sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | bedops 2.4.40+dfsg-1 (armel) Fri, 12 Nov 2021 21:04:37 +0000 | +==============================================================================+ Package: bedops Version: 2.4.40+dfsg-1 Source Version: 2.4.40+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-90bcb4af-9213-4b74-94a9-355624777033' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-WWf29p/resolver-9WgA0C' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [165 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [63.6 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-11-12-2001.29-F-2021-11-12-0801.42.pdiff [29.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-11-12-2001.29-F-2021-11-12-0801.42.pdiff [29.8 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-11-12-2001.29-F-2021-11-12-0801.42.pdiff [41.3 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-11-12-2001.29-F-2021-11-12-0801.42.pdiff [41.3 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main armel Packages [8478 kB] Fetched 8841 kB in 4s (2374 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://debian.oregonstate.edu/debian unstable/main bedops 2.4.40+dfsg-1 (dsc) [2178 B] Get:2 http://debian.oregonstate.edu/debian unstable/main bedops 2.4.40+dfsg-1 (tar) [13.4 MB] Get:3 http://debian.oregonstate.edu/debian unstable/main bedops 2.4.40+dfsg-1 (diff) [10.3 kB] Fetched 13.5 MB in 0s (121 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedops-WWf29p/bedops-2.4.40+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-WWf29p' 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:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel 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 [439 B] Get:5 copy:/<>/apt_archive ./ Packages [529 B] Fetched 1925 B in 0s (75.9 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-arm-linux-gnueabi bsdextrautils build-essential cpp-11-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-11 g++-11-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-11-arm-linux-gnueabi gcc-11-arm-linux-gnueabi-base gcc-11-base:armel gcc-11-cross-base gcc-9-base:armel gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:armel libasan6-armel-cross libatomic1:armel libatomic1-armel-cross libbz2-1.0:armel libbz2-dev:armel libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev-armel-cross libgcc-9-dev:armel libgcc-s1:armel libgcc-s1-armel-cross libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libicu67 libio-string-perl libjansson-dev:armel libjansson4:armel libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libnsl-dev libnsl-dev:armel libnsl2:armel libperl5.32 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsqlite3-0 libssl1.1:armel libstdc++-11-dev libstdc++-11-dev-armel-cross libstdc++-9-dev:armel libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtirpc-dev libtirpc-dev:armel libtirpc3:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db media-types perl perl-modules-5.32 po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.9 python3.9-minimal rpcsvc-proto sensible-utils ucf zlib1g:armel zlib1g-dev:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-11-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-11-multilib gcc-11-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armel libc-l10n:armel locales:armel libnss-nis:armel libnss-nisplus:armel glibc-doc manpages-dev:armel gnupg git bzr krb5-doc:armel krb5-user:armel libstdc++-11-doc libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binfmt-support Recommended packages: gnupg libalgorithm-merge-perl curl | wget | lynx bzip2-doc:armel libidn2-0:armel libfile-fcntllock-perl libarchive-cpio-perl krb5-locales:armel ca-certificates libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdextrautils build-essential cpp-11-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-11 g++-11-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-11-arm-linux-gnueabi gcc-11-arm-linux-gnueabi-base gcc-11-base:armel gcc-11-cross-base gcc-9-base:armel gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:armel libasan6-armel-cross libatomic1:armel libatomic1-armel-cross libbz2-1.0:armel libbz2-dev:armel libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev-armel-cross libgcc-9-dev:armel libgcc-s1:armel libgcc-s1-armel-cross libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libicu67 libio-string-perl libjansson-dev:armel libjansson4:armel libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libnsl-dev libnsl-dev:armel libnsl2:armel libperl5.32 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsqlite3-0 libssl1.1:armel libstdc++-11-dev libstdc++-11-dev-armel-cross libstdc++-9-dev:armel libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtirpc-dev libtirpc-dev:armel libtirpc3:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db media-types perl perl-modules-5.32 po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.9 python3.9-minimal rpcsvc-proto sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel 0 upgraded, 129 newly installed, 0 to remove and 0 not upgraded. Need to get 276 MB of archives. After this operation, 981 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://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.37.2-4 [143 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-7 [935 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.4-1 [36.2 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.32 all 5.32.1-6 [2824 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.32 amd64 5.32.1-6 [4106 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.32.1-6 [293 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.9-minimal amd64 3.9.8-2 [805 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.4.1-3 [104 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 python3.9-minimal amd64 3.9.8-2 [1927 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 python3-minimal amd64 3.9.7-1 [38.4 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 media-types all 4.0.0 [30.3 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.36.0-2 [815 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.9-stdlib amd64 3.9.8-2 [1681 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 python3.9 amd64 3.9.8-2 [484 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3-stdlib amd64 3.9.7-1 [21.6 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 python3 amd64 3.9.7-1 [38.