sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | perm 0.4.0-4 (arm64) Sun, 06 Oct 2019 09:41:33 +0000 | +==============================================================================+ Package: perm Version: 0.4.0-4 Source Version: 0.4.0-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-1b55b28f-a111-4c14-9f0e-60a31cdcf9cf' with '<>' I: NOTICE: Log filtering will replace 'build/perm-9a1pov/resolver-JCLoo8' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [139 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-10-06-0812.49.pdiff [3986 B] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-10-06-0812.49.pdiff [3986 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-10-06-0812.49.pdiff [33.2 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-10-06-0812.49.pdiff [33.2 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8046 kB] Fetched 8278 kB in 2s (4314 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: 'perm' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/perm.git Please use: git clone https://salsa.debian.org/med-team/perm.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 126 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main perm 0.4.0-4 (dsc) [1884 B] Get:2 http://debian.oregonstate.edu/debian unstable/main perm 0.4.0-4 (tar) [114 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main perm 0.4.0-4 (diff) [9912 B] Fetched 126 kB in 0s (0 B/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/perm-9a1pov/perm-0.4.0' with '<>' I: NOTICE: Log filtering will replace 'build/perm-9a1pov' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper (>= 11~), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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 [402 B] Get:5 copy:/<>/apt_archive ./ Packages [491 B] Fetched 1850 B in 0s (92.5 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdmainutils cpp-9-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-9-aarch64-linux-gnu gcc-9-aarch64-linux-gnu-base gcc-9-base:arm64 gcc-9-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:arm64 libasan5-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbsd0 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:arm64 libgcc-9-dev-arm64-cross libgcc1:arm64 libgcc1-arm64-cross libglib2.0-0 libgomp1:arm64 libgomp1-arm64-cross libicu63 libio-string-perl libitm1:arm64 libitm1-arm64-cross liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:arm64 libstdc++-9-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtool libtsan0:arm64 libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch gcc-9-doc libstdc++6-9-dbg-arm64-cross libgcc1-dbg-arm64-cross libgomp1-dbg-arm64-cross libitm1-dbg-arm64-cross libatomic1-dbg-arm64-cross libasan5-dbg-arm64-cross liblsan0-dbg-arm64-cross libtsan0-dbg-arm64-cross libubsan1-dbg-arm64-cross libquadmath0-dbg-arm64-cross manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64 manpages-dev:arm64 libstdc++-9-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:arm64 libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs 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-aarch64-linux-gnu bsdmainutils cpp-9-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-9-aarch64-linux-gnu gcc-9-aarch64-linux-gnu-base gcc-9-base:arm64 gcc-9-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:arm64 libasan5-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbsd0 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:arm64 libgcc-9-dev-arm64-cross libgcc1:arm64 libgcc1-arm64-cross libglib2.0-0 libgomp1:arm64 libgomp1-arm64-cross libicu63 libio-string-perl libitm1:arm64 libitm1-arm64-cross liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:arm64 libstdc++-9-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtool libtsan0:arm64 libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:arm64 sensible-utils ucf 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 62.9 MB of archives. After this operation, 262 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.7-3 [1300 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b5 [18.9 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-9-base arm64 9.2.1-8 [193 