sbuild (Debian sbuild) 0.81.2 (31 January 2021) on debian-ci-siliconvalley +==============================================================================+ | bedops 2.4.41+dfsg-1 (armel) Thu, 21 Jul 2022 01:53:42 +0000 | +==============================================================================+ Package: bedops Version: 2.4.41+dfsg-1 Source Version: 2.4.41+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/sid-amd64-sbuild-01262a41-91a9-4110-8cf5-6b2c77837717' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-V0DInB/resolver-7sFKZ4' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://localhost:3142/debian sid InRelease Get:2 http://localhost:3142/debian sid/main armel Packages [8831 kB] Fetched 8831 kB in 1s (6317 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://localhost:3142/debian sid/main bedops 2.4.41+dfsg-1 (dsc) [2178 B] Get:2 http://localhost:3142/debian sid/main bedops 2.4.41+dfsg-1 (tar) [13.5 MB] Get:3 http://localhost:3142/debian sid/main bedops 2.4.41+dfsg-1 (diff) [10.4 kB] Fetched 13.5 MB in 0s (188 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedops-V0DInB/bedops-2.4.41+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-V0DInB' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), 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 (= 13), 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 [440 B] Get:5 copy:/<>/apt_archive ./ Packages [527 B] Fetched 1924 B in 0s (0 B/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 cpp-11-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file 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-12-base:armel gcc-12-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:armel libasan6-armel-cross libatomic1:armel libatomic1-armel-cross libbz2-1.0:armel libbz2-dev:armel libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:armel libgcc-11-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libicu71 libio-string-perl libjansson-dev:armel libjansson4:armel libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libncursesw6 libnsl-dev:armel libnsl2:armel libpipeline1 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libreadline8 libsigsegv2 libsqlite3-0 libssl3:armel libstdc++-11-dev:armel libstdc++-11-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl 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 po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.10 python3.10-minimal readline-common 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 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 manpages-dev:armel krb5-doc:armel krb5-user:armel libstdc++-11-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.10-venv python3.10-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx bzip2-doc:armel libidn2-0:armel libarchive-cpio-perl krb5-locales:armel libgpm2 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdextrautils cpp-11-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file 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-12-base:armel gcc-12-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:armel libasan6-armel-cross libatomic1:armel libatomic1-armel-cross libbz2-1.0:armel libbz2-dev:armel libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:armel libgcc-11-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libicu71 libio-string-perl libjansson-dev:armel libjansson4:armel libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libncursesw6 libnsl-dev:armel libnsl2:armel libpipeline1 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libreadline8 libsigsegv2 libsqlite3-0 libssl3:armel libstdc++-11-dev:armel libstdc++-11-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl 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 po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.10 python3.10-minimal readline-common sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel 0 upgraded, 119 newly installed, 0 to remove and 0 not upgraded. Need to get 90.1 MB of archives. After this operation, 356 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [960 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4+b2 [19.2 kB] Get:3 http://localhost:3142/debian sid/main amd64 libpython3.10-minimal amd64 3.10.5-1 [828 kB] Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.4.8-1 [109 kB] Get:5 http://localhost:3142/debian sid/main amd64 python3.10-minimal amd64 3.10.5-1 [2093 kB] Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.10.5-3 [38.6 kB] Get:7 http://localhost:3142/debian sid/main amd64 media-types all 8.0.0 [33.4 kB] Get:8 http://localhost:3142/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:9 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.3+20220423-2 [133 kB] Get:10 http://localhost:3142/debian sid/main amd64 readline-common all 8.1.2-1.2 [73.9 kB] Get:11 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.1.2-1.2 [168 kB] Get:12 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.39.1-1 [836 kB] Get:13 http://localhost:3142/debian sid/main amd64 libpython3.10-stdlib amd64 3.10.5-1 [1704 kB] Get:14 http://localhost:3142/debian sid/main amd64 python3.10 amd64 3.10.5-1 [541 kB] Get:15 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.10.5-3 [21.7 kB] Get:16 http://localhost:3142/debian sid/main amd64 python3 amd64 3.10.5-3 [38.2 kB] Get:17 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.41-4 [295 kB] Get:19 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.41-4 [129 kB] Get:20 http://localhost:3142/debian sid/main amd64 file amd64 1:5.41-4 [67.0 kB] Get:21 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-6 [175 kB] Get:22 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:23 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-8 [936 kB] Get:24 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38-5 [144 kB] Get:25 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.6-1 [38.6 kB] Get:26 http://localhost:3142/debian sid/main amd64 man-db amd64 2.10.2-1 [1411 kB] Get:27 http://localhost:3142/debian sid/main amd64 ucf all 3.0043 [74.0 kB] Get:28 http://localhost:3142/debian sid/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB] Get:29 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:30 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:31 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:32 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:33 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-6 [510 kB] Get:34 http://localhost:3142/debian sid/main amd64 binutils-arm-linux-gnueabi amd64 2.38.90.20220713-2 [3175 kB] Get:35 http://localhost:3142/debian sid/main amd64 gcc-11-arm-linux-gnueabi-base amd64 11.3.0-3cross1 [209 kB] Get:36 http://localhost:3142/debian sid/main amd64 cpp-11-arm-linux-gnueabi amd64 11.3.0-3cross1 [8049 kB] Get:37 http://localhost:3142/debian sid/main amd64 cpp-arm-linux-gnueabi amd64 4:11.2.0-2 [17.0 kB] Get:38 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:39 http://localhost:3142/debian sid/main amd64 gcc-11-cross-base all 11.3.0-3cross1 [204 kB] Get:40 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base all 12.1.0-2cross1 [202 kB] Get:41 http://localhost:3142/debian sid/main amd64 libc6-armel-cross all 2.33-1cross1 [1130 kB] Get:42 http://localhost:3142/debian sid/main amd64 libgcc-s1-armel-cross all 12.1.0-2cross1 [38.5 kB] Get:43 http://localhost:3142/debian sid/main amd64 libgomp1-armel-cross all 12.1.0-2cross1 [96.8 kB] Get:44 http://localhost:3142/debian sid/main amd64 libatomic1-armel-cross all 12.1.0-2cross1 [8872 B] Get:45 http://localhost:3142/debian sid/main amd64 libasan6-armel-cross all 11.3.0-3cross1 [1937 kB] Get:46 http://localhost:3142/debian sid/main amd64 libstdc++6-armel-cross all 12.1.0-2cross1 [465 kB] Get:47 http://localhost:3142/debian sid/main amd64 libubsan1-armel-cross all 12.1.0-2cross1 [861 kB] Get:48 http://localhost:3142/debian sid/main amd64 libgcc-11-dev-armel-cross all 11.3.0-3cross1 [704 kB] Get:49 http://localhost:3142/debian sid/main amd64 gcc-11-arm-linux-gnueabi amd64 11.3.0-3cross1 [15.9 MB] Get:50 http://localhost:3142/debian sid/main amd64 gcc-arm-linux-gnueabi amd64 4:11.2.0-2 [1460 B] Get:51 http://localhost:3142/debian sid/main amd64 linux-libc-dev-armel-cross all 5.15.5-1cross1 [1541 kB] Get:52 http://localhost:3142/debian sid/main amd64 libc6-dev-armel-cross all 2.33-1cross1 [1810 kB] Get:53 http://localhost:3142/debian sid/main amd64 libstdc++-11-dev-armel-cross all 11.3.0-3cross1 [1972 kB] Get:54 http://localhost:3142/debian sid/main amd64 g++-11-arm-linux-gnueabi amd64 11.3.0-3cross1 [8933 kB] Get:55 http://localhost:3142/debian sid/main amd64 g++-arm-linux-gnueabi amd64 4:11.2.0-2 [1176 B] Get:56 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:57 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:58 http://localhost:3142/debian sid/main amd64 libicu71 amd64 71.1-3 [9218 kB] Get:59 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1 [708 kB] Get:60 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:61 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-2 [21.0 kB] Get:62 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:63 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1 [337 kB] Get:64 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:65 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:66 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:67 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-1 [17.3 kB] Get:68 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:69 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:70 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:71 http://localhost:3142/debian