sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | disulfinder 1.2.11-8 (arm64) Sat, 16 May 2020 04:22:17 +0000 | +==============================================================================+ Package: disulfinder Version: 1.2.11-8 Source Version: 1.2.11-8 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-e449cf7d-90ae-42d4-87a9-c41938f493f8' with '<>' I: NOTICE: Log filtering will replace 'build/disulfinder-4W88aA/resolver-18aveP' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [146 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 2020-05-15-0800.11.pdiff [14.1 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-15-1402.01.pdiff [15.2 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-15-2001.24.pdiff [21.1 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-16-0159.58.pdiff [14.3 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-15-0800.11.pdiff [1703 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-15-1402.01.pdiff [22.8 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-15-2001.24.pdiff [38.7 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-16-0159.58.pdiff [14.3 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-16-0159.58.pdiff [11.6 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-16-0159.58.pdiff [11.6 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8078 kB] Fetched 8419 kB in 2s (5139 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu libbinutils libctf-nobfd0 libctf0 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4329 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 libctf0 amd64 2.34-8 [45.7 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libctf-nobfd0 amd64 2.34-8 [101 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.34-8 [1589 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libbinutils amd64 2.34-8 [469 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 binutils amd64 2.34-8 [59.4 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-common amd64 2.34-8 [2065 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4329 kB in 0s (94.6 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12640 files and directories currently installed.) Preparing to unpack .../0-libctf0_2.34-8_amd64.deb ... Unpacking libctf0:amd64 (2.34-8) over (2.34-7) ... Preparing to unpack .../1-libctf-nobfd0_2.34-8_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.34-8) over (2.34-7) ... Preparing to unpack .../2-binutils-x86-64-linux-gnu_2.34-8_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.34-8) over (2.34-7) ... Preparing to unpack .../3-libbinutils_2.34-8_amd64.deb ... Unpacking libbinutils:amd64 (2.34-8) over (2.34-7) ... Preparing to unpack .../4-binutils_2.34-8_amd64.deb ... Unpacking binutils (2.34-8) over (2.34-7) ... Preparing to unpack .../5-binutils-common_2.34-8_amd64.deb ... Unpacking binutils-common:amd64 (2.34-8) over (2.34-7) ... Setting up binutils-common:amd64 (2.34-8) ... Setting up libctf-nobfd0:amd64 (2.34-8) ... Setting up libbinutils:amd64 (2.34-8) ... Setting up libctf0:amd64 (2.34-8) ... Setting up binutils-x86-64-linux-gnu (2.34-8) ... Setting up binutils (2.34-8) ... Processing triggers for libc-bin (2.30-8) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'disulfinder' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/disulfinder.git Please use: git clone https://salsa.debian.org/med-team/disulfinder.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2490 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main disulfinder 1.2.11-8 (dsc) [2180 B] Get:2 http://debian.oregonstate.edu/debian unstable/main disulfinder 1.2.11-8 (tar) [2481 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main disulfinder 1.2.11-8 (diff) [7588 B] Fetched 2490 kB in 0s (63.5 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/disulfinder-4W88aA/disulfinder-1.2.11' with '<>' I: NOTICE: Log filtering will replace 'build/disulfinder-4W88aA' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev, 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 [417 B] Get:5 copy:/<>/apt_archive ./ Packages [507 B] Fetched 1881 B in 0s (70.9 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdmainutils build-essential 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++ g++-9 g++-9-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-10-base:arm64 gcc-10-cross-base 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 libboost-dev:arm64 libboost-graph-dev:arm64 libboost-graph1.67-dev:arm64 libboost-graph1.67.0:arm64 libboost-regex1.67.0:arm64 libboost-serialization1.67-dev:arm64 libboost-serialization1.67.0:arm64 libboost-test1.67-dev:arm64 libboost-test1.67.0:arm64 libboost1.67-dev:arm64 libbsd0 libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64 libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libf2c2:arm64 libf2c2-dev:arm64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:arm64 libgcc-9-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libglib2.0-0 libgomp1:arm64 libgomp1-arm64-cross libicu63 libicu63:arm64 libio-string-perl libitm1:arm64 libitm1-arm64-cross liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libstdc++-9-dev 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 g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc:arm64 graphviz:arm64 libboost1.67-doc:arm64 libboost-atomic1.67-dev:arm64 libboost-chrono1.67-dev:arm64 libboost-container1.67-dev:arm64 libboost-context1.67-dev:arm64 libboost-contract1.67-dev:arm64 libboost-coroutine1.67-dev:arm64 libboost-date-time1.67-dev:arm64 libboost-exception1.67-dev:arm64 libboost-fiber1.67-dev:arm64 libboost-filesystem1.67-dev:arm64 libboost-graph-parallel1.67-dev:arm64 