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-5 [253 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-5 [119 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-5 [67.1 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.32.51.20190909-1 [2774 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-aarch64-linux-gnu-base amd64 9.2.1-8cross1 [193 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-aarch64-linux-gnu amd64 9.2.1-8cross1 [6536 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:9.2.1-3.1 [16.7 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-8cross1 [188 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.29-1cross7 [1253 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-arm64-cross all 1:9.2.1-8cross1 [34.0 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 9.2.1-8cross1 [76.6 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 9.2.1-8cross1 [24.3 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 9.2.1-8cross1 [8640 B] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-arm64-cross all 9.2.1-8cross1 [347 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 9.2.1-8cross1 [122 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 9.2.1-8cross1 [267 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 9.2.1-8cross1 [416 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 9.2.1-8cross1 [117 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-arm64-cross all 9.2.1-8cross1 [888 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-aarch64-linux-gnu amd64 9.2.1-8cross1 [6896 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:9.2.1-3.1 [1460 B] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 5.2.9-2cross7 [1310 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.29-1cross7 [2273 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-arm64-cross all 9.2.1-8cross1 [1632 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-aarch64-linux-gnu amd64 9.2.1-8cross1 [7113 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:9.2.1-3.1 [1180 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.8 [6644 B] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.66-2 [103 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.0-1 [23.3 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.0-1 [14.3 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-1 [81.8 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.6.1 [172 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.0-3 [1316 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20190803-1 [102 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.6.1 [993 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc1 arm64 1:9.2.1-8 [34.1 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.29-2 [2464 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main arm64 libasan5 arm64 9.2.1-8 [354 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 9.2.1-8 [8852 B] Get:82 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 5.2.17-1 [1230 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.29-2 [2287 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 9.2.1-8 [78.4 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 9.2.1-8 [24.7 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 9.2.1-8 [123 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 9.2.1-8 [274 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 9.2.1-8 [454 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 9.2.1-8 [118 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-9-dev arm64 9.2.1-8 [878 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-9-dev arm64 9.2.1-8 [1653 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.9 MB in 1s (60.7 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 14991 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.7-3_amd64.deb ... Unpacking man-db (2.8.7-3) ... 