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main armel gcc-11-base armel 11.2.0-10 [206 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.4.0-3 [200 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.39-3 [69.1 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.71-2 [343 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.5-1 [823 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.21-4 [510 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.37-8 [2860 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.26-1 [104 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 rpcsvc-proto amd64 1.4.2-4 [63.1 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.32-4 [2251 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-11-dev amd64 11.2.0-10 [1952 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 g++-11 amd64 11.2.0-10 [49.7 MB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:11.2.0-2 [1636 B] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.9 [1537 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.9 [2153 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.9 [7704 B] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-arm-linux-gnueabi-base amd64 11.2.0-9cross1 [206 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-11-arm-linux-gnueabi amd64 11.2.0-9cross1 [48.3 MB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:11.2.0-2 [17.0 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-cross-base all 11.2.0-9cross1 [201 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.32-1cross4 [1121 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 11.2.0-9cross1 [38.5 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 11.2.0-9cross1 [88.5 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 11.2.0-9cross1 [8812 B] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libasan6-armel-cross all 11.2.0-9cross1 [1937 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 11.2.0-9cross1 [426 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 11.2.0-9cross1 [798 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-11-dev-armel-cross all 11.2.0-9cross1 [703 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-arm-linux-gnueabi amd64 11.2.0-9cross1 [54.8 MB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:11.2.0-2 [1460 B] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.10.46-4cross4 [1436 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.32-1cross4 [1801 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-11-dev-armel-cross all 11.2.0-9cross1 [1954 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 g++-11-arm-linux-gnueabi amd64 11.2.0-9cross1 [52.4 MB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:11.2.0-2 [1176 B] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.12+dfsg-5 [696 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2+b1 [337 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.9 [6704 B] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.5.2 [192 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-15 [513 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.12.0-2 [15.5 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.185-2 [172 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.21-4 [1311 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.5.2 [1056 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 help2man amd64 1.48.5 [143 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 11.2.0-10 [38.4 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.32-4 [2349 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.4.0-3 [2703 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 11.2.0-10 [9020 B] Get:102 http://debian.oregonstate.edu/debian unstable/main armel libbz2-1.0 armel 1.0.8-4 [45.5 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.14.16-1 [1407 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.26-1 [97.2 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.26-1 [113 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armel libcom-err2 armel 1.46.4-1 [74.5 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armel libkrb5support0 armel 1.18.3-7 [62.4 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armel libk5crypto3 armel 1.18.3-7 [108 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armel libkeyutils1 armel 1.6.1-2 [14.5 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main armel libssl1.1 armel 1.1.1l-1 [1279 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main armel libkrb5-3 armel 1.18.3-7 [315 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main armel libgssapi-krb5-2 armel 1.18.3-7 [142 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main armel libtirpc3 armel 1.3.2-2 [71.6 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main armel libnsl2 armel 1.3.0-2 [33.0 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main armel libtirpc-dev armel 1.3.2-2 [182 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main armel libnsl-dev armel 1.3.0-2 [61.7 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.32-4 [1849 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main armel libbz2-dev armel 1.0.8-4 [28.2 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 11.2.0-10 [90.7 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 11.2.0-10 [467 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 11.2.0-10 [799 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.4.0-3 [641 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main armel libjansson4 armel 2.13.1-1.1 [36.1 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main