libboost-iostreams1.67-dev:arm64 libboost-locale1.67-dev:arm64 libboost-log1.67-dev:arm64 libboost-math1.67-dev:arm64 libboost-mpi1.67-dev:arm64 libboost-mpi-python1.67-dev:arm64 libboost-numpy1.67-dev:arm64 libboost-program-options1.67-dev:arm64 libboost-python1.67-dev:arm64 libboost-random1.67-dev:arm64 libboost-regex1.67-dev:arm64 libboost-signals1.67-dev:arm64 libboost-stacktrace1.67-dev:arm64 libboost-system1.67-dev:arm64 libboost-thread1.67-dev:arm64 libboost-timer1.67-dev:arm64 libboost-type-erasure1.67-dev:arm64 libboost-wave1.67-dev:arm64 libboost1.67-tools-dev:arm64 libmpfrc++-dev:arm64 libntl-dev:arm64 glibc-doc:arm64 libc-l10n:arm64 locales:arm64 glibc-doc manpages-dev:arm64 libstdc++-9-doc 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 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 build-essential 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++ g++-9 g++-9-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-10-base:arm64 gcc-10-cross-base 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 libboost-dev:arm64 libboost-graph-dev:arm64 libboost-graph1.67-dev:arm64 libboost-graph1.67.0:arm64 libboost-regex1.67.0:arm64 libboost-serialization1.67-dev:arm64 libboost-serialization1.67.0:arm64 libboost-test1.67-dev:arm64 libboost-test1.67.0:arm64 libboost1.67-dev:arm64 libbsd0 libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64 libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libf2c2:arm64 libf2c2-dev:arm64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:arm64 libgcc-9-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libglib2.0-0 libgomp1:arm64 libgomp1-arm64-cross libicu63 libicu63:arm64 libio-string-perl libitm1:arm64 libitm1-arm64-cross liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libstdc++-9-dev 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, 113 newly installed, 0 to remove and 0 not upgraded. Need to get 98.0 MB of archives. After this operation, 521 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 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 1.22.4-5 [920 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.1-1 [1308 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-10-base arm64 10.1.0-1 [197 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-9-base arm64 9.3.0-12 [196 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0039 [68.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-1 [775 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.34-8 [2790 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.16-1 [104 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.30-8 [2631 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-12 [1701 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.3.0-12 [10.7 MB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-aarch64-linux-gnu-base amd64 9.3.0-8cross1 [197 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-aarch64-linux-gnu amd64 9.3.0-8cross1 [6544 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:9.2.1-3.1 [16.7 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.3.0-8cross1 [192 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10-20200418-1cross1 [192 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.30-2cross1 [1246 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-arm64-cross all 10-20200418-1cross1 [34.7 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 10-20200418-1cross1 [87.9 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 10-20200418-1cross1 [22.9 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 10-20200418-1cross1 [8608 B] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-arm64-cross all 9.3.0-8cross1 [347 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 10-20200418-1cross1 [125 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 10-20200418-1cross1 [285 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 10-20200418-1cross1 [408 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 10-20200418-1cross1 [122 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-arm64-cross all 9.3.0-8cross1 [887 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-aarch64-linux-gnu amd64 9.3.0-8cross1 [6922 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:9.2.1-3.1 [1460 B] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 5.4.19-1cross1 [1153 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.30-2cross1 [2265 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-arm64-cross all 9.3.0-8cross1 [1637 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-aarch64-linux-gnu amd64 9.3.0-8cross1 [7127 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:9.2.1-3.1 [1180 B] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.8 [6644 B] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13 [184 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13 [1002 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-s1 arm64 10.1.0-1 [34.7 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt1 arm64 1:4.4.16-1 [90.4 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.30-8 [2468 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main arm64 libasan5 arm64 9.3.0-12 [354 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 10.1.0-1 [9476 B] Get:90 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 10.1.0-1 [91.0 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 10.1.0-1 [23.8 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 10.1.0-1 [126 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 10.1.0-1 [293 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 10.1.0-1 [450 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 