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Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up libarchive-zip-perl (1.66-2) ... Setting up libglib2.0-0:amd64 (2.62.0-3) ... No schema files found: doing nothing. Setting up gcc-9-aarch64-linux-gnu-base:amd64 (9.2.1-8cross1) ... Setting up libdebhelper-perl (12.6.1) ... Setting up libmagic1:amd64 (1:5.37-5) ... Setting up linux-libc-dev:arm64 (5.2.17-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up binutils-aarch64-linux-gnu (2.32.51.20190909-1) ... Setting up cpp-9-aarch64-linux-gnu (9.2.1-8cross1) ... Setting up file (1:5.37-5) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cpp-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libncurses6:amd64 (6.1+20190803-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libc6-arm64-cross (2.29-1cross7) ... Setting up autopoint (0.19.8.1-9) ... Setting up gcc-9-cross-base (9.2.1-8cross1) ... Setting up linux-libc-dev-arm64-cross (5.2.9-2cross7) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b5) ... Setting up gcc-9-base:arm64 (9.2.1-8) ... Setting up libatomic1-arm64-cross (9.2.1-8cross1) ... Setting up libgcc1-arm64-cross (1:9.2.1-8cross1) ... Setting up libfile-stripnondeterminism-perl (1.6.0-1) ... Setting up liblsan0-arm64-cross (9.2.1-8cross1) ... Setting up libgomp1-arm64-cross (9.2.1-8cross1) ... Setting up libtool (2.4.6-11) ... Setting up libtsan0-arm64-cross (9.2.1-8cross1) ... Setting up m4 (1.4.18-2) ... Setting up libc6-dev-arm64-cross (2.29-1cross7) ... Setting up libasan5-arm64-cross (9.2.1-8cross1) ... Setting up libstdc++6-arm64-cross (9.2.1-8cross1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libitm1-arm64-cross (9.2.1-8cross1) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.13-1) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libubsan1-arm64-cross (9.2.1-8cross1) ... Setting up libgcc-9-dev-arm64-cross (9.2.1-8cross1) ... Setting up man-db (2.8.7-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... 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 intltool-debian (0.35.0+20060710.5) ... Setting up gcc-9-aarch64-linux-gnu (9.2.1-8cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-9-dev-arm64-cross (9.2.1-8cross1) ... Setting up gcc-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up po-debconf (1.0.21) ... Setting up g++-9-aarch64-linux-gnu (9.2.1-8cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-arm64 (12.8) ... Setting up libc6:arm64 (2.29-2) ... Setting up libc6-dev:arm64 (2.29-2) ... Setting up libitm1:arm64 (9.2.1-8) ... Setting up libgcc1:arm64 (1:9.2.1-8) ... Setting up libgomp1:arm64 (9.2.1-8) ... Setting up dh-autoreconf (19) ... Setting up libasan5:arm64 (9.2.1-8) ... Setting up libatomic1:arm64 (9.2.1-8) ... Setting up dh-strip-nondeterminism (1.6.0-1) ... Setting up libstdc++6:arm64 (9.2.1-8) ... Setting up liblsan0:arm64 (9.2.1-8) ... Setting up libtsan0:arm64 (9.2.1-8) ... Setting up debhelper (12.6.1) ... Setting up libubsan1:arm64 (9.2.1-8) ... Setting up libgcc-9-dev:arm64 (9.2.1-8) ... Setting up libstdc++-9-dev:arm64 (9.2.1-8) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.29-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.32.51.20190909-1 dpkg-dev_1.19.7 g++-8_8.3.0-23 g++-9_9.2.1-8 gcc-8_8.3.0-23 gcc-9_9.2.1-8 libc6-dev_2.29-2 libstdc++-8-dev_8.3.0-23 libstdc++-9-dev_9.2.1-8 libstdc++-9-dev-arm64-cross_9.2.1-8cross1 libstdc++6_9.2.1-8 libstdc++6-arm64-cross_9.2.1-8cross1 linux-libc-dev_5.2.17-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.32.51.20190909-1 binutils-aarch64-linux-gnu_2.32.51.20190909-1 binutils-common_2.32.51.20190909-1 binutils-x86-64-linux-gnu_2.32.51.20190909-1 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-23 cpp-9_9.2.1-8 cpp-9-aarch64-linux-gnu_9.2.1-8cross1 cpp-aarch64-linux-gnu_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-arm64_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.6.1 debian-archive-keyring_2019.