armel libjansson-dev armel 2.13.1-1.1 [38.6 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.4.0-3 [1761 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main amd64 python3-lib2to3 all 3.9.8-1 [79.5 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main amd64 python3-distutils all 3.9.8-1 [146 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-2 [84.7 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-2 [185 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 276 MB in 2s (129 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10557 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-4_amd64.deb ... Unpacking bsdextrautils (2.37.2-4) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_amd64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.4-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.4-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package perl-modules-5.32. Preparing to unpack .../05-perl-modules-5.32_5.32.1-6_all.deb ... Unpacking perl-modules-5.32 (5.32.1-6) ... 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Setting up libpython3.9-minimal:amd64 (3.9.8-2) ... Setting up libexpat1:amd64 (2.4.1-3) ... Setting up python3.9-minimal (3.9.8-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.7-1_amd64.deb ... Unpacking python3-minimal (3.9.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-2_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-2) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../3-libsqlite3-0_3.36.0-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.36.0-2) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../4-libpython3.9-stdlib_3.9.8-2_amd64.deb ... 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Selecting previously unselected package libgcc-s1:armel. Preparing to unpack .../077-libgcc-s1_11.2.0-10_armel.deb ... Unpacking libgcc-s1:armel (11.2.0-10) ... Selecting previously unselected package libc6:armel. Preparing to unpack .../078-libc6_2.32-4_armel.deb ... Unpacking libc6:armel (2.32-4) ... Selecting previously unselected package libasan5:armel. Preparing to unpack .../079-libasan5_9.4.0-3_armel.deb ... Unpacking libasan5:armel (9.4.0-3) ... Selecting previously unselected package libatomic1:armel. Preparing to unpack .../080-libatomic1_11.2.0-10_armel.deb ... Unpacking libatomic1:armel (11.2.0-10) ... Selecting previously unselected package libbz2-1.0:armel. Preparing to unpack .../081-libbz2-1.0_1.0.8-4_armel.deb ... Unpacking libbz2-1.0:armel (1.0.8-4) ... Selecting previously unselected package linux-libc-dev:armel. Preparing to unpack .../082-linux-libc-dev_5.14.16-1_armel.deb ... Unpacking linux-libc-dev:armel (5.14.16-1) ... 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Unpacking libkeyutils1:armel (1.6.1-2) ... Selecting previously unselected package libssl1.1:armel. Preparing to unpack .../089-libssl1.1_1.1.1l-1_armel.deb ... Unpacking libssl1.1:armel (1.1.1l-1) ... Selecting previously unselected package libkrb5-3:armel. Preparing to unpack .../090-libkrb5-3_1.18.3-7_armel.deb ... Unpacking libkrb5-3:armel (1.18.3-7) ... Selecting previously unselected package libgssapi-krb5-2:armel. Preparing to unpack .../091-libgssapi-krb5-2_1.18.3-7_armel.deb ... Unpacking libgssapi-krb5-2:armel (1.18.3-7) ... Selecting previously unselected package libtirpc3:armel. Preparing to unpack .../092-libtirpc3_1.3.2-2_armel.deb ... Unpacking libtirpc3:armel (1.3.2-2) ... Selecting previously unselected package libnsl2:armel. Preparing to unpack .../093-libnsl2_1.3.0-2_armel.deb ... Unpacking libnsl2:armel (1.3.0-2) ... Selecting previously unselected package libtirpc-dev:armel. Preparing to unpack .../094-libtirpc-dev_1.3.2-2_armel.deb ... 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Unpacking libubsan1:armel (11.2.0-10) ... Selecting previously unselected package libgcc-9-dev:armel. Preparing to unpack .../101-libgcc-9-dev_9.4.0-3_armel.deb ... Unpacking libgcc-9-dev:armel (9.4.0-3) ... Selecting previously unselected package libjansson4:armel. Preparing to unpack .../102-libjansson4_2.13.1-1.1_armel.deb ... Unpacking libjansson4:armel (2.13.1-1.1) ... Selecting previously unselected package libjansson-dev:armel. Preparing to unpack .../103-libjansson-dev_2.13.1-1.1_armel.deb ... Unpacking libjansson-dev:armel (2.13.1-1.1) ... Selecting previously unselected package libstdc++-9-dev:armel. Preparing to unpack .../104-libstdc++-9-dev_9.4.0-3_armel.deb ... Unpacking libstdc++-9-dev:armel (9.4.0-3) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../105-python3-lib2to3_3.9.8-1_all.deb ... Unpacking python3-lib2to3 (3.9.8-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../106-python3-distutils_3.9.8-1_all.deb ... Unpacking python3-distutils (3.9.8-1) ... Selecting previously unselected package zlib1g:armel. Preparing to unpack .../107-zlib1g_1%3a1.2.11.dfsg-2_armel.deb ... Unpacking zlib1g:armel (1:1.2.11.dfsg-2) ... Selecting previously unselected package zlib1g-dev:armel. Preparing to unpack .../108-zlib1g-dev_1%3a1.2.11.dfsg-2_armel.deb ... Unpacking zlib1g-dev:armel (1:1.2.11.dfsg-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy:armel. Preparing to unpack .../109-sbuild-build-depends-main-dummy_0.invalid.0_armel.deb ... Unpacking sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:amd64 (1.5.4-1) ... Setting up gcc-11-base:armel (11.2.0-10) ... Setting up binutils-arm-linux-gnueabi (2.37-8) ... Setting up gcc-11-arm-linux-gnueabi-base:amd64 (11.2.0-9cross1) ... 