10.1.0-1 [123 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-9-dev arm64 9.3.0-12 [886 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 5.6.7-1 [1079 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt-dev arm64 1:4.4.16-1 [111 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.30-8 [2281 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-9-dev arm64 9.3.0-12 [1659 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main arm64 libboost1.67-dev arm64 1.67.0-17+b1 [8388 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-dev arm64 1.67.0.2+b1 [4484 B] Get:103 http://debian.oregonstate.edu/debian unstable/main arm64 libicu63 arm64 63.2-3 [8147 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-regex1.67.0 arm64 1.67.0-17+b1 [481 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-graph1.67.0 arm64 1.67.0-17+b1 [315 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-serialization1.67.0 arm64 1.67.0-17+b1 [310 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-serialization1.67-dev arm64 1.67.0-17+b1 [356 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-test1.67.0 arm64 1.67.0-17+b1 [436 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-test1.67-dev arm64 1.67.0-17+b1 [507 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-graph1.67-dev arm64 1.67.0-17+b1 [332 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-graph-dev arm64 1.67.0.2+b1 [4372 B] Get:112 http://debian.oregonstate.edu/debian unstable/main arm64 libf2c2 arm64 20130926-3 [110 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main arm64 libf2c2-dev arm64 20130926-3 [123 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 98.0 MB in 1s (113 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12640 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.1-1_amd64.deb ... Unpacking man-db (2.9.1-1) ... 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Selecting previously unselected package sbuild-build-depends-main-dummy:arm64. Preparing to unpack .../112-sbuild-build-depends-main-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-1) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.64.2-1) ... No schema files found: doing nothing. Setting up gcc-9-aarch64-linux-gnu-base:amd64 (9.3.0-8cross1) ... Setting up libdebhelper-perl (13) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up linux-libc-dev:arm64 (5.6.7-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up binutils-aarch64-linux-gnu (2.34-8) ... Setting up cpp-9-aarch64-linux-gnu (9.3.0-8cross1) ... Setting up file (1:5.38-4) ... Setting up libyaml-perl (1.30-1) ... Setting up libicu63:amd64 (63.2-3) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up gcc-10-base:arm64 (10.1.0-1) ... 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 libsigsegv2:amd64 (2.12-2) ... Setting up libc6-arm64-cross (2.30-2cross1) ... Setting up autopoint (0.19.8.1-10) ... Setting up gcc-9-cross-base (9.3.0-8cross1) ... Setting up gcc-10-cross-base (10-20200418-1cross1) ... Setting up linux-libc-dev-arm64-cross (5.4.19-1cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.16-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libc6-dev:amd64 (2.30-8) ... 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 (2.9.10+dfsg-5) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:arm64 (9.3.0-12) ... Setting up libgcc-s1-arm64-cross (10-20200418-1cross1) ... Setting up libatomic1-arm64-cross (10-20200418-1cross1) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up liblsan0-arm64-cross (10-20200418-1cross1) ... Setting up libgomp1-arm64-cross (10-20200418-1cross1) ... Setting up libstdc++-9-dev:amd64 (9.3.0-12) ... Setting up libtool (2.4.6-14) ... Setting up libtsan0-arm64-cross (10-20200418-1cross1) ... Setting up m4 (1.4.18-4) ... Setting up libc6-dev-arm64-cross (2.30-2cross1) ... Setting up libasan5-arm64-cross (9.3.0-8cross1) ... Setting up libstdc++6-arm64-cross (10-20200418-1cross1) ... 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 (10-20200418-1cross1) ... Setting up ucf (3.0039) ... Setting up g++-9 (9.3.0-12) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up build-essential (12.8) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up libubsan1-arm64-cross (10-20200418-1cross1) ... Setting up libgcc-9-dev-arm64-cross (9.3.0-8cross1) ... Setting up man-db (2.9.1-1) ... 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 (9.3.0-8cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2) ... 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 (9.3.0-8cross1) ... 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 (9.3.0-8cross1) ... 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 libcrypt1:arm64 (1:4.4.16-1) ... Setting up libgcc-s1:arm64 (10.1.0-1) ... Setting up dh-autoreconf (19) ... Setting up libc6:arm64 (2.30-8) ... Setting up libcrypt-dev:arm64 (1:4.4.16-1) ... Setting up libc6-dev:arm64 (2.30-8) ... Setting up libf2c2:arm64 (20130926-3) ... Setting up libf2c2-dev:arm64 (20130926-3) ... Setting up libstdc++6:arm64 (10.1.0-1) ... Setting up liblsan0:arm64 (10.1.0-1) ... Setting up libitm1:arm64 (10.1.0-1) ... Setting up libtsan0:arm64 (10.1.0-1) ... Setting up libboost-test1.67.0:arm64 (1.67.0-17+b1) ... Setting up debhelper (13) ... Setting up libgomp1:arm64 (10.1.0-1) ... Setting up libicu63:arm64 (63.2-3) ... Setting up libasan5:arm64 (9.3.0-12) ... Setting up libatomic1:arm64 (10.1.0-1) ... Setting up libubsan1:arm64 (10.1.0-1) ... Setting up libboost-serialization1.67.0:arm64 (1.67.0-17+b1) ... Setting up libboost-regex1.67.0:arm64 (1.67.0-17+b1) ... Setting up libboost-graph1.67.0:arm64 (1.67.0-17+b1) ... Setting up libgcc-9-dev:arm64 (9.3.0-12) ... Setting up libstdc++-9-dev:arm64 (9.3.0-12) ... Setting up libboost1.67-dev:arm64 (1.67.0-17+b1) ... Setting up libboost-serialization1.67-dev:arm64 (1.67.0-17+b1) ... Setting up libboost-test1.67-dev:arm64 (1.67.0-17+b1) ... Setting up libboost-graph1.67-dev:arm64 (1.67.0-17+b1) ... Setting up libboost-dev:arm64 (1.67.0.2+b1) ... Setting up libboost-graph-dev:arm64 (1.67.0.2+b1) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.30-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-8 dpkg-dev_1.19.7 g++-9_9.3.0-12 gcc-9_9.3.0-12 libc6-dev_2.30-8 libstdc++-9-dev_9.3.0-12 libstdc++-9-dev-arm64-cross_9.3.0-8cross1 libstdc++6_10.1.0-1 libstdc++6-arm64-cross_10-20200418-1cross1 linux-libc-dev_5.6.7-1 Package versions: adduser_3.118 apt_2.1.