sid/main amd64 crossbuild-essential-armel all 12.9 [6704 B] Get:72 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.8 [195 kB] Get:73 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-4 [526 kB] Get:74 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:75 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:76 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-3 [10.4 kB] Get:77 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Get:78 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Get:79 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.187-1 [179 kB] Get:80 http://localhost:3142/debian sid/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:81 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-6 [1310 kB] Get:82 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:83 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:84 http://localhost:3142/debian sid/main amd64 debhelper all 13.8 [1070 kB] Get:85 http://localhost:3142/debian sid/main armel gcc-11-base armel 11.3.0-5 [209 kB] Get:86 http://localhost:3142/debian sid/main armel gcc-12-base armel 12.1.0-7 [207 kB] Get:87 http://localhost:3142/debian sid/main amd64 help2man amd64 1.49.2 [202 kB] Get:88 http://localhost:3142/debian sid/main armel libgcc-s1 armel 12.1.0-7 [38.5 kB] Get:89 http://localhost:3142/debian sid/main armel libc6 armel 2.33-8 [2423 kB] Get:90 http://localhost:3142/debian sid/main armel libasan6 armel 11.3.0-5 [1944 kB] Get:91 http://localhost:3142/debian sid/main armel libatomic1 armel 12.1.0-7 [9164 B] Get:92 http://localhost:3142/debian sid/main armel libbz2-1.0 armel 1.0.8-5 [44.8 kB] Get:93 http://localhost:3142/debian sid/main armel linux-libc-dev armel 5.18.5-1 [1560 kB] Get:94 http://localhost:3142/debian sid/main armel libcrypt1 armel 1:4.4.28-2 [97.6 kB] Get:95 http://localhost:3142/debian sid/main armel libcrypt-dev armel 1:4.4.28-2 [127 kB] Get:96 http://localhost:3142/debian sid/main armel libcom-err2 armel 1.46.5-2 [74.9 kB] Get:97 http://localhost:3142/debian sid/main armel libkrb5support0 armel 1.19.2-2+b2 [62.8 kB] Get:98 http://localhost:3142/debian sid/main armel libk5crypto3 armel 1.19.2-2+b2 [108 kB] Get:99 http://localhost:3142/debian sid/main armel libkeyutils1 armel 1.6.3-1 [14.8 kB] Get:100 http://localhost:3142/debian sid/main armel libssl3 armel 3.0.4-2 [1646 kB] Get:101 http://localhost:3142/debian sid/main armel libkrb5-3 armel 1.19.2-2+b2 [316 kB] Get:102 http://localhost:3142/debian sid/main armel libgssapi-krb5-2 armel 1.19.2-2+b2 [143 kB] Get:103 http://localhost:3142/debian sid/main armel libtirpc3 armel 1.3.2-2 [71.6 kB] Get:104 http://localhost:3142/debian sid/main armel libnsl2 armel 1.3.0-2 [33.0 kB] Get:105 http://localhost:3142/debian sid/main armel libtirpc-dev armel 1.3.2-2 [182 kB] Get:106 http://localhost:3142/debian sid/main armel libnsl-dev armel 1.3.0-2 [61.7 kB] Get:107 http://localhost:3142/debian sid/main armel libc6-dev armel 2.33-8 [1857 kB] Get:108 http://localhost:3142/debian sid/main armel libbz2-dev armel 1.0.8-5 [27.4 kB] Get:109 http://localhost:3142/debian sid/main armel libgomp1 armel 12.1.0-7 [99.1 kB] Get:110 http://localhost:3142/debian sid/main armel libstdc++6 armel 12.1.0-7 [507 kB] Get:111 http://localhost:3142/debian sid/main armel libubsan1 armel 12.1.0-7 [862 kB] Get:112 http://localhost:3142/debian sid/main armel libgcc-11-dev armel 11.3.0-5 [704 kB] Get:113 http://localhost:3142/debian sid/main armel libjansson4 armel 2.14-2 [36.9 kB] Get:114 http://localhost:3142/debian sid/main armel libjansson-dev armel 2.14-2 [39.5 kB] Get:115 http://localhost:3142/debian sid/main armel libstdc++-11-dev armel 11.3.0-5 [1974 kB] Get:116 http://localhost:3142/debian sid/main amd64 python3-lib2to3 all 3.10.5-2 [80.9 kB] Get:117 http://localhost:3142/debian sid/main amd64 python3-distutils all 3.10.5-2 [147 kB] Get:118 http://localhost:3142/debian sid/main armel zlib1g armel 1:1.2.11.dfsg-4 [84.4 kB] Get:119 http://localhost:3142/debian sid/main armel zlib1g-dev armel 1:1.2.11.dfsg-4 [184 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 90.1 MB in 1s (171 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Selecting previously unselected package sbuild-build-depends-main-dummy:armel. Preparing to unpack .../104-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 (8.0.0) ... Setting up libpipeline1:amd64 (1.5.6-1) ... Setting up libicu71:amd64 (71.1-3) ... Setting up gcc-11-base:armel (11.3.0-5) ... Setting up libfile-which-perl (1.27-1) ... Setting up binutils-arm-linux-gnueabi (2.38.90.20220713-2) ... Setting up gcc-11-arm-linux-gnueabi-base:amd64 (11.3.0-3cross1) ... Setting up gcc-12-cross-base (12.1.0-2cross1) ... Setting up bsdextrautils (2.38-5) ... Setting up cpp-11-arm-linux-gnueabi (11.3.0-3cross1) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.8) ... Setting up libsqlite3-0:amd64 (3.39.1-1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up linux-libc-dev:armel (5.18.5-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-6) ... Setting up file (1:5.41-4) ... Setting up libyaml-perl (1.30-1) ... Setting up linux-libc-dev-armel-cross (5.15.5-1cross1) ... Setting up gcc-12-base:armel (12.1.0-7) ... Setting up libxml-sax-base-perl (1.09-2) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up cpp-arm-linux-gnueabi (4:11.2.0-2) ... Setting up libsigsegv2:amd64 (2.14-1) ... Setting up autopoint (0.21-6) ... Setting up libncursesw6:amd64 (6.3+20220423-2) ... Setting up libc6-armel-cross (2.33-1cross1) ... Setting up gcc-11-cross-base (11.3.0-3cross1) ... Setting up sensible-utils (0.0.17) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libsub-override-perl (0.09-3) ... Setting up libc6-dev-armel-cross (2.33-1cross1) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up libelf1:amd64 (0.187-1) ... Setting up readline-common (8.1.2-1.2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-4+b2) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up gettext (0.21-6) ... Setting up libgomp1-armel-cross (12.1.0-2cross1) ... Setting up libtool (2.4.7-4) ... Setting up libreadline8:amd64 (8.1.2-1.2) ... Setting up libgcc-s1-armel-cross (12.1.0-2cross1) ... Setting up m4 (1.4.18-5) ... Setting up libstdc++6-armel-cross (12.1.0-2cross1) ... Setting up libatomic1-armel-cross (12.1.0-2cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.49.2) ... Setting up libpython3.10-stdlib:amd64 (3.10.5-1) ... Setting up libubsan1-armel-cross (12.1.0-2cross1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-8) ... Setting up libasan6-armel-cross (11.3.0-3cross1) ... Setting up libpython3-stdlib:amd64 (3.10.5-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgcc-11-dev-armel-cross (11.3.0-3cross1) ... Setting up python3.10 (3.10.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.10.5-3) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up dh-autoreconf (20) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-11-dev-armel-cross (11.3.0-3cross1) ... Setting up python3-lib2to3 (3.10.5-2) ... Setting up python3-distutils (3.10.5-2) ... Setting up gcc-11-arm-linux-gnueabi (11.3.0-3cross1) ... Setting up debhelper (13.8) ... Setting up g++-11-arm-linux-gnueabi (11.3.0-3cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-arm-linux-gnueabi (4:11.2.0-2) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-arm-linux-gnueabi (4:11.2.0-2) ... 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 (12.1.0-7) ... Setting up libc6:armel (2.33-8) ... Setting up libbz2-1.0:armel (1.0.8-5) ... Setting up libstdc++6:armel (12.1.0-7) ... Setting up libkeyutils1:armel (1.6.3-1) ... Setting up zlib1g:armel (1:1.2.11.dfsg-4) ... Setting up libcrypt1:armel (1:4.4.28-2) ... Setting up libcom-err2:armel (1.46.5-2) ... Setting up libgomp1:armel (12.1.0-7) ... Setting up libasan6:armel (11.3.0-5) ... Setting up libjansson4:armel (2.14-2) ... Setting up libkrb5support0:armel (1.19.2-2+b2) ... Setting up libatomic1:armel (12.1.0-7) ... Setting up libk5crypto3:armel (1.19.2-2+b2) ... Setting up libubsan1:armel (12.1.0-7) ... Setting up libgcc-11-dev:armel (11.3.0-5) ... Setting up libcrypt-dev:armel (1:4.4.28-2) ... Setting up libjansson-dev:armel (2.14-2) ... Setting up libssl3:armel (3.0.4-2) ... Setting up libkrb5-3:armel (1.19.2-2+b2) ... Setting up libgssapi-krb5-2:armel (1.19.2-2+b2) ... 