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:amd64 (67.1-7) ... Setting up cpp-11-arm-linux-gnueabi (11.2.0-9cross1) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up perl-modules-5.32 (5.32.1-6) ... Setting up libsqlite3-0:amd64 (3.36.0-2) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up linux-libc-dev:armel (5.14.16-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up linux-libc-dev-armel-cross (5.10.46-4cross4) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libtirpc-dev:amd64 (1.3.2-2) ... Setting up cpp-arm-linux-gnueabi (4:11.2.0-2) ... Setting up rpcsvc-proto (1.4.2-4) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libperl5.32:amd64 (5.32.1-6) ... Setting up libc6-armel-cross (2.32-1cross4) ... Setting up gcc-11-cross-base (11.2.0-9cross1) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:amd64 (1:4.4.26-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libc6-dev:amd64 (2.32-4) ... Setting up libc6-dev-armel-cross (2.32-1cross4) ... Setting up libelf1:amd64 (0.185-2) ... Setting up libxml2:amd64 (2.9.12+dfsg-5) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libpython3.9-stdlib:amd64 (3.9.8-2) ... Setting up libpython3-stdlib:amd64 (3.9.7-1) ... Setting up gcc-9-base:armel (9.4.0-3) ... Setting up gettext (0.21-4) ... Setting up libgomp1-armel-cross (11.2.0-9cross1) ... Setting up libtool (2.4.6-15) ... Setting up libgcc-s1-armel-cross (11.2.0-9cross1) ... Setting up m4 (1.4.18-5) ... Setting up libstdc++6-armel-cross (11.2.0-9cross1) ... Setting up libatomic1-armel-cross (11.2.0-9cross1) ... Setting up perl (5.32.1-6) ... Setting up libubsan1-armel-cross (11.2.0-9cross1) ... Setting up ucf (3.0043) ... Setting up libdpkg-perl (1.20.9) ... Setting up autoconf (2.71-2) ... Setting up libstdc++-11-dev:amd64 (11.2.0-10) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up libsub-override-perl (0.09-2) ... Setting up python3.9 (3.9.8-2) ... Setting up libasan6-armel-cross (11.2.0-9cross1) ... 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 libfile-which-perl (1.23-1) ... Setting up libgcc-11-dev-armel-cross (11.2.0-9cross1) ... Setting up g++-11 (11.2.0-10) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.5.2) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up python3 (3.9.7-1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up dpkg-dev (1.20.9) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.5) ... Setting up dh-autoreconf (20) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up g++ (4:11.2.0-2) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up libstdc++-11-dev-armel-cross (11.2.0-9cross1) ... Setting up build-essential (12.9) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up python3-lib2to3 (3.9.8-1) ... Setting up python3-distutils (3.9.8-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up gcc-11-arm-linux-gnueabi (11.2.0-9cross1) ... Setting up po-debconf (1.0.21+nmu1) ... 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 g++-11-arm-linux-gnueabi (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 dh-strip-nondeterminism (1.12.0-2) ... Setting up gcc-arm-linux-gnueabi (4:11.2.0-2) ... Setting up debhelper (13.5.2) ... Setting up g++-arm-linux-gnueabi (4:11.2.0-2) ... Setting up libxml-simple-perl (2.25-1) ... 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-armel (12.9) ... Setting up libgcc-s1:armel (11.2.0-10) ... Setting up libc6:armel (2.32-4) ... Setting up libbz2-1.0:armel (1.0.8-4) ... Setting up libstdc++6:armel (11.2.0-10) ... Setting up libkeyutils1:armel (1.6.1-2) ... Setting up libssl1.1:armel (1.1.1l-1) ... Setting up zlib1g:armel (1:1.2.11.dfsg-2) ... Setting up libcrypt1:armel (1:4.4.26-1) ... Setting up libcom-err2:armel (1.46.4-1) ... Setting up libgomp1:armel (11.2.0-10) ... Setting up libjansson4:armel (2.13.1-1.1) ... Setting up libkrb5support0:armel (1.18.3-7) ... Setting up libasan5:armel (9.4.0-3) ... Setting up libatomic1:armel (11.2.0-10) ... Setting up libk5crypto3:armel (1.18.3-7) ... Setting up libubsan1:armel (11.2.0-10) ... Setting up libcrypt-dev:armel (1:4.4.26-1) ... Setting up libkrb5-3:armel (1.18.3-7) ... Setting up libjansson-dev:armel (2.13.1-1.1) ... Setting up libgcc-9-dev:armel (9.4.0-3) ... Setting up libgssapi-krb5-2:armel (1.18.3-7) ... Setting up libtirpc3:armel (1.3.2-2) ... Setting up libtirpc-dev:armel (1.3.2-2) ... Setting up libnsl2:armel (1.3.0-2) ... Setting up libnsl-dev:armel (1.3.0-2) ... Setting up libc6-dev:armel (2.32-4) ... Setting up libbz2-dev:armel (1.0.8-4) ... Setting up libstdc++-9-dev:armel (9.4.0-3) ... Setting up zlib1g-dev:armel (1:1.2.11.dfsg-2) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.32-4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) amd64 (x86_64) Toolchain package versions: binutils_2.37-8 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-armel-cross_11.2.0-9cross1 libstdc++-9-dev_9.4.0-3 libstdc++6_11.2.0-10 libstdc++6-armel-cross_11.2.0-9cross1 linux-libc-dev_5.14.16-1 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_5.1-3.1 binutils_2.37-8 binutils-arm-linux-gnueabi_2.37-8 binutils-common_2.37-8 binutils-x86-64-linux-gnu_2.37-8 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4.1 cpp_4:11.2.0-2 cpp-11_11.2.0-10 cpp-11-arm-linux-gnueabi_11.2.0-9cross1 cpp-8_8.4.0-7 cpp-arm-linux-gnueabi_4:11.2.0-2 cross-config_2.6.18+nmu2 crossbuild-essential-armel_12.9 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 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 e2fsprogs_1.46.4-1 fakeroot_1.26-1 fdisk_2.37.2-4 file_1:5.39-3 findutils_4.8.0-1 g++_4:11.2.0-2 g++-11_11.2.0-10 g++-11-arm-linux-gnueabi_11.2.0-9cross1 g++-arm-linux-gnueabi_4:11.2.0-2 gcc_4:11.2.0-2 gcc-10-base_10.3.0-12 gcc-11_11.2.0-10 gcc-11-arm-linux-gnueabi_11.2.0-9cross1 gcc-11-arm-linux-gnueabi-base_11.2.0-9cross1 gcc-11-base_11.2.0-10 gcc-11-cross-base_11.2.0-9cross1 gcc-8-base_8.4.0-7 gcc-9-base_9.4.0-3 gcc-arm-linux-gnueabi_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-pkg5.0_1.8.4 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan5_9.4.0-3 libasan6_11.2.0-10 libasan6-armel-cross_11.2.0-9cross1 libatomic1_11.2.0-10 libatomic1-armel-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_2.37-8 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-armel-cross_2.32-1cross4 libc6-dev_2.32-4 libc6-dev-armel-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_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-8 libctf0_2.37-8 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 libext2fs2_1.46.4-1 