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8 binutils-aarch64-linux-gnu_2.34-8 binutils-common_2.34-8 binutils-x86-64-linux-gnu_2.34-8 bsdmainutils_11.1.2+b1 bsdutils_1:2.35.1-5 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.4.0-3 cpp-9_9.3.0-12 cpp-9-aarch64-linux-gnu_9.3.0-8cross1 cpp-aarch64-linux-gnu_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-arm64_12.8 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-5 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-12 g++-9-aarch64-linux-gnu_9.3.0-8cross1 g++-aarch64-linux-gnu_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10.1.0-1 gcc-10-cross-base_10-20200418-1cross1 gcc-8-base_8.4.0-3 gcc-9_9.3.0-12 gcc-9-aarch64-linux-gnu_9.3.0-8cross1 gcc-9-aarch64-linux-gnu-base_9.3.0-8cross1 gcc-9-base_9.3.0-12 gcc-9-cross-base_9.3.0-8cross1 gcc-aarch64-linux-gnu_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-12 libasan5-arm64-cross_9.3.0-8cross1 libatomic1_10.1.0-1 libatomic1-arm64-cross_10-20200418-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.34-8 libblkid1_2.35.1-5 libboost-dev_1.67.0.2+b1 libboost-graph-dev_1.67.0.2+b1 libboost-graph1.67-dev_1.67.0-17+b1 libboost-graph1.67.0_1.67.0-17+b1 libboost-regex1.67.0_1.67.0-17+b1 libboost-serialization1.67-dev_1.67.0-17+b1 libboost-serialization1.67.0_1.67.0-17+b1 libboost-test1.67-dev_1.67.0-17+b1 libboost-test1.67.0_1.67.0-17+b1 libboost1.67-dev_1.67.0-17+b1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-8 libc-dev-bin_2.30-8 libc6_2.30-8 libc6-arm64-cross_2.30-2cross1 libc6-dev_2.30-8 libc6-dev-arm64-cross_2.30-2cross1 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10.1.0-1 libcom-err2_1.45.6-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000003-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8 libctf0_2.34-8 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libf2c2_20130926-3 libf2c2-dev_20130926-3 libfakeroot_1.24-1 libfdisk1_2.35.1-5 libffi6_3.2.1-9 libffi7_3.3-4 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.8.0-1 libfile-which-perl_1.23-1 libgcc-9-dev_9.3.0-12 libgcc-9-dev-arm64-cross_9.3.0-8cross1 libgcc-s1_10.1.0-1 libgcc-s1-arm64-cross_10-20200418-1cross1 libgcc1_1:10.1.0-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10.1.0-1 libgomp1-arm64-cross_10-20200418-1cross1 libgpg-error0_1.37-1 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10.1.0-1 libitm1-arm64-cross_10-20200418-1cross1 liblocale-gettext-perl_1.07-4 liblsan0_10.1.0-1 liblsan0-arm64-cross_10-20200418-1cross1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.35.1-5 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.4.0-3 libncursesw6_6.2-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libp11-kit0_0.23.20-1 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_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libquadmath0_10.1.0-1 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5 libss2_1.45.6-1 libstdc++-9-dev_9.3.0-12 libstdc++-9-dev-arm64-cross_9.3.0-8cross1 libstdc++6_10.1.0-1 libstdc++6-arm64-cross_10-20200418-1cross1 libsub-override-perl_0.09-2 libsystemd0_245.5-2 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10.1.0-1 libtsan0-arm64-cross_10-20200418-1cross1 libubsan1_10.1.0-1 libubsan1-arm64-cross_10-20200418-1cross1 libuchardet0_0.0.6-3 libudev1_245.5-2 libunistring2_0.9.10-2 libuuid1_2.35.1-5 libxml-libxml-perl_2.0134+dfsg-2 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_2.9.10+dfsg-5 libyaml-perl_1.30-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.6.7-1 linux-libc-dev-arm64-cross_5.4.19-1cross1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-2+b1 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.35.1-5 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-10 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0039 util-linux_2.35.1-5 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: disulfinder Binary: disulfinder, disulfinder-data Architecture: any all Version: 1.2.11-8 Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan , Andreas Tille Homepage: http://disulfind.dsi.unifi.it/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/disulfinder Vcs-Git: https://salsa.debian.org/med-team/disulfinder.