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 (2.33-8) ... Setting up libbz2-dev:armel (1.0.8-5) ... Setting up libstdc++-11-dev:armel (11.3.0-5) ... Setting up zlib1g-dev:armel (1:1.2.11.dfsg-4) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.33-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-15-amd64 #1 SMP Debian 5.10.120-1 (2022-06-09) amd64 (x86_64) Toolchain package versions: binutils_2.38.90.20220713-2 dpkg-dev_1.21.9 g++-11_11.3.0-5 gcc-11_11.3.0-5 libc6-dev_2.33-8 libstdc++-11-dev_11.3.0-5 libstdc++-11-dev-armel-cross_11.3.0-3cross1 libstdc++6_12.1.0-7 libstdc++6-armel-cross_12.1.0-2cross1 linux-libc-dev_5.18.5-1 Package versions: adduser_3.122 apt_2.5.1 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2 base-passwd_3.5.52 bash_5.1-6.1 binutils_2.38.90.20220713-2 binutils-arm-linux-gnueabi_2.38.90.20220713-2 binutils-common_2.38.90.20220713-2 binutils-x86-64-linux-gnu_2.38.90.20220713-2 bsdextrautils_2.38-5 bsdutils_1:2.38-5 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2 cpp-11_11.3.0-5 cpp-11-arm-linux-gnueabi_11.3.0-3cross1 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-8 debconf_1.5.79 debhelper_13.8 debian-archive-keyring_2021.1.1 debianutils_5.7-0.2 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dpkg_1.21.9 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.21.9 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:11.2.0-2 g++-11_11.3.0-5 g++-11-arm-linux-gnueabi_11.3.0-3cross1 g++-arm-linux-gnueabi_4:11.2.0-2 gcc_4:11.2.0-2 gcc-11_11.3.0-5 gcc-11-arm-linux-gnueabi_11.3.0-3cross1 gcc-11-arm-linux-gnueabi-base_11.3.0-3cross1 gcc-11-base_11.3.0-5 gcc-11-cross-base_11.3.0-3cross1 gcc-12-base_12.1.0-7 gcc-12-cross-base_12.1.0-2cross1 gcc-9-base_9.5.0-1 gcc-arm-linux-gnueabi_4:11.2.0-2 gettext_0.21-6 gettext-base_0.21-6 gpgv_2.2.35-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 help2man_1.49.2 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.5.1 libarchive-zip-perl_1.68-1 libasan6_11.3.0-5 libasan6-armel-cross_11.3.0-3cross1 libatomic1_12.1.0-7 libatomic1-armel-cross_12.1.0-2cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38.90.20220713-2 libblkid1_2.38-5 libbz2-1.0_1.0.8-5 libbz2-dev_1.0.8-5 libc-bin_2.33-8 libc-dev-bin_2.33-8 libc6_2.33-8 libc6-armel-cross_2.33-1cross1 libc6-dev_2.33-8 libc6-dev-armel-cross_2.33-1cross1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcc1-0_12.1.0-7 libcom-err2_1.46.5-2 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.38.90.20220713-2 libctf0_2.38.90.20220713-2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.263 libdebhelper-perl_13.8 libdebian-dpkgcross-perl_2.6.18+nmu2 libdpkg-perl_1.21.9 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.13.0-1 libfile-which-perl_1.27-1 libgcc-11-dev_11.3.0-5 libgcc-11-dev-armel-cross_11.3.0-3cross1 libgcc-s1_12.1.0-7 libgcc-s1-armel-cross_12.1.0-2cross1 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.6-2 libgomp1_12.1.0-7 libgomp1-armel-cross_12.1.0-2cross1 libgpg-error0_1.45-2 libgprofng0_2.38.90.20220713-2 libgssapi-krb5-2_1.19.2-2+b2 libhogweed6_3.7.3-1 libicu71_71.1-3 libidn2-0_2.3.3-1 libio-string-perl_1.08-3.1 libisl23_0.25-1 libitm1_12.1.0-7 libjansson-dev_2.14-2 libjansson4_2.14-2 libk5crypto3_1.19.2-2+b2 libkeyutils1_1.6.3-1 libkrb5-3_1.19.2-2+b2 libkrb5support0_1.19.2-2+b2 liblocale-gettext-perl_1.07-4+b2 liblsan0_12.1.0-7 liblz4-1_1.9.3-2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-5 libmpc3_1.2.1-2 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncursesw6_6.3+20220423-2 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-modules_1.4.0-13 libpam-modules-bin_1.4.0-13 libpam-runtime_1.4.0-13 libpam0g_1.4.0-13 libpcre2-8-0_10.40-1 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libpipeline1_1.5.6-1 libpython3-stdlib_3.10.5-3 libpython3.10-minimal_3.10.5-1 libpython3.10-stdlib_3.10.5-1 libquadmath0_12.1.0-7 libreadline8_8.1.2-1.2 libseccomp2_2.5.4-1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol2_3.4-2 libsigsegv2_2.14-1 libsmartcols1_2.38-5 libsqlite3-0_3.39.1-1 libss2_1.46.5-2 libssl3_3.0.4-2 libstdc++-11-dev_11.3.0-5 libstdc++-11-dev-armel-cross_11.3.0-3cross1 libstdc++6_12.1.0-7 libstdc++6-armel-cross_12.1.0-2cross1 libsub-override-perl_0.09-3 libsystemd0_251.3-1 libtasn1-6_4.18.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-4 libtsan0_11.3.0-5 libubsan1_12.1.0-7 libubsan1-armel-cross_12.1.0-2cross1 libuchardet0_0.0.7-1 libudev1_251.3-1 libunistring2_1.0-1 libuuid1_2.38-5 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-2 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libyaml-perl_1.30-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.18.5-1 linux-libc-dev-armel-cross_5.15.5-1cross1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.2 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38-5 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 po-debconf_1.0.21+nmu1 python3_3.10.5-3 python3-distutils_3.10.5-2 python3-lib2to3_3.10.5-2 python3-minimal_3.10.5-3 python3.10_3.10.5-1 python3.10-minimal_3.10.5-1 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 sysvinit-utils_3.03-1 tar_1.34+dfsg-1 tzdata_2022a-1 ucf_3.0043 util-linux_2.38-5 util-linux-extra_2.38-5 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4 zlib1g-dev_1:1.2.11.dfsg-4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bedops Binary: bedops, bedops-doc Architecture: any all Version: 2.4.41+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Homepage: https://github.com/bedops/bedops Standards-Version: 4.6.1 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 (= 13), 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: 4f982f219bbf756e2502ca38e8a512b2f5c8c157 13466240 bedops_2.4.41+dfsg.orig.tar.xz c1fc191dcefb9f7d30a3d4fdc24b7902c1187c22 10448 bedops_2.4.41+dfsg-1.debian.tar.xz Checksums-Sha256: 76b239863512daa8e934b1565eee974977de440e4adca0d6f8039d9376a007f4 13466240 bedops_2.4.41+dfsg.orig.tar.xz d40cd2d31f382653bce7fa430f813e6db252420c6b8d15702031a92793087355 10448 bedops_2.4.41+dfsg-1.debian.tar.xz Files: d2e57e5c93e9d612d7457092e112ffa5 13466240 bedops_2.4.41+dfsg.orig.tar.xz dbc0c7ab1986702a1c3d3e310341e1a1 10448 bedops_2.4.41+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmLVIdwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGS8A/9Fnfa/lU6SRBoqJHXciU4E6sUWLDZWF/A SFjvdjvMVgO+459qZ0kLn0MiWNIz9rAEEktaqjJ2Q7HToV6DaZG23YZHnTampcTj 1GN8aMHm8msCFH1KZUItCHIB/AA4R9kPiB73Gpc4NGpzl3a0N1PwZ2GXr+3/D9ll LXu6l0wWpE+eNfradW9OG8kJILZFcs+CkpTanruPERbw3eMXC73vPEu+Pabtd8hL ZYJCRmO47N7wqjB0UH3CQkdoOdiHOuGClH03Bu421l8sb+9aiJvR+m5z0GROx1By F6OX3jPsEnU/j8L8gDdIAXixuzU/uutjUgL76A9muTumu9I6W080aqgAcidzUosr boH5lsdPCt17QIVQfJY7HSCy405VJTJXaMWA92vzRZc7NA+JQXtVaa8ghcqoiMmn QtORJTa0Uvj+ZbmZtEK+sMgSSzbTbST5qAmVEhG1PyEyflttkk0zvndgxggT5Pdr IxXfRtiTe4XzjwX1uWL+/NmpToUq/bVDMDHFDjKLUEGrkgno6b00PPr/vX6w0Oea AmmMeFS81QYr/HLNGBDQX2yU477bxfpOKWHDUrCDsfdCT0SWqr8TZVGTCeSc60x9 hfzq+DBbkW0ERSKgr35hEEOYOI0mMfP4AHIoDc9qrk8EiY5YkUnz9AyxDKafLhy4 gySxQN6GgUA= =w9Uq -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.MI4dtvAi/trustedkeys.kbx': General error gpgv: Signature made Mon Jul 18 09:03:24 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./bedops_2.4.41+dfsg-1.dsc dpkg-source: info: extracting bedops in /<> dpkg-source: info: unpacking bedops_2.4.41+dfsg.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.41+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=crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-01262a41-91a9-4110-8cf5-6b2c77837717 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.41+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-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 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 binary-arch dh binary-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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 = 512]’ 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 = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:267:24, inlined from ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’ at BedReader.hpp:78:13: ../../../../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 member function ‘FeatDist::BedReader::BedType* FeatDist::BedReader::ReadLine() [with IterType = Bed::bed_check_iterator*, 512>]’: ../../../../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/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:6716:103: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 6716 | 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:6716:109: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘long unsigned int’ [-Wformat=] 6716 | 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:6716:115: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘long unsigned int’ [-Wformat=] 6716 | 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: In function ‘c2b_line_convert_sam_to_bed_unsorted_with_split_operation’: convert2bed.c:5017:25: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 5017 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:5043:21: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 5043 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:5061:21: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 5061 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:4950:25: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 4950 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:4974:21: warning: ‘sprintf’ argument 3 overlaps destination object ‘’ [-Wrestrict] 4974 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/bedops-2.4.41\+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="2.4.41+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/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/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 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/closest-features 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_2.4.41+dfsg-1_armel.deb'. dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.41+dfsg-1_armel.deb'. dpkg-genbuildinfo --build=any -O../bedops_2.4.41+dfsg-1_armel.buildinfo dpkg-genchanges --build=any -O../bedops_2.4.41+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 2022-07-21T02:00:36Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bedops_2.4.41+dfsg-1_armel.changes: ----------------------------------- Format: 1.8 Date: Mon, 18 Jul 2022 10:29:31 +0200 Source: bedops Binary: bedops bedops-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 2.4.41+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bedops - high-performance genomic feature operations Changes: bedops (2.4.41+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Repository, Repository-Browse. Checksums-Sha1: b195562fec1a5662a90ad2bdbdefa40148dd2d52 79280 bedops-dbgsym_2.4.41+dfsg-1_armel.deb bfccc9135060afbb8f639f84f43d3a9e72d41b23 5720 bedops_2.4.41+dfsg-1_armel.buildinfo 15a1ad02d11b244c6bcf67e332f0fe052f4c4bbe 1162548 bedops_2.4.41+dfsg-1_armel.deb Checksums-Sha256: 8bdb267af139d0850573099a81e6f7d54bbbea0ed3d2746225f049a09a9ff27d 79280 bedops-dbgsym_2.4.41+dfsg-1_armel.deb 33655575f6fe9810115744da750ca7b721495c4dac009167d42d8a78f257d7ae 5720 bedops_2.4.41+dfsg-1_armel.buildinfo 9cef09bb5e3272d6a6633c310e51e04742e8c6f222b83a63b527302f16526c00 1162548 bedops_2.4.41+dfsg-1_armel.deb Files: d922c81f21dfc6c2db5df92fb0cbe159 79280 debug optional bedops-dbgsym_2.4.41+dfsg-1_armel.deb 2e2fc6e663ac7589d3200d3cf50d2344 5720 science optional bedops_2.4.41+dfsg-1_armel.buildinfo d1ab0cf994f0c0ec4f362572404a1075 1162548 science optional bedops_2.4.41+dfsg-1_armel.deb /<>/bedops_2.4.41+dfsg-1_armel.changes.new could not be renamed to /<>/bedops_2.4.41+dfsg-1_armel.