libfakeroot_1.26-1 libfdisk1_2.37.2-4 libffi6_3.2.1-9 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-armel-cross_11.2.0-9cross1 libgcc-9-dev_9.4.0-3 libgcc-s1_11.2.0-10 libgcc-s1-armel-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-armel-cross_11.2.0-9cross1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl19_0.20-2 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 libmpx2_8.4.0-7 libncursesw6_6.2+20210905-1 libnettle6_3.5.1+really3.4.1-1 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_10.39-2 libpcre3_2:8.39-13 libperl5.28_5.28.1-6 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libpython3-stdlib_3.9.7-1 libpython3.9-minimal_3.9.8-2 libpython3.9-stdlib_3.9.8-2 libquadmath0_11.2.0-10 libreadline8_8.1-2 libseccomp2_2.5.2-2 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage1_3.1-2 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10 libstdc++-11-dev-armel-cross_11.2.0-9cross1 libstdc++-9-dev_9.4.0-3 libstdc++6_11.2.0-10 libstdc++6-armel-cross_11.2.0-9cross1 libsub-override-perl_0.09-2 libsystemd0_249.6-1 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 libubsan1_11.2.0-10 libubsan1-armel-cross_11.2.0-9cross1 libuchardet0_0.0.7-1 libudev1_249.6-1 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_5.14.16-1 linux-libc-dev-armel-cross_5.10.46-4cross4 login_1:4.8.1-2 logsave_1.46.4-1 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_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.28_5.28.1-6 perl-modules-5.32_5.32.1-6 po-debconf_1.0.21+nmu1 python3_3.9.7-1 python3-distutils_3.9.8-1 python3-lib2to3_3.9.8-1 python3-minimal_3.9.7-1 python3.9_3.9.8-2 python3.9-minimal_3.9.8-2 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----- 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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 User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-90bcb4af-9213-4b74-94a9-355624777033 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -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 arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel 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=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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; 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; 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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:28, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/11/algorithm:62, from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:28, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:37: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h: In function ‘void std::nth_element(_RAIter, _RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]’: /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:4754:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 4754 | nth_element(_RandomAccessIterator __first, _RandomAccessIterator __nth, | ^~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:4754:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/11/bits/stl_algo.h:4754:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/11/vector:72, from Bedmap.cpp:35: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34, from Bedmap.cpp:37: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor, true>, double, true>, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor, Bed::NoPool::Bed5, true>, double, true> >; ExceptionType = Ext::Exception, 2>]’: ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:100:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 100 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:103:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 103 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:108:25: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 108 | std::nth_element(vec.begin(), n, vec.end()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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; 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::BedPadReader::CleanAll() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedPadReader.hpp:183:28, inlined from ‘static void BedOperations::createWork, Bed::bed_check_iterator >::run(const BedOperations::Input&) [with BedType1 = Bed::BasicCoords; BedType2 = Bed::BasicCoords; unsigned int Sz = 512]’ at Bedops.cpp:401:30: ../../../../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 static member function ‘static void BedOperations::createWork, Bed::bed_check_iterator >::run(const BedOperations::Input&) [with BedType1 = Bed::BasicCoords; BedType2 = Bed::BasicCoords; unsigned int Sz = 512]’: ../../../../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; 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; 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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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_process_intermediate_bytes_by_lines’: convert2bed.c:6631:103: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 6631 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int long unsigned int | %lu convert2bed.c:6631:109: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘long unsigned int’ [-Wformat=] 6631 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int long unsigned int | %lu convert2bed.c:6631:115: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘long unsigned int’ [-Wformat=] 6631 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int 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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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 && arm-linux-gnueabi-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_JSONMetadataExists(FILE**, const char*)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1089:20: warning: comparison is always true due to limited range of data type [-Wtype-limits] 1089 | } while (currC != EOF); | ^ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1090:63: