= 5.32.1-6), perl-modules-5.32 (= 5.32.1-6), po-debconf (= 1.0.21+nmu1), python3 (= 3.9.2-3), python3-distutils (= 3.9.7-1), python3-lib2to3 (= 3.9.7-1), python3-minimal (= 3.9.2-3), python3.9 (= 3.9.7-4), python3.9-minimal (= 3.9.7-4), readline-common (= 8.1-2), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.00-1), tar (= 1.34+dfsg-1), tzdata (= 2021e-1), util-linux (= 2.37.2-4), xz-utils (= 5.2.5-2), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1635061815" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedops-dbgsym_2.4.40+dfsg-1_amd64.deb ------------------------------------- new Debian package, version 2.0. size 85580 bytes: control archive=540 bytes. 378 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: bedops-dbgsym Source: bedops Version: 2.4.40+dfsg-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 102 Depends: bedops (= 2.4.40+dfsg-1) Section: debug Priority: optional Description: debug symbols for bedops Build-Ids: d82b22e1d4e88ec4f60ce4273aa0023a1ef35156 drwxr-xr-x root/root 0 2021-10-24 07:50 ./ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/lib/debug/.build-id/d8/ -rw-r--r-- root/root 94008 2021-10-24 07:50 ./usr/lib/debug/.build-id/d8/2b22e1d4e88ec4f60ce4273aa0023a1ef35156.debug drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/ lrwxrwxrwx root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops-dbgsym -> bedops bedops_2.4.40+dfsg-1_amd64.deb ------------------------------ new Debian package, version 2.0. size 1574084 bytes: control archive=6152 bytes. 731 bytes, 15 lines control 21485 bytes, 236 lines md5sums Package: bedops Version: 2.4.40+dfsg-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 10267 Depends: libbz2-1.0, libc6 (>= 2.28), libgcc-s1 (>= 3.0), libjansson4 (>= 2.3), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4), python3, tcsh Section: science Priority: optional Homepage: https://github.com/bedops/bedops Description: high-performance genomic feature operations BEDOPS is a suite of tools to address common questions raised in genomic studies, mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data. drwxr-xr-x root/root 0 2021-10-24 07:50 ./ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/bin/ -rwxr-xr-x root/root 4711 2021-10-24 07:50 ./usr/bin/bam2bed -rwxr-xr-x root/root 4501 2021-10-24 07:50 ./usr/bin/bam2bed_gnuParallel -rwxr-xr-x root/root 5022 2021-10-24 07:50 ./usr/bin/bam2bed_sge -rwxr-xr-x root/root 5021 2021-10-24 07:50 ./usr/bin/bam2bed_slurm -rwxr-xr-x root/root 5842 2021-10-24 07:50 ./usr/bin/bam2starch -rwxr-xr-x root/root 4507 2021-10-24 07:50 ./usr/bin/bam2starch_gnuParallel -rwxr-xr-x root/root 5076 2021-10-24 07:50 ./usr/bin/bam2starch_sge -rwxr-xr-x root/root 5014 2021-10-24 07:50 ./usr/bin/bam2starch_slurm -rwxr-xr-x root/root 199960 2021-10-24 07:50 ./usr/bin/bedextract -rwxr-xr-x root/root 8326624 2021-10-24 07:50 ./usr/bin/bedmap -rwxr-xr-x root/root 425384 2021-10-24 07:50 ./usr/bin/bedops -rwxr-xr-x root/root 88992 2021-10-24 07:50 ./usr/bin/bedops-starch -rwxr-xr-x root/root 236880 2021-10-24 07:50 ./usr/bin/closest-features -rwxr-xr-x root/root 139160 2021-10-24 07:50 ./usr/bin/convert2bed -rwxr-xr-x root/root 3773 2021-10-24 07:50 ./usr/bin/gff2bed -rwxr-xr-x root/root 4904 2021-10-24 07:50 ./usr/bin/gff2starch -rwxr-xr-x root/root 3532 2021-10-24 07:50 ./usr/bin/gtf2bed -rwxr-xr-x root/root 4663 2021-10-24 07:50 ./usr/bin/gtf2starch -rwxr-xr-x root/root 3773 2021-10-24 07:50 ./usr/bin/gvf2bed -rwxr-xr-x root/root 4904 2021-10-24 07:50 ./usr/bin/gvf2starch -rwxr-xr-x root/root 3976 2021-10-24 07:50 ./usr/bin/psl2bed -rwxr-xr-x root/root 5107 2021-10-24 07:50 ./usr/bin/psl2starch -rwxr-xr-x root/root 3776 2021-10-24 07:50 ./usr/bin/rmsk2bed -rwxr-xr-x root/root 4907 2021-10-24 07:50 ./usr/bin/rmsk2starch -rwxr-xr-x root/root 4711 2021-10-24 07:50 ./usr/bin/sam2bed -rwxr-xr-x root/root 5842 2021-10-24 07:50 ./usr/bin/sam2starch -rwxr-xr-x root/root 220512 2021-10-24 07:50 ./usr/bin/sort-bed -rwxr-xr-x root/root 10163 2021-10-24 07:50 ./usr/bin/starch-diff -rwxr-xr-x root/root 166848 2021-10-24 07:50 ./usr/bin/starchcat -rwxr-xr-x root/root 4299 2021-10-24 07:50 ./usr/bin/starchcluster_gnuParallel -rwxr-xr-x root/root 4810 2021-10-24 07:50 ./usr/bin/starchcluster_sge -rwxr-xr-x root/root 4716 2021-10-24 07:50 ./usr/bin/starchcluster_slurm -rwxr-xr-x root/root 97056 2021-10-24 07:50 ./usr/bin/starchstrip -rwxr-xr-x root/root 125568 2021-10-24 07:50 ./usr/bin/unstarch -rwxr-xr-x root/root 32686 2021-10-24 07:50 ./usr/bin/update-sort-bed-migrate-candidates -rwxr-xr-x root/root 20701 2021-10-24 07:50 ./usr/bin/update-sort-bed-slurm -rwxr-xr-x root/root 22682 2021-10-24 07:50 ./usr/bin/update-sort-bed-starch-slurm -rwxr-xr-x root/root 4675 2021-10-24 07:50 ./usr/bin/vcf2bed -rwxr-xr-x root/root 5806 2021-10-24 07:50 ./usr/bin/vcf2starch -rwxr-xr-x root/root 4598 2021-10-24 07:50 ./usr/bin/wig2bed -rwxr-xr-x root/root 5729 2021-10-24 07:50 ./usr/bin/wig2starch drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/ -rw-r--r-- root/root 267 2021-10-24 07:33 ./usr/share/doc/bedops/README.Debian -rw-r--r-- root/root 1618 2021-10-24 07:50 ./usr/share/doc/bedops/changelog.Debian.gz -rw-r--r-- root/root 22054 2021-07-27 21:43 ./usr/share/doc/bedops/changelog.gz -rw-r--r-- root/root 1156 2021-10-24 07:33 ./usr/share/doc/bedops/copyright drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/ -rw-r--r-- root/root 954 2021-07-27 21:43 ./usr/share/doc/bedops/tests/Makefile drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/bedops/ -rw-r--r-- root/root 2166 2021-10-24 07:50 ./usr/share/doc/bedops/tests/bedops/Makefile.gz drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/ -rw-r--r-- root/root 197 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001.expected -rw-r--r-- root/root 44 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001a.test -rw-r--r-- root/root 53 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001b.test -rw-r--r-- root/root 24 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.chrom.001.expected -rw-r--r-- root/root 26 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.complement.001.expected -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.difference.001.expected -rw-r--r-- root/root 23 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.ec.001a.test -rw-r--r-- root/root 69 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.element-of.001.expected -rw-r--r-- root/root 91 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001.expected -rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001a.test -rw-r--r-- root/root 104 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001b.test -rw-r--r-- root/root 37 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.expected -rw-r--r-- root/root 111 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.test -rw-r--r-- root/root 368 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.named-pipe.001.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.not-element-of.001.expected -rw-r--r-- root/root 148 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001.expected -rw-r--r-- root/root 39 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001a.test -rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001b.test -rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001c.test -rw-r--r-- root/root 257 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.stdin.001.expected -rw-r--r-- root/root 130 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.symdiff.001.expected -rw-r--r-- root/root 134 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.expected -rw-r--r-- root/root 126 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.test -rw-r--r-- root/root 171 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.chop.002.expected -rw-r--r-- root/root 20 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.chrom.002.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.complement.002.expected -rw-r--r-- root/root 2172 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002.expected -rw-r--r-- root/root 3033 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002a.test -rw-r--r-- root/root 2941 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002b.test -rw-r--r-- root/root 18 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.element-of.002.expected -rw-r--r-- root/root 13 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.expected -rw-r--r-- root/root 26 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.test -rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.merge.002.expected -rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.not-element-of.002.expected -rw-r--r-- root/root 376 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002.expected -rw-r--r-- root/root 48 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002a.test -rw-r--r-- root/root 49 2021-07-27 21:43 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./usr/share/doc/bedops/tests/bedops/data/003.difference.003.expected -rw-r--r-- root/root 42 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.element-of.003.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.intersection.003.expected -rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.expected -rw-r--r-- root/root 46 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.test -rw-r--r-- root/root 21 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003.expected -rw-r--r-- root/root 63 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003a.test -rw-r--r-- root/root 42 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003b.test -rw-r--r-- root/root 153 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.expected -rw-r--r-- root/root 398 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.test -rw-r--r-- root/root 22 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003.expected -rw-r--r-- root/root 18 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003a.test -rw-r--r-- root/root 29 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003b.test -rw-r--r-- root/root 9 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003c.test -rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003d.test -rw-r--r-- root/root 355 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.expected -rw-r--r-- root/root 360 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.test -rw-r--r-- root/root 257 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.chop.004.expected -rw-r--r-- root/root 24 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.chrom.004.expected -rw-r--r-- root/root 111 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004.expected -rw-r--r-- root/root 46 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004a.test -rw-r--r-- root/root 132 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004b.test -rw-r--r-- root/root 94 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004c.test -rw-r--r-- root/root 30 