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-5 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-8_8.3.0-23 g++-9_9.2.1-8 g++-9-aarch64-linux-gnu_9.2.1-8cross1 g++-aarch64-linux-gnu_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-8_8.3.0-23 gcc-8-base_8.3.0-23 gcc-9_9.2.1-8 gcc-9-aarch64-linux-gnu_9.2.1-8cross1 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libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.0-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-23 libgcc-9-dev_9.2.1-8 libgcc-9-dev-arm64-cross_9.2.1-8cross1 libgcc1_1:9.2.1-8 libgcc1-arm64-cross_1:9.2.1-8cross1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.0-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-5 libgomp1_9.2.1-8 libgomp1-arm64-cross_9.2.1-8cross1 libgpg-error0_1.36-7 libhogweed4_3.5.1+really3.4.1-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl21_0.21-2 libitm1_9.2.1-8 libitm1-arm64-cross_9.2.1-8cross1 liblocale-gettext-perl_1.07-3+b5 liblsan0_9.2.1-8 liblsan0-arm64-cross_9.2.1-8cross1 liblz4-1_1.8.3-1+b1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-23 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.5.1+really3.4.1-1 libp11-kit0_0.23.17-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.32-5+b1 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-5 libpipeline1_1.5.1-2 libquadmath0_9.2.1-8 libseccomp2_2.4.1-2 libselinux1_2.9-2+b2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2+b2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.4-1 libstdc++-8-dev_8.3.0-23 libstdc++-9-dev_9.2.1-8 libstdc++-9-dev-arm64-cross_9.2.1-8cross1 libstdc++6_9.2.1-8 libstdc++6-arm64-cross_9.2.1-8cross1 libsub-override-perl_0.09-2 libsystemd0_242-7 libtasn1-6_4.14-3 libtinfo6_6.1+20190803-1 libtool_2.4.6-11 libtsan0_9.2.1-8 libtsan0-arm64-cross_9.2.1-8cross1 libubsan1_9.2.1-8 libubsan1-arm64-cross_9.2.1-8cross1 libuchardet0_0.0.6-3 libudev1_242-7 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1+b1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.29-1 libzstd1_1.4.3+dfsg-1 linux-libc-dev_5.2.17-1 linux-libc-dev-arm64-cross_5.2.9-2cross7 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20190803-1 ncurses-bin_6.1+20190803-1 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-5 perl-base_5.30.0-5 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-5 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96~beta-3 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: perm Binary: perm Architecture: any Version: 0.4.0-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://omictools.com/perm-tool Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/perm Vcs-Git: https://salsa.debian.org/med-team/perm.git Build-Depends: debhelper (>= 11~) Package-List: perm deb science optional arch=any Checksums-Sha1: b89025fe3ac6d6ab48c7a8a898a592119eb62037 114025 perm_0.4.0.orig.tar.gz 4cf7d62fdf548b2209d01b2fc210a2299bb5d09c 9912 perm_0.4.0-4.debian.tar.xz Checksums-Sha256: 31384ffe5abc1eabd68d6d5a331da761891a99da9e8502b1db8f0178e5df6b18 114025 perm_0.4.0.orig.tar.gz c51333d840f0713c2bba38d724de6761f8b420c256b45f6c1f74eb8375bed4b9 9912 perm_0.4.0-4.debian.tar.xz Files: 302f5828a0f15b7ae4c85390e8fe747d 114025 perm_0.4.0.orig.tar.gz 5c42dcb33b3e56ef3a8acaf79f68b4d4 9912 perm_0.4.0-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlunrBkRHHRpbGxlQGRl 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F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./perm_0.4.0-4.dsc dpkg-source: info: extracting perm in /<> dpkg-source: info: unpacking perm_0.4.0.orig.tar.gz dpkg-source: info: unpacking perm_0.4.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying make_dynamic_executable.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying gcc7.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.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-1b55b28f-a111-4c14-9f0e-60a31cdcf9cf SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package perm dpkg-buildpackage: info: source version 0.4.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu 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 arm64 fakeroot debian/rules clean dh clean dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' rm -f *.o *.exe cut out perm perm.tar.gz make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc make[1]: Entering directory '/<>' make clean make[2]: Entering directory '/<>' rm -f *.o *.exe cut out perm perm.tar.gz make[2]: Leaving directory '/<>' aarch64-linux-gnu-gcc -o perm -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp AlignmentsQ.cpp Filename.cpp GenomeNTdata.cpp ReadInBits.cpp PerM.cpp chromosomeNTdata.cpp bitsOperationUtil.cpp FileOutputBuffer.cpp HashIndexT.cpp ReadInBitsSet.cpp