warning: comparison is always false due to limited range of data type [-Wtype-limits] 1090 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) { | ^ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1306:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] 1306 | } while (currC != EOF); | ^ ../../../../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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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 && arm-linux-gnueabi-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; 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; 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; 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; 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; 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; 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; 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; 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; 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 && arm-linux-gnueabi-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 arm-linux-gnueabi-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 arm-linux-gnueabi-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 arm-linux-gnueabi-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::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’: ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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 arm-linux-gnueabi-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_JSONMetadataExists(FILE**, const char*)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1089:20: warning: comparison is always true due to limited range of data type [-Wtype-limits] 1089 | } while (currC != EOF); | ^ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1090:63: warning: comparison is always false due to limited range of data type [-Wtype-limits] 1090 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) { | ^ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’: ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1306:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] 1306 | } while (currC != EOF); | ^ ../../../../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 arm-linux-gnueabi-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 arm-linux-gnueabi-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 arm-linux-gnueabi-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 arm-linux-gnueabi-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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-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 arm-linux-gnueabi-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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-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 arm-linux-gnueabi-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/arm-linux-gnueabi/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:2131:78: warning: left shift count >= width of type [-Wshift-count-overflow] 2131 | bzOutBytesWritten = static_cast( bzOutBytesWrittenHi32 ) << 32 | bzOutBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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/arm-linux-gnueabi/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/arm-linux-gnueabi/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); | ~~~~~~^~~~~~~ arm-linux-gnueabi-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 arm-linux-gnueabi-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 )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-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 dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedextract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bedops/usr/bin/sort-bed contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bedops/usr/bin/closest-features contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedops contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedmap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'bedops' in '../bedops_2.4.40+dfsg-1_armel.deb'. dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.40+dfsg-1_armel.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bedops_2.4.40+dfsg-1_armel.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 2021-11-12T21:14:24Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedops_2.4.40+dfsg-1_armel.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: armel 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: b6e3c01924d8846d186fce032295bc9bac5d5127 78552 bedops-dbgsym_2.4.40+dfsg-1_armel.deb bda9890770f35df09ba34d26303fb43070d2ab94 5560 bedops_2.4.40+dfsg-1_armel.buildinfo 0776320128e4c78e59c1444cfbf904b54736a063 1157384 bedops_2.4.40+dfsg-1_armel.deb Checksums-Sha256: 61d8015a47c700d84fa67fb50458d201c45a1f3b6d85a0431d9a9aaa45d5c163 78552 bedops-dbgsym_2.4.40+dfsg-1_armel.deb 760b7011958aa7c7a023032a74ab77ae7d11437d870968541c050e1e3332fee2 5560 bedops_2.4.40+dfsg-1_armel.buildinfo 28fceb66447554f463eeab0ad88a21c9c181d44bf81189701bfc37a043778bd8 1157384 bedops_2.4.40+dfsg-1_armel.deb Files: 962def0f9e5aedc7cb6ccd1f3503e122 78552 debug optional bedops-dbgsym_2.4.40+dfsg-1_armel.deb 8728ed845c9d5397d2af4baf11a68352 5560 science optional bedops_2.4.40+dfsg-1_armel.buildinfo b32b868f4a5af495cae27c77429e8f2b 1157384 science optional bedops_2.4.40+dfsg-1_armel.