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004.expected -rw-r--r-- root/root 30 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004a.test -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004b.test -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004.expected -rw-r--r-- root/root 92 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004a.test -rw-r--r-- root/root 23 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004b.test -rw-r--r-- root/root 49 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004.expected -rw-r--r-- root/root 103 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004a.test -rw-r--r-- root/root 85 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004b.test -rw-r--r-- root/root 47 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004c.test -rw-r--r-- root/root 72 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.merge.004.expected -rw-r--r-- root/root 117 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.expected -rw-r--r-- root/root 117 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.test -rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.symdiff.004.expected -rw-r--r-- root/root 22 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.expected -rw-r--r-- root/root 32 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.test -rw-r--r-- root/root 385 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.expected -rw-r--r-- root/root 87 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.test -rw-r--r-- root/root 20 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.expected -rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.test -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.difference.005.expected -rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.expected -rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.test -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.symdiff.005.expected -rw-r--r-- root/root 11 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/005.union.005.expected -rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.complement.006.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.difference.006.expected -rw-r--r-- root/root 41 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006.expected -rw-r--r-- root/root 37 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006a.test -rw-r--r-- root/root 35 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006b.test -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006c.test -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/006.union.006.expected -rw-r--r-- root/root 9 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.complement.007.expected -rw-r--r-- root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.difference.007.expected -rw-r--r-- root/root 55 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007.expected -rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007a.test -rw-r--r-- root/root 69 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007b.test -rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/007.union.007.expected -rw-r--r-- root/root 79 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.complement.008.expected -rw-r--r-- root/root 197 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.merge.008.expected -rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/008.union.008.expected -rw-r--r-- root/root 175 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.complement.009.expected -rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.merge.009.expected -rw-r--r-- root/root 33 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.expected -rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.test drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/conversion/ -rw-r--r-- root/root 1159 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/Makefile.gz drwxr-xr-x root/root 0 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/ -rw-r--r-- root/root 398 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 352 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 368 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 322 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 102 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 52 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 102 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.expected -rw-r--r-- root/root 60 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.wig -rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 49 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 93 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.expected -rw-r--r-- root/root 56 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.wig -rw-r--r-- root/root 170 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 85 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 34 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.expected -rw-r--r-- root/root 43 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.wig -rw-r--r-- root/root 155 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 82 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 31 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.expected -rw-r--r-- root/root 40 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.wig -rw-r--r-- root/root 538 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.expected -rw-r--r-- root/root 454 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.wig -rw-r--r-- root/root 