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bedops Binary: bedops bedops-dbgsym Architecture: armel Version: 2.4.41+dfsg-1 Checksums-Md5: d922c81f21dfc6c2db5df92fb0cbe159 79280 bedops-dbgsym_2.4.41+dfsg-1_armel.deb d1ab0cf994f0c0ec4f362572404a1075 1162548 bedops_2.4.41+dfsg-1_armel.deb Checksums-Sha1: b195562fec1a5662a90ad2bdbdefa40148dd2d52 79280 bedops-dbgsym_2.4.41+dfsg-1_armel.deb 15a1ad02d11b244c6bcf67e332f0fe052f4c4bbe 1162548 bedops_2.4.41+dfsg-1_armel.deb Checksums-Sha256: 8bdb267af139d0850573099a81e6f7d54bbbea0ed3d2746225f049a09a9ff27d 79280 bedops-dbgsym_2.4.41+dfsg-1_armel.deb 9cef09bb5e3272d6a6633c310e51e04742e8c6f222b83a63b527302f16526c00 1162548 bedops_2.4.41+dfsg-1_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 21 Jul 2022 02:00:36 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2), base-passwd (= 3.5.52), bash (= 5.1-6.1), binutils (= 2.38.90.20220713-2), binutils-common (= 2.38.90.20220713-2), binutils-x86-64-linux-gnu (= 2.38.90.20220713-2), bsdextrautils (= 2.38-5), bsdutils (= 1:2.38-5), build-essential (= 12.9), bzip2 (= 1.0.8-5), coreutils (= 8.32-4.1), cpp (= 4:11.2.0-2), cpp-11 (= 11.3.0-5), dash (= 0.5.11+git20210903+057cd650a4ed-8), debconf (= 1.5.79), debhelper (= 13.8), debianutils (= 5.7-0.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.7-5), dpkg (= 1.21.9), dpkg-dev (= 1.21.9), dwz (= 0.14-1), file (= 1:5.41-4), findutils (= 4.9.0-3), g++ (= 4:11.2.0-2), g++-11 (= 11.3.0-5), gcc (= 4:11.2.0-2), gcc-11 (= 11.3.0-5), gcc-11-base (= 11.3.0-5), gcc-12-base (= 12.1.0-7), gettext (= 0.21-6), gettext-base (= 0.21-6), grep (= 3.7-1), groff-base (= 1.22.4-8), gzip (= 1.12-1), help2man (= 1.49.2), hostname (= 3.23), init-system-helpers (= 1.64), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.3.0-5), libatomic1 (= 12.1.0-7), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.7-1), libaudit1 (= 1:3.0.7-1+b1), libbinutils (= 2.38.90.20220713-2), libblkid1 (= 2.38-5), libbz2-1.0 (= 1.0.8-5), libbz2-dev (= 1.0.8-5), libc-bin (= 2.33-8), libc-dev-bin (= 2.33-8), libc6 (= 2.33-8), libc6-dev (= 2.33-8), libcap-ng0 (= 0.8.3-1), libcap2 (= 1:2.44-1), libcc1-0 (= 12.1.0-7), libcom-err2 (= 1.46.5-2), libcrypt-dev (= 1:4.4.28-2), libcrypt1 (= 1:4.4.28-2), libctf-nobfd0 (= 2.38.90.20220713-2), libctf0 (= 2.38.90.20220713-2), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.263), libdebhelper-perl (= 13.8), libdpkg-perl (= 1.21.9), libelf1 (= 0.187-1), libexpat1 (= 2.4.8-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.3.0-5), libgcc-s1 (= 12.1.0-7), libgcrypt20 (= 1.10.1-2), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgmp10 (= 2:6.2.1+dfsg1-1), libgomp1 (= 12.1.0-7), libgpg-error0 (= 1.45-2), libgprofng0 (= 2.38.90.20220713-2), libgssapi-krb5-2 (= 1.19.2-2+b2), libicu71 (= 71.1-3), libisl23 (= 0.25-1), libitm1 (= 12.1.0-7), libjansson-dev (= 2.14-2), libjansson4 (= 2.14-2), libk5crypto3 (= 1.19.2-2+b2), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.19.2-2+b2), libkrb5support0 (= 1.19.2-2+b2), liblocale-gettext-perl (= 1.07-4+b2), liblsan0 (= 12.1.0-7), liblz4-1 (= 1.9.3-2), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38-5), libmpc3 (= 1.2.1-2), libmpdec3 (= 2.5.1-2), libmpfr6 (= 4.1.0-3), libncursesw6 (= 6.3+20220423-2), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libpam-modules (= 1.4.0-13), libpam-modules-bin (= 1.4.0-13), libpam-runtime (= 1.4.0-13), libpam0g (= 1.4.0-13), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-5), libpipeline1 (= 1.5.6-1), libpython3-stdlib (= 3.10.5-3), libpython3.10-minimal (= 3.10.5-1), libpython3.10-stdlib (= 3.10.5-1), libquadmath0 (= 12.1.0-7), libreadline8 (= 8.1.2-1.2), libseccomp2 (= 2.5.4-1), libselinux1 (= 3.4-1), libsigsegv2 (= 2.14-1), libsmartcols1 (= 2.38-5), libsqlite3-0 (= 3.39.1-1), libssl3 (= 3.0.4-2), libstdc++-11-dev (= 11.3.0-5), libstdc++6 (= 12.1.0-7), libsub-override-perl (= 0.09-3), libsystemd0 (= 251.3-1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-5), libubsan1 (= 12.1.0-7), libuchardet0 (= 0.0.7-1), libudev1 (= 251.3-1), libunistring2 (= 1.0-1), libuuid1 (= 2.38-5), libxml2 (= 2.9.14+dfsg-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.18.5-1), login (= 1:4.11.1+dfsg1-2), lsb-base (= 11.2), m4 (= 1.4.18-5), make (= 4.3-4.1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3.1), media-types (= 8.0.0), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7), perl (= 5.34.0-5), perl-base (= 5.34.0-5), perl-modules-5.34 (= 5.34.0-5), po-debconf (= 1.0.21+nmu1), python3 (= 3.10.5-3), python3-distutils (= 3.10.5-2), python3-lib2to3 (= 3.10.5-2), python3-minimal (= 3.10.5-3), python3.10 (= 3.10.5-1), python3.10-minimal (= 3.10.5-1), readline-common (= 8.1.2-1.2), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.03-1), tar (= 1.34+dfsg-1), util-linux (= 2.38-5), util-linux-extra (= 2.38-5), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-4), zlib1g-dev (= 1:1.2.11.dfsg-4) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1658132971" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bedops-dbgsym_2.4.41+dfsg-1_armel.deb ------------------------------------- new Debian package, version 2.0. size 79280 bytes: control archive=536 bytes. 377 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: bedops-dbgsym Source: bedops Version: 2.4.41+dfsg-1 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 95 Depends: bedops (= 2.4.41+dfsg-1) Section: debug Priority: optional Description: debug symbols for bedops Build-Ids: ab2bcc97ff35eef26e0c344effef235b3cc9dabb drwxr-xr-x root/root 0 2022-07-18 08:29 ./ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/lib/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/lib/debug/.build-id/ab/ -rw-r--r-- root/root 86780 2022-07-18 08:29 ./usr/lib/debug/.build-id/ab/2bcc97ff35eef26e0c344effef235b3cc9dabb.debug drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops-dbgsym -> bedops bedops_2.4.41+dfsg-1_armel.deb ------------------------------ new Debian package, version 2.0. size 1162548 bytes: control archive=6144 bytes. 731 bytes, 15 lines control 21485 bytes, 236 lines md5sums Package: bedops Version: 2.4.41+dfsg-1 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 8189 Depends: libbz2-1.0, libc6 (>= 2.33), libgcc-s1 (>= 3.5), libjansson4 (>= 2.14), 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 2022-07-18 08:29 ./ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/bin/ -rwxr-xr-x root/root 4711 2022-07-18 08:29 ./usr/bin/bam2bed -rwxr-xr-x root/root 4501 2022-07-18 08:29 ./usr/bin/bam2bed_gnuParallel -rwxr-xr-x root/root 5022 2022-07-18 08:29 ./usr/bin/bam2bed_sge -rwxr-xr-x root/root 5021 2022-07-18 08:29 ./usr/bin/bam2bed_slurm -rwxr-xr-x root/root 5842 2022-07-18 08:29 ./usr/bin/bam2starch -rwxr-xr-x root/root 4507 2022-07-18 08:29 ./usr/bin/bam2starch_gnuParallel -rwxr-xr-x root/root 5076 2022-07-18 08:29 ./usr/bin/bam2starch_sge -rwxr-xr-x root/root 5014 2022-07-18 08:29 ./usr/bin/bam2starch_slurm -rwxr-xr-x root/root 198960 2022-07-18 08:29 ./usr/bin/bedextract -rwxr-xr-x root/root 5976480 2022-07-18 08:29 ./usr/bin/bedmap -rwxr-xr-x root/root 461492 2022-07-18 08:29 ./usr/bin/bedops -rwxr-xr-x root/root 133044 2022-07-18 08:29 ./usr/bin/bedops-starch -rwxr-xr-x root/root 264712 2022-07-18 08:29 ./usr/bin/closest-features -rwxr-xr-x root/root 133488 2022-07-18 08:29 ./usr/bin/convert2bed -rwxr-xr-x root/root 3773 2022-07-18 08:29 ./usr/bin/gff2bed -rwxr-xr-x root/root 4904 2022-07-18 08:29 ./usr/bin/gff2starch -rwxr-xr-x root/root 4061 2022-07-18 08:29 ./usr/bin/gtf2bed -rwxr-xr-x root/root 5195 2022-07-18 08:29 ./usr/bin/gtf2starch -rwxr-xr-x root/root 3773 2022-07-18 08:29 ./usr/bin/gvf2bed -rwxr-xr-x root/root 4904 2022-07-18 08:29 ./usr/bin/gvf2starch -rwxr-xr-x root/root 3976 2022-07-18 08:29 ./usr/bin/psl2bed -rwxr-xr-x root/root 5107 2022-07-18 08:29 ./usr/bin/psl2starch -rwxr-xr-x root/root 3776 2022-07-18 08:29 ./usr/bin/rmsk2bed -rwxr-xr-x root/root 4907 2022-07-18 08:29 ./usr/bin/rmsk2starch -rwxr-xr-x root/root 4711 2022-07-18 08:29 ./usr/bin/sam2bed -rwxr-xr-x root/root 5842 2022-07-18 08:29 ./usr/bin/sam2starch -rwxr-xr-x root/root 264508 2022-07-18 08:29 ./usr/bin/sort-bed -rwxr-xr-x root/root 10163 2022-07-18 08:29 ./usr/bin/starch-diff -rwxr-xr-x root/root 198600 2022-07-18 08:29 ./usr/bin/starchcat -rwxr-xr-x root/root 4299 2022-07-18 08:29 ./usr/bin/starchcluster_gnuParallel -rwxr-xr-x root/root 4810 2022-07-18 08:29 ./usr/bin/starchcluster_sge -rwxr-xr-x root/root 4716 2022-07-18 08:29 ./usr/bin/starchcluster_slurm -rwxr-xr-x root/root 132976 2022-07-18 08:29 ./usr/bin/starchstrip -rwxr-xr-x root/root 132904 2022-07-18 08:29 ./usr/bin/unstarch -rwxr-xr-x root/root 32686 2022-07-18 08:29 ./usr/bin/update-sort-bed-migrate-candidates -rwxr-xr-x root/root 20701 2022-07-18 08:29 ./usr/bin/update-sort-bed-slurm -rwxr-xr-x root/root 22682 2022-07-18 08:29 ./usr/bin/update-sort-bed-starch-slurm -rwxr-xr-x root/root 4675 2022-07-18 