SeedPattern.cpp boolFlagArray.cpp GenomeInBits.cpp Index_Table.cpp ReadsMapping.cpp PairedReadsMapping.cpp ShortReadUtil.cpp chdir.cpp Genome_Index.cpp MismatchScores.cpp stdafx.cpp Flags.cpp ParseReadsOpts.cpp ColorSpaceRead.cpp Genome_Index_Table.cpp ParameterList.cpp ReadsMappingStats.cpp FileInputBuffer.cpp Genome_Index_TableQ.cpp ReadsQualScores.cpp ChrIndex2GeneName.cpp ReadsFileParser.cpp PairedReadsSet.cpp MappingResult.cpp refInBinFile.cpp LongReadsSet.cpp -lm -lstdc++ -Wl,-z,relro -Wl,-z,now chromosomeNTdata.cpp: In member function ‘unsigned int CchromosomeNTdata::removedNonACGTNBaseAndCollectGeneName()’: chromosomeNTdata.cpp:211:25: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 211 | sprintf(caGeneName, "%s:%d", caGeneName, (int)this->geneVec.table.size()); | ^~~~~~~~~~ ~~~~~~~~~~ chromosomeNTdata.cpp:211:41: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 2047 [-Wformat-overflow=] 211 | sprintf(caGeneName, "%s:%d", caGeneName, (int)this->geneVec.table.size()); | ^~ chromosomeNTdata.cpp:211:37: note: using the range [-2147483648, 2147483647] for directive argument 211 | sprintf(caGeneName, "%s:%d", caGeneName, (int)this->geneVec.table.size()); | ^~~~~~~ chromosomeNTdata.cpp:211:24: note: ‘sprintf’ output between 3 and 2060 bytes into a destination of size 2048 211 | sprintf(caGeneName, "%s:%d", caGeneName, (int)this->geneVec.table.size()); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadsMapping.cpp: In function ‘void getQualityScore4SOLiD(unsigned int, CReadInBits&, CAlignmentsQ&, CMappingResult&, bool)’: ReadsMapping.cpp:907:19: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 907 | sprintf(m.TAG, "%s\tCS:Z:%s\tCQ:Z:%s", m.TAG, m.caRead, m.QScores); | ~~^~~ ~~~~~ ReadsMapping.cpp: In constructor ‘CReadsMapping::CReadsMapping(MappingOpts)’: ReadsMapping.cpp:102:46: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 102 | sprintf(this->opt.outputDir, "%s/", P.outputDir); | ^ ReadsMapping.cpp:102:20: note: ‘sprintf’ output between 2 and 4097 bytes into a destination of size 4096 102 | sprintf(this->opt.outputDir, "%s/", P.outputDir); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadsMapping.cpp: In function ‘std::string getOutputFileNamePrefix(const char*, const CGenome_Index_TableQ&, MappingOpts&)’: ReadsMapping.cpp:594:33: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 2048 [-Wformat-overflow=] 594 | sprintf(outputPrefixStr, "%s%s_%c_%u_%d",\ | ^~ ReadsMapping.cpp:594:12: note: ‘sprintf’ output 7 or more bytes (assuming 4102) into a destination of size 2048 594 | sprintf(outputPrefixStr, "%s%s_%c_%u_%d",\ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 595 | dir, table.caRefName, excludeAmbiguous, table.chosenSeedId, opt.subDiffThreshold); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadsMapping.cpp: In member function ‘std::string CReadsMapping::getMappingFileN(const char*, const CGenome_Index_TableQ&)’: ReadsMapping.cpp:730:30: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 2048 [-Wformat-overflow=] 730 | sprintf(outputPath, "%s%s", this->opt.outputDir, this->opt.outputFileN); | ^~ ReadsMapping.cpp:730:16: note: ‘sprintf’ output between 1 and 8191 bytes into a destination of size 2048 730 | sprintf(outputPath, "%s%s", this->opt.outputDir, this->opt.outputFileN); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadsMapping.cpp:723:59: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 2020 [-Wformat-overflow=] 723 | sprintf(msg, "The specified output format %s is unrecognizable.\n", extN); | ^~ ReadsMapping.cpp:723:24: note: ‘sprintf’ output between 49 and 4144 bytes into a destination of size 2048 723 | sprintf(msg, "The specified output format %s is unrecognizable.\n", extN); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadsMapping.cpp:719:40: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 2046 [-Wformat-overflow=] 719 | sprintf(outputPath, "%s_%s.%s", outFileNPrefix.c_str(), fileNameOfReadSet.c_str(), extN); | ^~ ReadsMapping.cpp:719:20: note: ‘sprintf’ output 3 or more bytes (assuming 4098) into a destination of size 2048 719 | sprintf(outputPath, "%s_%s.