583 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.002.expected -rw-r--r-- root/root 700 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.003.expected -rw-r--r-- root/root 763 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.004.expected -rw-r--r-- root/root 493 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.expected -rw-r--r-- root/root 421 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.wig -rw-r--r-- root/root 538 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.002.expected -rw-r--r-- root/root 652 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.003.expected -rw-r--r-- root/root 715 2021-07-27 21:43 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.004.expected drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/ -rw-r--r-- root/root 1078 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/Makefile.gz drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/data/ -rw-r--r-- root/root 1935 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.expected -rw-r--r-- root/root 2813 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.test.gz -rw-r--r-- root/root 772 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1.001.test -rw-r--r-- root/root 1166 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1andChr2.001.expected -rw-r--r-- root/root 772 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr2.001.test -rw-r--r-- root/root 764 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.expected -rw-r--r-- root/root 2851 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.test.gz -rw-r--r-- root/root 218 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.expected -rw-r--r-- root/root 2254 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.test.gz -rw-r--r-- root/root 109 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/README -rw-r--r-- root/root 426 2021-07-27 21:43 ./usr/share/doc/bedops/tests/starch/data/hg38.bed -rw-r--r-- root/root 1516 2021-10-24 07:50 ./usr/share/doc/bedops/tests/starch/generate_random_intervals.sh drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/man/ drwxr-xr-x root/root 0 2021-10-24 07:50 ./usr/share/man/man1/ -rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/bam2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/bam2starch.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/bedextract.1.gz -rw-r--r-- root/root 353 2021-10-24 07:50 ./usr/share/man/man1/bedmap.1.gz -rw-r--r-- root/root 362 2021-10-24 07:50 ./usr/share/man/man1/bedops-starch.1.gz -rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/bedops.1.gz -rw-r--r-- root/root 366 2021-10-24 07:50 ./usr/share/man/man1/closest-features.1.gz -rw-r--r-- root/root 369 2021-10-24 07:50 ./usr/share/man/man1/convert2bed.1.gz -rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/gff2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/gff2starch.1.gz -rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/gtf2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/gtf2starch.1.gz -rw-r--r-- root/root 349 2021-10-24 07:50 ./usr/share/man/man1/gvf2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/gvf2starch.1.gz -rw-r--r-- root/root 347 2021-10-24 07:50 ./usr/share/man/man1/psl2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/psl2starch.1.gz -rw-r--r-- root/root 350 2021-10-24 07:50 ./usr/share/man/man1/rmsk2bed.1.gz -rw-r--r-- root/root 357 2021-10-24 07:50 ./usr/share/man/man1/rmsk2starch.1.gz -rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/sam2bed.1.gz -rw-r--r-- root/root 355 2021-10-24 07:50 ./usr/share/man/man1/sam2starch.1.gz -rw-r--r-- root/root 353 2021-10-24 07:50 ./usr/share/man/man1/sort-bed.1.gz -rw-r--r-- root/root 720 2021-10-24 07:50 ./usr/share/man/man1/starch-diff.1.gz -rw-r--r-- root/root 352 2021-10-24 07:50 ./usr/share/man/man1/starchcat.1.gz -rw-r--r-- root/root 367 2021-10-24 07:50 ./usr/share/man/man1/starchstrip.1.gz -rw-r--r-- root/root 361 2021-10-24 07:50 ./usr/share/man/man1/unstarch.1.gz -rw-r--r-- root/root 1764 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz -rw-r--r-- root/root 1330 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-slurm.1.gz -rw-r--r-- root/root 1383 2021-10-24 07:50 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz -rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/vcf2bed.1.gz -rw-r--r-- root/root 356 2021-10-24 07:50 ./usr/share/man/man1/vcf2starch.1.gz -rw-r--r-- root/root 348 2021-10-24 07:50 ./usr/share/man/man1/wig2bed.1.gz -rw-r--r-- root/root 356 2021-10-24 07:50 ./usr/share/man/man1/wig2starch.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 [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [573 B] Get:5 copy:/<>/apt_archive ./ Packages [656 B] Fetched 2192 B in 0s (51.6 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-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 libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils t1utils unzip Suggested packages: libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libwww-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg liblist-someutils-xs-perl libpackage-stash-xs-perl libref-util-perl libtype-tiny-xs-perl The following NEW packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-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 libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils sbuild-build-depends-lintian-dummy:amd64 t1utils unzip 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 6664 kB of archives. After this