08:29 ./usr/bin/vcf2bed -rwxr-xr-x root/root 5806 2022-07-18 08:29 ./usr/bin/vcf2starch -rwxr-xr-x root/root 4598 2022-07-18 08:29 ./usr/bin/wig2bed -rwxr-xr-x root/root 5729 2022-07-18 08:29 ./usr/bin/wig2starch drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/ -rw-r--r-- root/root 267 2022-07-18 08:29 ./usr/share/doc/bedops/README.Debian -rw-r--r-- root/root 1699 2022-07-18 08:29 ./usr/share/doc/bedops/changelog.Debian.gz -rw-r--r-- root/root 22675 2022-07-13 08:18 ./usr/share/doc/bedops/changelog.gz -rw-r--r-- root/root 1156 2022-07-18 08:29 ./usr/share/doc/bedops/copyright drwxr-xr-x root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/ -rw-r--r-- root/root 954 2022-07-13 08:18 ./usr/share/doc/bedops/tests/Makefile drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/tests/bedops/ -rw-r--r-- root/root 2166 2022-07-18 08:29 ./usr/share/doc/bedops/tests/bedops/Makefile.gz drwxr-xr-x root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/ -rw-r--r-- root/root 197 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001.expected -rw-r--r-- root/root 44 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001a.test -rw-r--r-- root/root 53 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001b.test -rw-r--r-- root/root 24 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.chrom.001.expected -rw-r--r-- root/root 26 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.complement.001.expected -rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.difference.001.expected -rw-r--r-- root/root 23 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.ec.001a.test -rw-r--r-- root/root 69 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.element-of.001.expected -rw-r--r-- root/root 91 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001.expected -rw-r--r-- root/root 52 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001a.test -rw-r--r-- root/root 104 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001b.test -rw-r--r-- root/root 37 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.expected -rw-r--r-- root/root 111 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.test -rw-r--r-- root/root 368 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.named-pipe.001.expected -rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.not-element-of.001.expected -rw-r--r-- root/root 148 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001.expected -rw-r--r-- root/root 39 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001a.test -rw-r--r-- root/root 56 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001b.test -rw-r--r-- root/root 40 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001c.test -rw-r--r-- root/root 257 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.stdin.001.expected -rw-r--r-- root/root 130 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.symdiff.001.expected -rw-r--r-- root/root 134 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.expected -rw-r--r-- root/root 126 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.test -rw-r--r-- root/root 171 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.chop.002.expected -rw-r--r-- root/root 20 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.chrom.002.expected -rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.complement.002.expected -rw-r--r-- root/root 2172 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002.expected -rw-r--r-- root/root 3033 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002a.test -rw-r--r-- root/root 2941 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002b.test -rw-r--r-- root/root 18 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.element-of.002.expected -rw-r--r-- root/root 13 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.expected -rw-r--r-- root/root 26 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.test -rw-r--r-- root/root 11 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.merge.002.expected -rw-r--r-- root/root 11 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.not-element-of.002.expected -rw-r--r-- root/root 376 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002.expected -rw-r--r-- root/root 48 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002a.test -rw-r--r-- root/root 49 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002b.test -rw-r--r-- root/root 101 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002c.test -rw-r--r-- root/root 39 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002d.test -rw-r--r-- root/root 131 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002e.test -rw-r--r-- root/root 118 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.symdiff.002.expected -rw-r--r-- root/root 56 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/002.union.002.expected -rw-r--r-- root/root 368 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.chop.003.expected -rw-r--r-- root/root 24 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.chrom.003.expected -rw-r--r-- root/root 61 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.complement.003.expected -rw-r--r-- root/root 3794 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.difference.003.expected -rw-r--r-- root/root 42 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.element-of.003.expected -rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.intersection.003.expected -rw-r--r-- root/root 35 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.expected -rw-r--r-- root/root 46 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.test -rw-r--r-- root/root 21 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003.expected -rw-r--r-- root/root 63 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003a.test -rw-r--r-- root/root 42 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003b.test -rw-r--r-- root/root 153 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.expected -rw-r--r-- root/root 398 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.test -rw-r--r-- root/root 22 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003.expected -rw-r--r-- root/root 18 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003a.test -rw-r--r-- root/root 29 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003b.test -rw-r--r-- root/root 9 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003c.test -rw-r--r-- root/root 11 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003d.test -rw-r--r-- root/root 355 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.expected -rw-r--r-- root/root 360 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.test -rw-r--r-- root/root 257 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.chop.004.expected -rw-r--r-- root/root 24 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.chrom.004.expected -rw-r--r-- root/root 111 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004.expected -rw-r--r-- root/root 46 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004a.test -rw-r--r-- root/root 132 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004b.test -rw-r--r-- root/root 94 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004c.test -rw-r--r-- root/root 30 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004.expected -rw-r--r-- root/root 30 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004a.test -rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004b.test -rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004.expected -rw-r--r-- root/root 92 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004a.test -rw-r--r-- root/root 23 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004b.test -rw-r--r-- root/root 49 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004.expected -rw-r--r-- root/root 103 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004a.test -rw-r--r-- root/root 85 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004b.test -rw-r--r-- root/root 47 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004c.test -rw-r--r-- root/root 72 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.merge.004.expected -rw-r--r-- root/root 117 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.expected -rw-r--r-- root/root 117 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.test -rw-r--r-- root/root 52 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.symdiff.004.expected -rw-r--r-- root/root 22 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.expected -rw-r--r-- root/root 32 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.test -rw-r--r-- root/root 385 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.expected -rw-r--r-- root/root 87 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.test -rw-r--r-- root/root 20 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.expected -rw-r--r-- root/root 40 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.test -rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.difference.005.expected -rw-r--r-- root/root 93 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.expected -rw-r--r-- root/root 43 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.test -rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.symdiff.005.expected -rw-r--r-- root/root 11 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/005.union.005.expected -rw-r--r-- root/root 35 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.complement.006.expected -rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.difference.006.expected -rw-r--r-- root/root 41 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006.expected -rw-r--r-- root/root 37 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006a.test -rw-r--r-- root/root 35 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006b.test -rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006c.test -rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/006.union.006.expected -rw-r--r-- root/root 9 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.complement.007.expected -rw-r--r-- root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.difference.007.expected -rw-r--r-- root/root 55 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007.expected -rw-r--r-- root/root 56 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007a.test -rw-r--r-- root/root 69 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007b.test -rw-r--r-- root/root 33 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/007.union.007.expected -rw-r--r-- root/root 79 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/008.complement.008.expected -rw-r--r-- root/root 197 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/008.merge.008.expected -rw-r--r-- root/root 33 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/008.union.008.expected -rw-r--r-- root/root 175 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/009.complement.009.expected -rw-r--r-- root/root 52 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/009.merge.009.expected -rw-r--r-- root/root 33 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.expected -rw-r--r-- root/root 43 2022-07-13 08:18 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.test drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/tests/conversion/ -rw-r--r-- root/root 1159 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/Makefile.gz drwxr-xr-x root/root 0 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/ -rw-r--r-- root/root 398 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 352 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/001.wig2bed_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 368 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 322 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/002.wig2bed_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 102 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 52 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 102 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.expected -rw-r--r-- root/root 60 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/003.wig2bed_fixedStep_with_chr_prefix_no_header.002.wig -rw-r--r-- root/root 93 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 49 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 93 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.expected -rw-r--r-- root/root 56 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/004.wig2bed_fixedStep_no_chr_prefix_no_header.002.wig -rw-r--r-- root/root 170 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.expected -rw-r--r-- root/root 85 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.001.wig -rw-r--r-- root/root 34 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.expected -rw-r--r-- root/root 43 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/005.wig2bed_variableStep_with_chr_prefix_no_header.002.wig -rw-r--r-- root/root 155 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.expected -rw-r--r-- root/root 82 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.001.wig -rw-r--r-- root/root 31 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.expected -rw-r--r-- root/root 40 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/006.wig2bed_variableStep_no_chr_prefix_no_header.002.wig -rw-r--r-- root/root 538 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.expected -rw-r--r-- root/root 454 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.001.wig -rw-r--r-- root/root 583 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.002.expected -rw-r--r-- root/root 700 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.003.expected -rw-r--r-- root/root 763 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/007.wig2bed_multipleTracks_with_chr_prefix_with_header.004.expected -rw-r--r-- root/root 493 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.expected -rw-r--r-- root/root 421 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.001.wig -rw-r--r-- root/root 538 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.002.expected -rw-r--r-- root/root 652 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.003.expected -rw-r--r-- root/root 715 2022-07-13 08:18 ./usr/share/doc/bedops/tests/conversion/data/008.wig2bed_multipleTracks_no_chr_prefix_with_header.004.expected drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/tests/starch/ -rw-r--r-- root/root 1078 2022-07-18 08:29 ./usr/share/doc/bedops/tests/starch/Makefile.gz drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/doc/bedops/tests/starch/data/ -rw-r--r-- root/root 1935 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.expected -rw-r--r-- root/root 2813 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.test.gz -rw-r--r-- root/root 772 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1.001.test -rw-r--r-- root/root 1166 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1andChr2.001.expected -rw-r--r-- root/root 772 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr2.001.test -rw-r--r-- root/root 764 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.expected -rw-r--r-- root/root 2851 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.test.gz -rw-r--r-- root/root 218 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.expected -rw-r--r-- root/root 2254 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.test.gz -rw-r--r-- root/root 109 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/README -rw-r--r-- root/root 426 2022-07-13 08:18 ./usr/share/doc/bedops/tests/starch/data/hg38.bed -rw-r--r-- root/root 1516 2022-07-18 08:29 ./usr/share/doc/bedops/tests/starch/generate_random_intervals.sh drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/man/ drwxr-xr-x root/root 0 2022-07-18 08:29 ./usr/share/man/man1/ -rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/bam2bed.1.gz -rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/bam2starch.1.gz -rw-r--r-- root/root 362 2022-07-18 08:29 ./usr/share/man/man1/bedextract.1.gz -rw-r--r-- root/root 358 2022-07-18 08:29 ./usr/share/man/man1/bedmap.1.gz -rw-r--r-- root/root 372 2022-07-18 08:29 ./usr/share/man/man1/bedops-starch.1.gz -rw-r--r-- root/root 355 2022-07-18 08:29 ./usr/share/man/man1/bedops.1.gz -rw-r--r-- root/root 376 2022-07-18 08:29 ./usr/share/man/man1/closest-features.1.gz -rw-r--r-- root/root 368 2022-07-18 08:29 ./usr/share/man/man1/convert2bed.1.gz -rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/gff2bed.1.gz -rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/gff2starch.1.gz -rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/gtf2bed.1.gz -rw-r--r-- root/root 353 2022-07-18 08:29 ./usr/share/man/man1/gtf2starch.1.gz -rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/gvf2bed.1.gz -rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/gvf2starch.1.gz -rw-r--r-- root/root 346 2022-07-18 08:29 ./usr/share/man/man1/psl2bed.1.gz -rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/psl2starch.1.gz -rw-r--r-- root/root 349 2022-07-18 08:29 ./usr/share/man/man1/rmsk2bed.1.gz -rw-r--r-- root/root 356 2022-07-18 08:29 ./usr/share/man/man1/rmsk2starch.1.gz -rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/sam2bed.1.gz -rw-r--r-- root/root 354 2022-07-18 08:29 ./usr/share/man/man1/sam2starch.1.gz -rw-r--r-- root/root 365 2022-07-18 08:29 ./usr/share/man/man1/sort-bed.1.gz -rw-r--r-- root/root 720 2022-07-18 08:29 ./usr/share/man/man1/starch-diff.1.gz -rw-r--r-- root/root 364 2022-07-18 08:29 ./usr/share/man/man1/starchcat.1.gz -rw-r--r-- root/root 366 2022-07-18 08:29 ./usr/share/man/man1/starchstrip.1.gz -rw-r--r-- root/root 358 2022-07-18 08:29 ./usr/share/man/man1/unstarch.1.gz -rw-r--r-- root/root 1763 2022-07-18 08:29 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz -rw-r--r-- root/root 1329 2022-07-18 08:29 ./usr/share/man/man1/update-sort-bed-slurm.1.gz -rw-r--r-- root/root 1383 2022-07-18 08:29 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz -rw-r--r-- root/root 347 2022-07-18 08:29 ./usr/share/man/man1/vcf2bed.1.gz -rw-r--r-- root/root 355 2022-07-18 08:29 ./usr/share/man/man1/vcf2starch.1.gz -rw-r--r-- root/root 346 2022-07-18 08:29 ./usr/share/man/man1/wig2bed.1.gz -rw-r--r-- root/root 355 2022-07-18 08:29 ./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 [572 B] Get:5 copy:/<>/apt_archive ./ Packages [657 B] Fetched 2192 B in 0s (0 B/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: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhttp-server-simple-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl 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 libregexp-ipv6-perl libregexp-wildcards-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 libsyntax-keyword-try-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 libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhttp-server-simple-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl 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 libregexp-ipv6-perl libregexp-wildcards-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 libsyntax-keyword-try-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 libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:armel t1utils unzip 0 upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 13.2 MB of archives. After this operation, 49.8 