%s", outFileNPrefix.c_str(), fileNameOfReadSet.c_str(), extN); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadsMapping.cpp: In function ‘void getSingleMappingSeqAndQ4SOLiD(const CGenome_Index_TableQ&, CAlignmentsQ&, CMappingResult&, bool)’: ReadsMapping.cpp:907:27: warning: ‘ CS:Z:’ directive writing 6 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 907 | sprintf(m.TAG, "%s\tCS:Z:%s\tCQ:Z:%s", m.TAG, m.caRead, m.QScores); | ^~~~~~~ ReadsMapping.cpp:907:16: note: ‘sprintf’ output between 13 and 4876 bytes into a destination of size 4096 907 | sprintf(m.TAG, "%s\tCS:Z:%s\tCQ:Z:%s", m.TAG, m.caRead, m.QScores); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ParameterList.cpp: In member function ‘void MappingOpts::setDefaults()’: ParameterList.cpp:31:9: warning: unused variable ‘mismatchScoreThreshold’ [-Wunused-variable] 31 | int mismatchScoreThreshold = -1; // No filtering by sum of mismatch score | ^~~~~~~~~~~~~~~~~~~~~~ Genome_Index_TableQ.cpp: In member function ‘unsigned int CGenome_Index_TableQ::extendAlignment(CAlignmentsQ&, CReadInBits) const’: Genome_Index_TableQ.cpp:364:10: warning: variable ‘extendForward’ set but not used [-Wunused-but-set-variable] 364 | bool extendForward = true; | ^~~~~~~~~~~~~ In file included from ReadsQualScores.h:3, from ReadsQualScores.cpp:1: In function ‘char* myStrCpy(char*, const char*, int)’, inlined from ‘unsigned int CReadsQualScores::getQualityScoresFromQUAL(std::vector*)’ at ReadsQualScores.cpp:86:25: stdafx.h:184:28: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 257 bytes from a string of length 2047 [-Wstringop-truncation] 184 | char* returnV = strncpy(caBuf, str, iBufSizeMinus1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ReadsQualScores.h:3, from ReadsFileParser.h:19, from ReadsFileParser.cpp:1: In function ‘char* myStrCpy(char*, const char*, int)’, inlined from ‘int CReadsFileParser::initialization()’ at ReadsFileParser.cpp:28:13: stdafx.h:184:28: warning: ‘char* strncpy(char*, const char*, size_t)’ writing 4095 bytes into a region of size 2048 overflows the destination [-Wstringop-overflow=] 184 | char* returnV = strncpy(caBuf, str, iBufSizeMinus1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* myStrCpy(char*, const char*, int)’, inlined from ‘bool CReadsFileParser::getNextSeqNameInFq(FileInputBuffer*, char*)’ at ReadsFileParser.cpp:191:5, inlined from ‘char* CReadsFileParser::get_Next_Read_From_Fastq()’ at ReadsFileParser.cpp:264:43: stdafx.h:184:28: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4095 bytes from a string of length 4999 [-Wstringop-truncation] 184 | char* returnV = strncpy(caBuf, str, iBufSizeMinus1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* myStrCpy(char*, const char*, int)’, inlined from ‘bool CReadsFileParser::getNextSeqNameInFq(FileInputBuffer*, char*)’ at ReadsFileParser.cpp:191:5, inlined from ‘char* CReadsFileParser::get_Next_Read_From_csFastq()’ at ReadsFileParser.cpp:302:43: stdafx.h:184:28: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4095 bytes from a string of length 4999 [-Wstringop-truncation] 184 | char* returnV = strncpy(caBuf, str, iBufSizeMinus1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* myStrCpy(char*, const char*, int)’, inlined from ‘char* CReadsFileParser::get_Next_Read_From_csFasta()’ at ReadsFileParser.cpp:346:25: stdafx.h:184:28: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4095 bytes from a string of length 4999 [-Wstringop-truncation] 184 | char* returnV = strncpy(caBuf, str, iBufSizeMinus1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from MappingResult.h:2, from MappingResult.cpp:1: In function ‘char* myStrCpy(char*, const char*, int)’, inlined from ‘CMappingResult::CMappingResult(CAlignmentsQ&, unsigned int)’ at MappingResult.cpp:13:13: stdafx.h:184:28: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 184 | char* returnV = strncpy(caBuf, str, iBufSizeMinus1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ #aarch64-linux-gnu-gcc -o perm *.o -lm -lstdc++ make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' # make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'perm' in '../perm_0.4.0-4_arm64.deb'. dpkg-deb: building package 'perm-dbgsym' in '../perm-dbgsym_0.4.0-4_arm64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../perm_0.4.0-4_arm64.