operation, 20.0 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [856 B] Get:2 http://mirror.einval.org/debian sid/main arm64 diffstat arm64 1.64-1 [34.6 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libassuan0 arm64 2.5.5-1 [49.3 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 gpgconf arm64 2.2.27-2 [540 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.27-2 [883 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 libaliased-perl all 0.34-1.1 [14.1 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40 [69.4 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-1+b3 [11.2 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.008-1+b2 [15.8 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-1+b3 [25.5 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:16 http://mirror.einval.org/debian sid/main arm64 libvariable-magic-perl arm64 0.62-1+b3 [44.2 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libb-hooks-endofscope-perl all 0.25-1 [19.5 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:20 http://mirror.einval.org/debian sid/main arm64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-3+b7 [36.9 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 libclone-perl arm64 0.45-1+b1 [15.3 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 libconfig-tiny-perl all 2.27-1 [17.1 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-1+b1 [25.3 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libconst-fast-perl all 0.014-1.1 [8552 B] Get:29 http://mirror.einval.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.27-1 [126 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 libiterator-perl all 0.03+ds1-1.1 [18.4 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-2 [36.8 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.01-2 [34.3 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libdevel-size-perl arm64 0.83-1+b2 [25.8 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.04-1+b3 [26.7 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libnumber-compare-perl all 0.03-2 [7448 B] Get:46 http://mirror.einval.org/debian sid/main arm64 libtext-glob-perl all 0.11-2 [8992 B] Get:47 http://mirror.einval.org/debian sid/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libio-prompt-tiny-perl all 0.003-1 [9150 B] Get:53 http://mirror.einval.org/debian sid/main arm64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.005004-2 [60.4 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b1 [170 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-1+b3 [11.9 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-1+b1 [13.5 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.118-1 [53.5 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.19-1+b7 [17.0 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.008-1+b1 [11.8 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.634-1 [46.1 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 4.018+ds-1+b1 [95.3 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 4.018+ds-1+b1 [98.3 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libsort-versions-perl all 1.62-1 [11.0 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-1+b2 [27.3 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-4+b8 [8680 B] Get:79 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.13-1 [13.1 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.8-1+b1 [195 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-1+b3 [75.1 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libtype-tiny-perl all 1.012004-1 [351 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b2 [19.8 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.08-1 [90.6 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.83+ds-1 [34.2 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 lzip arm64 1.22-4 [84.6 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:93 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-26 [165 kB] Get:94 http://mirror.einval.org/debian sid/main arm64 lintian all 2.110.0 [1338 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6664 kB in 1s (7626 kB/s) Selecting previously unselected package diffstat. (Reading database ... 19674 files and directories currently installed.) Preparing to unpack .../00-diffstat_1.64-1_arm64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../01-libassuan0_2.5.5-1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.5-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../02-gpgconf_2.2.27-2_arm64.deb ... Unpacking gpgconf (2.2.27-2) ... Selecting previously unselected package gpg. Preparing to unpack .../03-gpg_2.2.27-2_arm64.deb ... Unpacking gpg (2.2.27-2) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../04-libaliased-perl_0.34-1.1_all.deb ... Unpacking libaliased-perl (0.34-1.1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../05-libapt-pkg-perl_0.1.40_arm64.deb ... Unpacking libapt-pkg-perl (0.1.40) ... Selecting previously unselected package libb-hooks-op-check-perl. 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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: 55580 Build-Time: 1671 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 68 Job: bedops_2.4.40+dfsg-1 Lintian: pass Machine Architecture: arm64 Package: bedops Package-Time: 1779 Source-Version: 2.4.40+dfsg-1 Space: 55580 Status: successful Version: 2.4.40+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-10-27T03:04:12Z Build needed 00:29:39, 55580k disk space