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bedops Binary: bedops bedops-dbgsym Architecture: armel Version: 2.4.40+dfsg-1 Checksums-Md5: 962def0f9e5aedc7cb6ccd1f3503e122 78552 bedops-dbgsym_2.4.40+dfsg-1_armel.deb b32b868f4a5af495cae27c77429e8f2b 1157384 bedops_2.4.40+dfsg-1_armel.deb Checksums-Sha1: b6e3c01924d8846d186fce032295bc9bac5d5127 78552 bedops-dbgsym_2.4.40+dfsg-1_armel.deb 0776320128e4c78e59c1444cfbf904b54736a063 1157384 bedops_2.4.40+dfsg-1_armel.deb Checksums-Sha256: 61d8015a47c700d84fa67fb50458d201c45a1f3b6d85a0431d9a9aaa45d5c163 78552 bedops-dbgsym_2.4.40+dfsg-1_armel.deb 28fceb66447554f463eeab0ad88a21c9c181d44bf81189701bfc37a043778bd8 1157384 bedops_2.4.40+dfsg-1_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Fri, 12 Nov 2021 21:14:24 +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 (= 5.1-3.1), binutils (= 2.37-8), binutils-common (= 2.37-8), binutils-x86-64-linux-gnu (= 2.37-8), bsdextrautils (= 2.37.2-4), bsdutils (= 1:2.37.2-4), build-essential (= 12.9), bzip2 (= 1.0.8-4), coreutils (= 8.32-4.1), cpp (= 4:11.2.0-2), cpp-11 (= 11.2.0-10), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), 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 (= 2.37-8), 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 (= 1:4.4.26-1), libcrypt1 (= 1:4.4.26-1), libctf-nobfd0 (= 2.37-8), libctf0 (= 2.37-8), 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 (= 10.39-2), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.1-6), libpipeline1 (= 1.5.4-1), libpython3-stdlib (= 3.9.7-1), libpython3.9-minimal (= 3.9.8-2), libpython3.9-stdlib (= 3.9.8-2), libquadmath0 (= 11.2.0-10), libreadline8 (= 8.1-2), libseccomp2 (= 2.5.2-2), libselinux1 (= 3.3-1), 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++6 (= 11.2.0-10), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.6-1), 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 (= 249.6-1), 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 (= 5.14.16-1), login (= 1:4.8.1-2), 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 (= 3.9.7-1), python3-distutils (= 3.9.8-1), python3-lib2to3 (= 3.9.8-1), python3-minimal (= 3.9.7-1), python3.9 (= 3.9.8-2), python3.9-minimal (= 3.9.8-2), 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_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1635061815" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedops-dbgsym_2.4.40+dfsg-1_armel.deb ------------------------------------- new Debian package, version 2.0. size 78552 bytes: control archive=540 bytes. 377 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: armel Maintainer: Debian Med Packaging Team Installed-Size: 95 Depends: bedops (= 2.4.40+dfsg-1) Section: debug Priority: optional Description: debug symbols for bedops Build-Ids: a0c2e8841954209b5d0881d21f1413bcec94e6c7 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/a0/ -rw-r--r-- root/root 86076 2021-10-24 07:50 ./usr/lib/debug/.build-id/a0/c2e8841954209b5d0881d21f1413bcec94e6c7.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_armel.deb ------------------------------ new Debian package, version 2.0. size 1157384 bytes: control archive=6148 bytes. 730 bytes, 15 lines control 21485 bytes, 236 lines md5sums Package: bedops Version: 2.4.40+dfsg-1 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 7911 Depends: libbz2-1.0, libc6 (>= 2.28), libgcc-s1 (>= 3.5), 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 194864 2021-10-24 07:50 ./usr/bin/bedextract -rwxr-xr-x root/root 5980576 2021-10-24 07:50 ./usr/bin/bedmap -rwxr-xr-x root/root 404148 2021-10-24 07:50 ./usr/bin/bedops -rwxr-xr-x root/root 87988 2021-10-24 07:50 ./usr/bin/bedops-starch -rwxr-xr-x root/root 236040 2021-10-24 07:50 ./usr/bin/closest-features -rwxr-xr-x root/root 125296 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 207164 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 161736 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 92016 2021-10-24 07:50 ./usr/bin/starchstrip -rwxr-xr-x root/root 124712 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 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./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 365 2021-10-24 07:50 ./usr/share/man/man1/bedextract.1.gz -rw-r--r-- root/root 358 2021-10-24 07:50 ./usr/share/man/man1/bedmap.1.gz -rw-r--r-- root/root 372 2021-10-24 07:50 ./usr/share/man/man1/bedops-starch.1.gz -rw-r--r-- root/root 357 2021-10-24 07:50 ./usr/share/man/man1/bedops.1.gz -rw-r--r-- root/root 375 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 363 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 363 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:amd64 Filtered Build-Depends: lintian:amd64 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 [657 B] Fetched 2193 B in 0s (86.0 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 libbusiness-isbn-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:armel t1utils unzip 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 6788 kB of archives. After this operation, 20.3 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.64-1 [36.6 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.5-1 [51.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.27-2 [547 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.27-2 [927 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libaliased-perl all 0.34-1.1 [14.1 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.40 [72.2 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b3 [11.3 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b2 [15.9 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b3 [25.7 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b3 [45.7 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.25-1 [19.5 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-3+b7 [38.1 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.45-1+b1 [15.4 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-tiny-perl all 2.27-1 [17.1 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-util-perl amd64 1.102-1+b1 [25.6 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libconst-fast-perl all 0.014-1.1 [8552 B] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.27-1 [129 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libiterator-perl all 0.03+ds1-1.1 [18.4 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-xs-perl amd64 0.430-2 [40.9 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-messagepack-perl amd64 1.01-2 [35.5 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-size-perl amd64 0.83-1+b2 [26.1 