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://localhost:3142/debian sid/main amd64 netbase all 6.3 [19.9 kB] Get:3 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.4-2 [1421 kB] Get:4 http://localhost:3142/debian sid/main amd64 ca-certificates all 20211016 [156 kB] Get:5 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.64-1 [36.6 kB] Get:6 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.5-4 [51.3 kB] Get:7 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.35-3 [578 kB] Get:8 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.35-3 [961 kB] Get:9 http://localhost:3142/debian sid/main amd64 iso-codes all 4.10.0-1 [2825 kB] Get:10 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-2 [14.2 kB] Get:11 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b1 [72.1 kB] Get:12 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2 [11.2 kB] Get:13 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-2 [13.1 kB] Get:14 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-1+b3 [16.0 kB] Get:15 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2 [25.6 kB] Get:16 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:17 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-1 [24.2 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:19 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-2 [8044 B] Get:20 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.62-2 [45.7 kB] Get:21 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:22 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-1+b2 [124 kB] Get:23 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:24 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:25 http://localhost:3142/debian sid/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:26 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.12-1 [93.7 kB] Get:27 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.78-1 [105 kB] Get:28 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.54-1 [224 kB] Get:29 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:30 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:31 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-3+b8 [37.7 kB] Get:32 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.45-1+b2 [15.5 kB] Get:33 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.28-1 [17.3 kB] Get:34 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-1+b2 [25.7 kB] Get:35 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.928-2 [11.0 kB] Get:36 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:37 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:38 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:39 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.30-1 [130 kB] Get:40 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:41 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:42 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:43 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:44 http://localhost:3142/debian sid/main amd64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:45 http://localhost:3142/debian sid/main amd64 liblist-moreutils-xs-perl amd64 0.430-3 [40.3 kB] Get:46 http://localhost:3142/debian sid/main amd64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:47 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:48 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1 [35.7 kB] Get:49 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-2 [33.7 kB] Get:50 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:51 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:52 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0001-1 [32.2 kB] Get:53 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2 [104 kB] Get:54 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:55 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:56 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-1+b3 [26.1 kB] Get:57 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.04-1+b4 [28.0 kB] Get:58 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-2 [13.5 kB] Get:59 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:60 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:61 http://localhost:3142/debian sid/main amd64 libnumber-compare-perl all 0.03-2 [7448 B] Get:62 http://localhost:3142/debian sid/main amd64 libtext-glob-perl all 0.11-2 [8992 B] Get:63 http://localhost:3142/debian sid/main amd64 libfile-find-rule-perl all 0.34-2 [28.4 kB] Get:64 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:65 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.05-1 [10.4 kB] Get:66 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:67 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:68 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:69 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get:70 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.37-1 [80.9 kB] Get:71 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.07-1 [22.9 kB] Get:72 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-2 [21.6 kB] Get:73 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get:74 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:75 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:76 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:77 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2 [343 kB] Get:78 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.074-2 [220 kB] Get:79 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get:80 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:81 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:82 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.67-1 [194 kB] Get:83 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:84 http://localhost:3142/debian sid/main amd64 libhttp-server-simple-perl all 0.52-2 [29.4 kB] Get:85 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:86 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:87 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:88 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:89 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:90 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:91 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-1 [16.1 kB] Get:92 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-4 [42.0 kB] Get:93 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:94 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:95 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-3 [18.8 kB] Get:96 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:97 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:98 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005004-3 [60.5 kB] Get:99 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:100 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:101 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b2 [173 kB] Get:102 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:103 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-2 [11.9 kB] Get:104 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.26-1+b2 [13.9 kB] Get:105 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:106 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.122-1 [56.0 kB] Get:107 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1 [17.5 kB] Get:108 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.009-1+b1 [12.2 kB] Get:109 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.634-1+b1 [46.9 kB] Get:110 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-2 [14.1 kB] Get:111 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 4.023+ds-1 [99.7 kB] Get:112 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 4.023+ds-1 [104 kB] Get:113 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-2 [10.7 kB] Get:114 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.24-1 [53.0 kB] Get:115 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.27-1 [28.5 kB] Get:116 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-1+b3 [27.8 kB] Get:117 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5 [8656 B] Get:118 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.13-1+b1 [13.6 kB] Get:119 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b1 [197 kB] Get:120 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:121 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-1+b4 [75.8 kB] Get:122 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-1+b3 [20.3 kB] Get:123 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.10-1 [116 kB] Get:124 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:125 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.83+ds-1+b1 [35.9 kB] Get:126 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-4 [64.0 kB] Get:127 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:128 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:129 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:130 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-26 [171 kB] Get:131 http://localhost:3142/debian sid/main amd64 lintian all 2.115.2 [1416 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.2 MB in 0s (101 MB/s) Selecting previously unselected package netbase. (Reading database ... 