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev Package-List: disulfinder deb science optional arch=any disulfinder-data deb science optional arch=all Checksums-Sha1: 275abbe8b4ac8e7f83d8a38c81c7f75c0ec7481e 2480613 disulfinder_1.2.11.orig.tar.gz 6f1b8adf28a7f68eb9ab1017d404cc8ff219000b 7588 disulfinder_1.2.11-8.debian.tar.xz Checksums-Sha256: d653aaac3ea26e9f6106a371de4f43d05b781a8b8b690c97820e4b27ea9d3495 2480613 disulfinder_1.2.11.orig.tar.gz 8a101f70997f8df0fcf75ae44be28548ffed2128ead3ad7cc9b60655f8b8630d 7588 disulfinder_1.2.11-8.debian.tar.xz Files: a4f0ed137b56fc0674a207351b659eba 2480613 disulfinder_1.2.11.orig.tar.gz c28edeb4b97d4c55fcc1e4b94796db9b 7588 disulfinder_1.2.11-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluntPgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGNlg//d8PAW3d5XTdQVkWgT3Z9Q6jOJ72yU8hn XPmnFWXI60NfpaBpfUi/JjxyY0FxpAJme5S0+A4Dbj/luqKetvQNMdglf5W53n6V DrEh3OQvVI92PBm/d2cvxk7PrLDUsQZiRFj4djGVMxltgH2HusCklHTR91svF2A2 GT91vG3Vf/1DKTMaSUoWCl9WqhCJorNkZ/n2vRMfsmqANkb1vFoVlLGYJAh0mxqI 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disulfinder_1.2.11.orig.tar.gz dpkg-source: info: unpacking disulfinder_1.2.11-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying variable_length_array dpkg-source: info: applying unknown_escape dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying gcc-7.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-e449cf7d-90ae-42d4-87a9-c41938f493f8 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 disulfinder dpkg-buildpackage: info: source version 1.2.11-8 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 distclean make[1]: Entering directory '/<>' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory '/<>/disulfind/src' make -C NN clean make[3]: Entering directory '/<>/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Leaving directory '/<>/disulfind/src/NN' make -C Common clean make[3]: Entering directory '/<>/disulfind/src/Common' make -C eig clean make[4]: Entering directory '/<>/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[4]: Leaving directory '/<>/disulfind/src/Common/eig' rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory '/<>/disulfind/src/Common' make -C SVM clean make[3]: Entering directory '/<>/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/<>/disulfind/src/SVM' cd SVM && make clean make[3]: Entering directory '/<>/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/<>/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory '/<>/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory '/<>/disulfind/src/Input' cd Output && make clean make[3]: Entering directory '/<>/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory '/<>/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory '/<>/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory '/<>/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory '/<>/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory '/<>/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory '/<>/disulfind/src' rm -f *.[12345678] *.[12345678].gz #if [ -d "disulfind" ]; then rm -rf disulfind; fi if [ -d "disulfinder-1.2.11" ]; then rm -rf "disulfinder-1.2.11"; fi rm -rf patch-stamp \ initial-clean-stamp \ "disulfinder-1.2.11.tar.gz" \ .pc make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars debian/files rm -fr -- debian/disulfinder/ debian/tmp/ debian/disulfinder-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build --no-parallel 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[2]: Entering directory '/<>' make -C disulfind/src disulfinder make[3]: Entering directory '/<>/disulfind/src' aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/GlobalDescriptor.cpp -o Input/GlobalDescriptor.o In file included from Input/utils.h:2, from Input/GlobalDescriptor.cpp:3: Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ Input/Protein.h:16:20: warning: ‘aa_codes’ defined but not used [-Wunused-variable] 16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files | ^~~~~~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o In file included from Input/utils.h:2, from Input/createBRNNDataset.h:1, from Input/createBRNNDataset.cpp:2: Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ Input/Protein.h:16:20: warning: ‘aa_codes’ defined but not used [-Wunused-variable] 16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files | ^~~~~~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o In file included from Input/utils.h:2, from Input/createKernelDataset.h:1, from Input/createKernelDataset.cpp:2: Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o Output/makeHTMLOutput.cpp: In function ‘void makeHTMLOutput(std::string, const char*, int, std::string, std::ostream&)’: Output/makeHTMLOutput.cpp:162:24: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 162 | char * altname[2] = {"Second","Third"}; | ^~~~~~~~ Output/makeHTMLOutput.cpp:162:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 162 | char * altname[2] = {"Second","Third"}; | ^~~~~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o Output/makeASCIIOutput.cpp: In function ‘void makeASCIIOutput(std::string, const char*, int, std::string, std::ostream&)’: Output/makeASCIIOutput.cpp:144:24: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 144 | char * altname[2] = {"SECOND","THIRD"}; | ^~~~~~~~ Output/makeASCIIOutput.cpp:144:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 144 | char * altname[2] = {"SECOND","THIRD"}; | ^~~~~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/viterbi_aligner.cpp -o FSA-Alignment/viterbi_aligner.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/multi-array.cpp -o NN/multi-array.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/array.cpp -o NN/array.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-model.cpp -o NN/brnn-model.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-test.cpp -o NN/brnn-test.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Node.cpp -o BRNN/RNNs/Node.