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-address-xs-perl amd64 1.04-1+b3 [28.0 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-2 [7448 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.11-2 [8992 B] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libio-prompt-tiny-perl all 0.003-1 [9150 B] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.005004-2 [60.4 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libmouse-perl amd64 2.5.10-1+b1 [172 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b3 [12.0 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1+b1 [13.8 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.120-1 [54.7 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-gzip-perl amd64 0.19-1+b7 [17.4 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.008-1+b1 [12.0 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libproc-processtable-perl amd64 0.634-1 [46.5 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.018+ds-1+b1 [99.3 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.018+ds-1+b1 [103 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libsort-versions-perl all 1.62-1 [11.0 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-1+b2 [27.8 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-4+b8 [8724 B] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.13-1 [13.2 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.9-1 [197 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-moment-perl amd64 0.44-1+b3 [75.8 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.012004-1 [351 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b2 [20.3 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 5.10-1 [91.0 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.83+ds-1 [35.5 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 lzip amd64 1.22-4 [88.2 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 unzip amd64 6.0-26 [171 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.111.0 [1340 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6788 kB in 0s (30.7 MB/s) Selecting previously unselected package diffstat. (Reading database ... 22116 files and directories currently installed.) Preparing to unpack .../00-diffstat_1.64-1_amd64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../01-libassuan0_2.5.5-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.5-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../02-gpgconf_2.2.27-2_amd64.deb ... Unpacking gpgconf (2.2.27-2) ... Selecting previously unselected package gpg. Preparing to unpack .../03-gpg_2.2.27-2_amd64.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_amd64.deb ... Unpacking libapt-pkg-perl (0.1.40) ... Selecting previously unselected package libb-hooks-op-check-perl. 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Unpacking libsub-identify-perl (0.14-1+b3) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../66-libsub-name-perl_0.26-1+b1_amd64.deb ... Unpacking libsub-name-perl (0.26-1+b1) ... Selecting previously unselected package libnamespace-clean-perl. Preparing to unpack .../67-libnamespace-clean-perl_0.27-1_all.deb ... Unpacking libnamespace-clean-perl (0.27-1) ... Selecting previously unselected package libpath-tiny-perl. Preparing to unpack .../68-libpath-tiny-perl_0.120-1_all.deb ... Unpacking libpath-tiny-perl (0.120-1) ... Selecting previously unselected package libperlio-gzip-perl. Preparing to unpack .../69-libperlio-gzip-perl_0.19-1+b7_amd64.deb ... Unpacking libperlio-gzip-perl (0.19-1+b7) ... Selecting previously unselected package libperlio-utf8-strict-perl. Preparing to unpack .../70-libperlio-utf8-strict-perl_0.008-1+b1_amd64.deb ... Unpacking libperlio-utf8-strict-perl (0.008-1+b1) ... Selecting previously unselected package libproc-processtable-perl:amd64. Preparing to unpack .../71-libproc-processtable-perl_0.634-1_amd64.deb ... Unpacking libproc-processtable-perl:amd64 (0.634-1) ... Selecting previously unselected package libsereal-decoder-perl. Preparing to unpack .../72-libsereal-decoder-perl_4.018+ds-1+b1_amd64.deb ... Unpacking libsereal-decoder-perl (4.018+ds-1+b1) ... Selecting previously unselected package libsereal-encoder-perl. Preparing to unpack .../73-libsereal-encoder-perl_4.018+ds-1+b1_amd64.deb ... Unpacking libsereal-encoder-perl (4.018+ds-1+b1) ... Selecting previously unselected package libsort-versions-perl. Preparing to unpack .../74-libsort-versions-perl_1.62-1_all.deb ... Unpacking libsort-versions-perl (1.62-1) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../75-libterm-readkey-perl_2.38-1+b2_amd64.deb ... Unpacking libterm-readkey-perl (2.38-1+b2) ... Selecting previously unselected package libtext-levenshteinxs-perl. Preparing to unpack .../76-libtext-levenshteinxs-perl_0.03-4+b8_amd64.deb ... Unpacking libtext-levenshteinxs-perl (0.03-4+b8) ... Selecting previously unselected package libtext-markdown-discount-perl:amd64. Preparing to unpack .../77-libtext-markdown-discount-perl_0.13-1_amd64.deb ... Unpacking libtext-markdown-discount-perl:amd64 (0.13-1) ... Selecting previously unselected package libtext-xslate-perl:amd64. Preparing to unpack .../78-libtext-xslate-perl_3.5.9-1_amd64.deb ... Unpacking libtext-xslate-perl:amd64 (3.5.9-1) ... Selecting previously unselected package libtime-duration-perl. Preparing to unpack .../79-libtime-duration-perl_1.21-1_all.deb ... Unpacking libtime-duration-perl (1.21-1) ... Selecting previously unselected package libtime-moment-perl. Preparing to unpack .../80-libtime-moment-perl_0.44-1+b3_amd64.deb ... Unpacking libtime-moment-perl (0.44-1+b3) ... 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 47108 Build-Time: 528 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 43 Job: bedops_2.4.40+dfsg-1 Lintian: pass Machine Architecture: amd64 Package: bedops Package-Time: 587 Source-Version: 2.4.40+dfsg-1 Space: 47108 Status: successful Version: 2.4.40+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-11-12T21:14:24Z Build needed 00:09:47, 47108k disk space