19617 files and directories currently installed.) Preparing to unpack .../000-netbase_6.3_all.deb ... Unpacking netbase (6.3) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.0.4-2_amd64.deb ... Unpacking openssl (3.0.4-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../002-ca-certificates_20211016_all.deb ... Unpacking ca-certificates (20211016) ... Selecting previously unselected package diffstat. Preparing to unpack .../003-diffstat_1.64-1_amd64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../004-libassuan0_2.5.5-4_amd64.deb ... Unpacking libassuan0:amd64 (2.5.5-4) ... Selecting previously unselected package gpgconf. Preparing to unpack .../005-gpgconf_2.2.35-3_amd64.deb ... Unpacking gpgconf (2.2.35-3) ... Selecting previously unselected package gpg. Preparing to unpack .../006-gpg_2.2.35-3_amd64.deb ... Unpacking gpg (2.2.35-3) ... Selecting previously unselected package iso-codes. Preparing to unpack .../007-iso-codes_4.10.0-1_all.deb ... Unpacking iso-codes (4.10.0-1) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../008-libaliased-perl_0.34-2_all.deb ... Unpacking libaliased-perl (0.34-2) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../009-libapt-pkg-perl_0.1.40+b1_amd64.deb ... Unpacking libapt-pkg-perl (0.1.40+b1) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../010-libb-hooks-op-check-perl_0.22-2_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../011-libdynaloader-functions-perl_0.003-2_all.deb ... Unpacking libdynaloader-functions-perl (0.003-2) ... Selecting previously unselected package libdevel-callchecker-perl. 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Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../028-libclass-method-modifiers-perl_2.13-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.13-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../029-libclass-xsaccessor-perl_1.19-3+b8_amd64.deb ... Unpacking libclass-xsaccessor-perl (1.19-3+b8) ... Selecting previously unselected package libclone-perl. Preparing to unpack .../030-libclone-perl_0.45-1+b2_amd64.deb ... Unpacking libclone-perl (0.45-1+b2) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../031-libconfig-tiny-perl_2.28-1_all.deb ... Unpacking libconfig-tiny-perl (2.28-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../032-libparams-util-perl_1.102-1+b2_amd64.deb ... Unpacking libparams-util-perl (1.102-1+b2) ... Selecting previously unselected package libsub-install-perl. 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Unpacking libdevel-stacktrace-perl (2.0400-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../039-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../040-libiterator-perl_0.03+ds1-2_all.deb ... Unpacking libiterator-perl (0.03+ds1-2) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../041-libiterator-util-perl_0.02+ds1-2_all.deb ... Unpacking libiterator-util-perl (0.02+ds1-2) ... Selecting previously unselected package libexporter-tiny-perl. Preparing to unpack .../042-libexporter-tiny-perl_1.002002-1_all.deb ... Unpacking libexporter-tiny-perl (1.002002-1) ... Selecting previously unselected package liblist-moreutils-xs-perl. Preparing to unpack .../043-liblist-moreutils-xs-perl_0.430-3_amd64.deb ... Unpacking liblist-moreutils-xs-perl (0.430-3) ... 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Preparing to unpack .../049-libnet-ipv6addr-perl_1.02-1_all.deb ... Unpacking libnet-ipv6addr-perl (1.02-1) ... Selecting previously unselected package libnet-netmask-perl. Preparing to unpack .../050-libnet-netmask-perl_2.0001-1_all.deb ... Unpacking libnet-netmask-perl (2.0001-1) ... Selecting previously unselected package libnetaddr-ip-perl. Preparing to unpack .../051-libnetaddr-ip-perl_4.079+dfsg-2_amd64.deb ... Unpacking libnetaddr-ip-perl (4.079+dfsg-2) ... Selecting previously unselected package libdata-validate-ip-perl. Preparing to unpack .../052-libdata-validate-ip-perl_0.30-1_all.deb ... Unpacking libdata-validate-ip-perl (0.30-1) ... Selecting previously unselected package libdata-validate-uri-perl. Preparing to unpack .../053-libdata-validate-uri-perl_0.07-2_all.deb ... Unpacking libdata-validate-uri-perl (0.07-2) ... Selecting previously unselected package libdevel-size-perl. Preparing to unpack .../054-libdevel-size-perl_0.83-1+b3_amd64.deb ... Unpacking libdevel-size-perl (0.83-1+b3) ... Selecting previously unselected package libemail-address-xs-perl. Preparing to unpack .../055-libemail-address-xs-perl_1.04-1+b4_amd64.deb ... Unpacking libemail-address-xs-perl (1.04-1+b4) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../056-libencode-locale-perl_1.05-2_all.deb ... Unpacking libencode-locale-perl (1.05-2) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../057-libipc-system-simple-perl_1.30-1_all.deb ... Unpacking libipc-system-simple-perl (1.30-1) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../058-libfile-basedir-perl_0.09-1_all.deb ... Unpacking libfile-basedir-perl (0.09-1) ... Selecting previously unselected package libnumber-compare-perl. Preparing to unpack .../059-libnumber-compare-perl_0.03-2_all.deb ... Unpacking libnumber-compare-perl (0.03-2) ... 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Setting up plzip (1.10-4) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-1+b3) ... Setting up libmouse-perl (2.5.10-1+b2) ... Setting up libdata-messagepack-perl (1.02-1) ... Setting up libdynaloader-functions-perl (0.003-2) ... Setting up libtext-glob-perl (0.11-2) ... Setting up libclass-method-modifiers-perl (2.13-1) ... Setting up liblist-compare-perl (0.55-1) ... Setting up libclone-perl (0.45-1+b2) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-2) ... Setting up libcpanel-json-xs-perl:amd64 (4.30-1) ... Setting up libhtml-tagset-perl (3.20-4) ... Setting up libdevel-size-perl (0.83-1+b3) ... Setting up unzip (6.0-26) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libyaml-libyaml-perl (0.83+ds-1+b1) ... Setting up libio-interactive-perl (1.023-1) ... Setting up libtry-tiny-perl (0.31-1) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-3) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-1+b4) ... Setting up libencode-locale-perl (1.05-2) ... Setting up libassuan0:amd64 (2.5.5-4) ... Setting up libconfig-tiny-perl (2.28-1) ... Setting up libsereal-encoder-perl:amd64 (4.023+ds-1) ... Setting up liblist-utilsby-perl (0.12-1) ... Setting up libnet-netmask-perl (2.0001-1) ... Setting up libsub-install-perl (0.928-2) ... Setting up libnumber-compare-perl (0.03-2) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004003-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.24-1) ... Setting up libfile-find-rule-perl (0.34-2) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libnet-domain-tld-perl (1.75-2) ... Setting up libperlio-utf8-strict-perl (0.009-1+b1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.62-2) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2) ... Setting up liblist-moreutils-xs-perl (0.430-3) ... Setting up libparams-util-perl (1.102-1+b2) ... Setting up libtime-duration-perl (1.21-1) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b1) ... Setting up libsub-exporter-progressive-perl (0.001013-2) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libsub-name-perl (0.26-1+b2) ... Setting up libsyntax-keyword-try-perl (0.27-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.634-1+b1) ... Setting up libpath-tiny-perl (0.122-1) ... Setting up lzop (1.04-2) ... Setting up gpgconf (2.2.35-3) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-2) ... Setting up libregexp-wildcards-perl (1.05-2) ... Setting up libaliased-perl (0.34-2) ... Setting up netbase (6.3) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b8) ... Setting up libsort-versions-perl (1.62-2) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libterm-readkey-perl (2.38-1+b3) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.4-2) ... Setting up libtext-levenshteinxs-perl (0.03-5) ... Setting up libperlio-gzip-perl (0.20-1) ... Setting up libhtml-html5-entities-perl (0.004-2) ... Setting up libsereal-decoder-perl (4.023+ds-1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.12-1) ... Setting up iso-codes (4.10.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up gpg (2.2.35-3) ... Setting up libdata-validate-ip-perl (0.30-1) ... Setting up libemail-address-xs-perl (1.04-1+b4) ... Setting up libnet-ssleay-perl:amd64 (1.92-2) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libfile-basedir-perl (0.09-1) ... Setting up libfile-listing-perl (6.15-1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libnet-http-perl (6.22-1) ... Setting up libtext-markdown-discount-perl:amd64 (0.13-1+b1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl (0.008-1+b3) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 127 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.78-1) ... Setting up libio-socket-ssl-perl (2.074-2) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libhttp-message-perl (6.37-1) ... Setting up libhtml-form-perl (6.07-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl:amd64 (0.015-2) ... Setting up libcgi-pm-perl (4.54-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libhttp-server-simple-perl (0.52-2) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.67-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.10-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Processing triggers for libc-bin (2.33-8) ... Processing triggers for man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for sgml-base (1.30) ... Setting up lintian (2.115.2) ... Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 47480 Build-Time: 393 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 12 Job: bedops_2.4.41+dfsg-1 Lintian: pass Machine Architecture: amd64 Package: bedops Package-Time: 414 Source-Version: 2.4.41+dfsg-1 Space: 47480 Status: successful Version: 2.4.41+dfsg-1 -------------------------------------------------------------------------------- Finished at 2022-07-21T02:00:36Z Build needed 00:06:54, 47480k disk space