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/StructureSearch.cpp -o BRNN/RNNs/StructureSearch.o aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DataSet.cpp -o BRNN/RNNs/DataSet.o In file included from BRNN/RNNs/DataSet.cpp:1: BRNN/RNNs/DataSet.h:19:1: warning: ‘typedef’ was ignored in this declaration 19 | typedef struct StructuredInstanceTemplate { | ^~~~~~~ In file included from BRNN/RNNs/DataSet.cpp:1: BRNN/RNNs/DataSet.h: In constructor ‘DataSet::iterator::iterator(DataSet&)’: BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h: In member function ‘bool DataSet::iterator::operator++()’: BRNN/RNNs/DataSet.h:116:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 116 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h:135:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.cpp: In constructor ‘DataSet::DataSet(const char*, const char*)’: BRNN/RNNs/DataSet.cpp:69:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 69 | if(pos == string::npos) | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.cpp: In member function ‘bool DataSet::loadInstances(const char*)’: BRNN/RNNs/DataSet.cpp:141:7: warning: unused variable ‘ng’ [-Wunused-variable] 141 | int ng = 1; | ^~ BRNN/RNNs/DataSet.cpp: At global scope: BRNN/RNNs/DataSet.cpp:14:12: warning: ‘int one(const dirent*)’ defined but not used [-Wunused-function] 14 | static int one(const struct dirent* unused) { | ^~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DPAG.cpp -o BRNN/RNNs/DPAG.o BRNN/RNNs/DPAG.cpp: In function ‘float PRMeasure(const DPAG&, const DPAG&, std::vector&)’: BRNN/RNNs/DPAG.cpp:48:7: warning: unused variable ‘global_predicted_positives’ [-Wunused-variable] 48 | int global_predicted_positives = boost::num_edges(g), | ^~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:49:5: warning: unused variable ‘global_actual_positives’ [-Wunused-variable] 49 | global_actual_positives = boost::num_edges(gtarget), | ^~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:52:12: warning: unused variable ‘graphNode’ [-Wunused-variable] 52 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘float PrecisionMeasure(const DPAG&, const DPAG&, std::vector&)’: BRNN/RNNs/DPAG.cpp:302:12: warning: unused variable ‘graphNode’ [-Wunused-variable] 302 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘std::pair globalPRMeasure(const DPAG&, const DPAG&, int&, int&, int&, int&, int&, int&, float&)’: BRNN/RNNs/DPAG.cpp:361:12: warning: unused variable ‘graphNode’ [-Wunused-variable] 361 | Vertex_d graphNode, targetNode, targetNode1; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘ConfusionTable getPredictionIndexes(const DPAG&, const DPAG&, std::vector&)’: BRNN/RNNs/DPAG.cpp:560:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::vertices_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 559 | require(true_positives + true_negatives + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | false_positives + false_negatives == | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 561 | boost::num_vertices(gpred) * (boost::num_vertices(gpred)-1) / 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:471:9: warning: unused variable ‘weight’ [-Wunused-variable] 471 | float weight = 1.0 / boost::num_vertices(gpred); | ^~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘float RecallMeasure(const DPAG&, const DPAG&, std::vector&)’: BRNN/RNNs/DPAG.cpp:573:12: warning: unused variable ‘graphNode’ [-Wunused-variable] 573 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘bool equal(const DPAG&, const DPAG&)’: BRNN/RNNs/DPAG.cpp:746:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 746 | for(int i=0; i, boost::property >, boost::adjacency_list, boost::property > > dpag_to_rnndpag(const DPAG&)’: BRNN/RNNs/DPAG.cpp:832:24: warning: comparison of integer expressions of different signedness: ‘boost::vec_adj_list_vertex_id_map, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 832 | if(vertex_id[*v_i] != n_vertices-1) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:839:22: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} and ‘boost::vec_adj_list_vertex_id_map, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 839 | if(children.front() == vertex_id[*v_i]+1) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:844:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 844 | for(int i=0; i, int>::value_type’ {aka ‘int’} and ‘boost::vec_adj_list_vertex_id_map, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 862 | if((*it).second.front() == vertex_id[*v_i]-1) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:867:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 867 | for(int i=0; i<(*it).second.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:813:12: warning: unused variable ‘node’ [-Wunused-variable] 813 | Vertex_d node; | ^~~~ BRNN/RNNs/DPAG.cpp: In function ‘DPAG rnndpag_to_dpag(const std::pair, boost::property >, boost::adjacency_list, boost::property > >&)’: BRNN/RNNs/DPAG.cpp:878:12: warning: variable ‘vertex_id’ set but not used [-Wunused-but-set-variable] 878 | VertexId vertex_id = boost::get(boost::vertex_index, g);; | ^~~~~~~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Options.cpp -o BRNN/RNNs/Options.o BRNN/RNNs/Options.cpp: In member function ‘virtual void Options::parse_config(const string&)’: BRNN/RNNs/Options.cpp:30:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 30 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:36:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 36 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:42:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 42 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:47:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 47 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:61:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 61 