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 2019-10-06T09:42:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ perm_0.4.0-4_arm64.changes: --------------------------- Format: 1.8 Date: Sun, 23 Sep 2018 17:04:23 +0200 Source: perm Binary: perm perm-dbgsym Built-For-Profiles: cross nocheck Architecture: arm64 Version: 0.4.0-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: perm - efficient mapping of short reads with periodic spaced seeds Changes: perm (0.4.0-4) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: 454bc26d2eb1267e0a3fef10fc46dc724e555870 1344516 perm-dbgsym_0.4.0-4_arm64.deb f7aec10f6d4bd54b7608030b52b70a9723bfd445 4636 perm_0.4.0-4_arm64.buildinfo e75ee29753102af2f8801e800bac59fff31cc328 114720 perm_0.4.0-4_arm64.deb Checksums-Sha256: 2e718701df5ff3c9b63a7b25d77d5aa4eeb21e3d86b2e737000afeda6d1ad26a 1344516 perm-dbgsym_0.4.0-4_arm64.deb 4f7f558521191f86675d029311e135863a2d069bdf8a421b5c96f5751d7002c2 4636 perm_0.4.0-4_arm64.buildinfo c65785fe89d2829940a235abbdd39063898b9c9e380c8572d8abc2b152ef3e25 114720 perm_0.4.0-4_arm64.deb Files: b0eca8c18389b7dd3d2222f3b5cb0d85 1344516 debug optional perm-dbgsym_0.4.0-4_arm64.deb bc26962c2d8bb98a5182a54c7ff7d13f 4636 science optional perm_0.4.0-4_arm64.buildinfo 9dbd7cfcc9c112132a0fe1e3719725a6 114720 science optional perm_0.4.0-4_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: perm Binary: perm Architecture: arm64 Version: 0.4.0-4 Checksums-Md5: b0eca8c18389b7dd3d2222f3b5cb0d85 1344516 perm-dbgsym_0.4.0-4_arm64.deb 9dbd7cfcc9c112132a0fe1e3719725a6 114720 perm_0.4.0-4_arm64.deb Checksums-Sha1: 454bc26d2eb1267e0a3fef10fc46dc724e555870 1344516 perm-dbgsym_0.4.0-4_arm64.deb e75ee29753102af2f8801e800bac59fff31cc328 114720 perm_0.4.0-4_arm64.deb Checksums-Sha256: 2e718701df5ff3c9b63a7b25d77d5aa4eeb21e3d86b2e737000afeda6d1ad26a 1344516 perm-dbgsym_0.4.0-4_arm64.deb c65785fe89d2829940a235abbdd39063898b9c9e380c8572d8abc2b152ef3e25 114720 perm_0.4.0-4_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 06 Oct 2019 09:42:51 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.32.51.20190909-1), binutils-common (= 2.32.51.20190909-1), binutils-x86-64-linux-gnu (= 2.32.51.20190909-1), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.8), bzip2 (= 1.0.8-2), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-8 (= 8.3.0-23), cpp-9 (= 9.2.1-8), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.6.1), debianutils (= 4.9), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.0-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-1), fdisk (= 2.34-0.1), file (= 1:5.37-5), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.2.1-8), gcc (= 4:9.2.1-3.1), gcc-8 (= 8.3.0-23), gcc-8-base (= 8.3.0-23), gcc-9 (= 9.2.1-8), gcc-9-base (= 9.2.1-8), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3+b1), hostname (= 3.22+b1), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-5), libarchive-zip-perl (= 1.66-2), libasan5 (= 9.2.1-8), libatomic1 (= 9.2.1-8), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.32.51.20190909-1), libblkid1 (= 2.34-0.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.29-2), libc-dev-bin (= 2.29-2), libc6 (= 2.29-2), libc6-dev (= 2.29-2), libcap-ng0 (= 0.7.9-2+b1), libcc1-0 (= 9.2.1-8), libcroco3 (= 0.6.13-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.249), libdebhelper-perl (= 12.6.1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.6.0-1), libgcc-8-dev (= 8.3.0-23), libgcc-9-dev (= 9.2.1-8), libgcc1 (= 1:9.2.1-8), libgcrypt20 (= 1.8.5-3), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.62.0-3), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 9.2.1-8), libgpg-error0 (= 1.36-7), libicu63 (= 63.2-2), libisl21 (= 0.21-2), libitm1 (= 9.2.1-8), liblsan0 (= 9.2.1-8), liblz4-1 (= 1.8.3-1+b1), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.37-5), libmagic1 (= 1:5.37-5), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-23), libncurses6 (= 6.1+20190803-1), libncursesw6 (= 6.1+20190803-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.32-5+b1), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.0-5), libpipeline1 (= 1.5.1-2), libquadmath0 (= 9.2.1-8), libseccomp2 (= 2.4.1-2), libselinux1 (= 2.9-2+b2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libstdc++-9-dev (= 9.2.1-8), libstdc++6 (= 9.2.1-8), libsub-override-perl (= 0.09-2), libsystemd0 (= 242-7), libtinfo6 (= 6.1+20190803-1), libtool (= 2.4.6-11), libtsan0 (= 9.2.1-8), libubsan1 (= 9.2.1-8), libuchardet0 (= 0.0.6-3), libudev1 (= 242-7), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 5.2.17-1), login (= 1:4.7-2), lsb-base (= 11.1.0), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.7-3), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20190803-1), ncurses-bin (= 6.1+20190803-1), patch (= 2.7.6-6), perl (= 5.30.0-5), perl-base (= 5.30.0-5), perl-modules-5.30 (= 5.30.0-5), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.96~beta-3), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1537715063" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ perm-dbgsym_0.4.0-4_arm64.deb ----------------------------- new Debian package, version 2.0. size 1344516 bytes: control archive=532 bytes. 359 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: perm-dbgsym Source: perm Version: 0.4.0-4 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 1382 Depends: perm (= 0.4.0-4) Section: debug Priority: optional Description: debug symbols for perm Build-Ids: ffea75d02b26dfb39970a92d8f8b69b9c3f76537 drwxr-xr-x root/root 0 2018-09-23 15:04 ./ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/lib/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/lib/debug/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/lib/debug/.build-id/ff/ -rw-r--r-- root/root 1403944 2018-09-23 15:04 ./usr/lib/debug/.build-id/ff/ea75d02b26dfb39970a92d8f8b69b9c3f76537.debug drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/share/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/share/doc/ lrwxrwxrwx root/root 0 2018-09-23 15:04 ./usr/share/doc/perm-dbgsym -> perm perm_0.4.0-4_arm64.deb ---------------------- new Debian package, version 2.0. size 114720 bytes: control archive=860 bytes. 747 bytes, 15 lines control 246 bytes, 4 lines md5sums Package: perm Version: 0.4.0-4 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 301 Depends: libc6 (>= 2.29), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: https://omictools.com/perm-tool Description: efficient mapping of short reads with periodic spaced seeds PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads. drwxr-xr-x root/root 0 2018-09-23 15:04 ./ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/bin/ lrwxrwxrwx root/root 0 2018-09-23 15:04 ./usr/bin/PerM -> perm -rwxr-xr-x root/root 288880 2018-09-23 15:04 ./usr/bin/perm drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/share/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/share/doc/perm/ -rw-r--r-- root/root 812 2018-09-23 15:04 ./usr/share/doc/perm/changelog.Debian.gz -rw-r--r-- root/root 913 2018-09-23 15:04 ./usr/share/doc/perm/copyright drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/share/man/ drwxr-xr-x root/root 0 2018-09-23 15:04 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2018-09-23 15:04 ./usr/share/man/man1/PerM.1.gz -> perm.1.gz -rw-r--r-- root/root 5110 2018-09-23 15:04 ./usr/share/man/man1/perm.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 [532 B] Get:5 copy:/<>/apt_archive ./ Packages [619 B] Fetched 2114 B in 0s (109 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: sbuild-build-depends-lintian-dummy:arm64 : Depends: lintian:amd64 E: Unable to correct problems, you have held broken packages. apt-get failed. E: Package installation failed Not removing build depends: cloned chroot in use +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 8408 Build-Time: 49 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 17 Job: perm_0.4.0-4 Lintian: error Machine Architecture: amd64 Package: perm Package-Time: 78 Source-Version: 0.4.0-4 Space: 8408 Status: successful Version: 0.4.0-4 -------------------------------------------------------------------------------- Finished at 2019-10-06T09:42:51Z Build needed 00:01:18, 8408k disk space