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:79:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 79 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:85:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 85 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:90:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 90 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:99:29: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 99 | if(_input_mask.size() != _input_dimension) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp: In member function ‘virtual void Options::parse_args(int, char**)’: BRNN/RNNs/Options.cpp:138:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 138 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:144:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 144 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:150:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 150 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:155:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 155 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:169:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 169 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:187:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 187 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:193:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 193 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:198:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 198 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:207:29: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 207 | if(_input_mask.size() != _input_dimension) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/protein_util.cpp -o BRNN/protein_util.o In file included from BRNN/protein_util.cpp:1: BRNN/protein_util.h: In constructor ‘Residue::Residue(int, int, char, float, float, float, float, float, char)’: BRNN/protein_util.h:209:16: warning: ‘Residue::_coord’ will be initialized after [-Wreorder] 209 | Coordinate3D _coord; // residue representative coordinates | ^~~~~~ BRNN/protein_util.h:208:9: warning: ‘float Residue::_hydr’ [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): | ^~~~~~~ BRNN/protein_util.h:208:16: warning: ‘Residue::_acc’ will be initialized after [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~ BRNN/protein_util.h:207:17: warning: ‘char Residue::_ssbridge’ [-Wreorder] 207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator | ^~~~~~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): | ^~~~~~~ BRNN/protein_util.h: In copy constructor ‘Residue::Residue(const Residue&)’: BRNN/protein_util.h:209:16: warning: ‘Residue::_coord’ will be initialized after [-Wreorder] 209 | Coordinate3D _coord; // residue representative coordinates | ^~~~~~ BRNN/protein_util.h:208:9: warning: ‘float Residue::_hydr’ [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h:208:16: warning: ‘Residue::_acc’ will be initialized after [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~ BRNN/protein_util.h:207:17: warning: ‘char Residue::_ssbridge’ [-Wreorder] 207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator | ^~~~~~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h:211:13: warning: ‘Residue::_bp2’ will be initialized after [-Wreorder] 211 | int _bp1, _bp2; // bridge partners | ^~~~ BRNN/protein_util.h:206:24: warning: ‘int Residue::_ssp’ [-Wreorder] 206 | int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner | ^~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h: In constructor ‘SSegment::SSegment(char)’: BRNN/protein_util.h:241:16: warning: ‘SSegment::_baricentre’ will be initialized after [-Wreorder] 241 | Coordinate3D _baricentre; // baricentrum of C_alpha atoms set | ^~~~~~~~~~~ BRNN/protein_util.h:239:18: warning: ‘SSegment::Hydrophobicity SSegment::_hydr’ [-Wreorder] 239 | Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment | ^~~~~ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] 245 | SSegment(char symbol): | ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/9/cassert:44, from BRNN/protein_util.cpp:2: BRNN/protein_util.cpp: In member function ‘void Chain::setSShydrophobicity()’: BRNN/protein_util.cpp:365:31: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 365 | assert(resHydrScales.size() == numResidues()); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ BRNN/protein_util.cpp:380:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 380 | if(r_i >= resHydrScales.size()) r_i = resHydrScales.size()-1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/9/cassert:44, from BRNN/protein_util.cpp:2: BRNN/protein_util.cpp:386:24: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 386 | assert(hAvg.size() == (*c_it).numResidues()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ BRNN/protein_util.cpp:391:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 391 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 401 | assert(seq_pos == resHydrScales.size()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/blast_util.cpp -o BRNN/blast_util.o BRNN/blast_util.cpp: In member function ‘void PSSM::parsePsiBlastReport(const char*)’: BRNN/blast_util.cpp:34:13: warning: unused variable ‘prof’ [-Wunused-variable] 34 | Profile prof; | ^~~~ aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/rnn_util.cpp -o BRNN/rnn_util.o In file included from BRNN/rnn_util.cpp:4: BRNN/RNNs/DataSet.h:19:1: warning: ‘typedef’ was ignored in this declaration 19 | typedef struct StructuredInstanceTemplate { | ^~~~~~~ In file included from BRNN/rnn_util.cpp:4: BRNN/RNNs/DataSet.h: In constructor ‘DataSet::iterator::iterator(DataSet&)’: BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h: In member function ‘bool DataSet::iterator::operator++()’: BRNN/RNNs/DataSet.h:116:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 116 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h:135:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from BRNN/rnn_util.cpp:7: BRNN/protein_util.h: In constructor ‘Residue::Residue(int, int, char, float, float, float, float, float, char)’: BRNN/protein_util.h:209:16: warning: ‘Residue::_coord’ will be initialized after [-Wreorder] 209 | Coordinate3D _coord; // residue representative coordinates | ^~~~~~ BRNN/protein_util.h:208:9: warning: ‘float Residue::_hydr’ [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): | ^~~~~~~ BRNN/protein_util.h:208:16: warning: ‘Residue::_acc’ will be initialized after [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~ BRNN/protein_util.h:207:17: warning: ‘char Residue::_ssbridge’ [-Wreorder] 207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator | ^~~~~~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): | ^~~~~~~ BRNN/protein_util.h: In copy constructor ‘Residue::Residue(const Residue&)’: BRNN/protein_util.h:209:16: warning: ‘Residue::_coord’ will be initialized after [-Wreorder] 209 | Coordinate3D _coord; // residue representative coordinates | ^~~~~~ BRNN/protein_util.h:208:9: warning: ‘float Residue::_hydr’ [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h:208:16: warning: ‘Residue::_acc’ will be initialized after [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~ BRNN/protein_util.h:207:17: warning: ‘char Residue::_ssbridge’ [-Wreorder] 207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator | ^~~~~~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h:211:13: warning: ‘Residue::_bp2’ will be initialized after [-Wreorder] 211 | int _bp1, _bp2; // bridge partners | ^~~~ BRNN/protein_util.h:206:24: warning: ‘int Residue::_ssp’ [-Wreorder] 206 | int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner | ^~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h: In constructor ‘SSegment::SSegment(char)’: BRNN/protein_util.h:241:16: warning: ‘SSegment::_baricentre’ will be initialized after [-Wreorder] 241 | Coordinate3D _baricentre; // baricentrum of C_alpha atoms set | ^~~~~~~~~~~ BRNN/protein_util.h:239:18: warning: ‘SSegment::Hydrophobicity SSegment::_hydr’ [-Wreorder] 239 | Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment | ^~~~~ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] 245 | SSegment(char symbol): | ^~~~~~~~ BRNN/rnn_util.cpp: In function ‘void create_connectivity_input_data(const string&, const string&, int, int, const string&)’: BRNN/rnn_util.cpp:233:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 233 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 277 | if(i >=0 && i < pssm.size()) | ~~^~~~~~~~~~~~~ BRNN/rnn_util.cpp: In function ‘void rnn_predict_disulphides(const string&, const string&, const string&, const string&, const string&, const string&, int)’: BRNN/rnn_util.cpp:359:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::edges_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 359 | require(B == boost::num_edges(candidate) && | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:348:16: warning: variable ‘vertex_id’ set but not used [-Wunused-but-set-variable] 348 | VertexId vertex_id = boost::get(boost::vertex_index, candidate); | ^~~~~~~~~ BRNN/rnn_util.cpp:405:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, boost::property > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 405 | for(int j=0; j, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::edges_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 406 | require(B == boost::num_edges(bestPatterns[j]) && | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:407:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::vertices_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 407 | B == boost::num_vertices(bestPatterns[j]) / 2, | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:378:18: warning: unused variable ‘nodes’ [-Wunused-variable] 378 | vector *nodes = it.currenTONodes(); | ^~~~~ In file included from BRNN/rnn_util.cpp:5: BRNN/RNNs/RecursiveNN.h: In instantiation of ‘RecursiveNN::RecursiveNN(const char*) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]’: BRNN/rnn_util.cpp:88:73: required from here BRNN/RNNs/RecursiveNN.h:1018:13: warning: unused variable ‘trasd’ [-Wunused-variable] 1018 | TrasdType trasd = Options::instance()->getTrasductionType(); | ^~~~~ In file included from BRNN/rnn_util.cpp:5: BRNN/RNNs/RecursiveNN.h:1026:23: warning: variable ‘indexes’ set but not used [-Wunused-but-set-variable] 1026 | std::pair indexes = Options::instance()->getLayersIndexes(); | ^~~~~~~ BRNN/RNNs/RecursiveNN.h:1047:7: warning: unused variable ‘default_precision’ [-Wunused-variable] 1047 | int default_precision = is.precision(); | ^~~~~~~~~~~~~~~~~ In file included from BRNN/rnn_util.cpp:6: BRNN/RNNs/StructureSearch.h: In instantiation of ‘std::vector, boost::property > > StructureSearch::ConnectivityPatternSearch(RNN*, const std::vector, boost::property > >&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]’: BRNN/rnn_util.cpp:396:65: required from here BRNN/RNNs/StructureSearch.h:977:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 977 | for(int i=0; i<_nodesInputs.size(); ++i) | ~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/StructureSearch.h:984:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, boost::property > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 984 | for(int i=0; i::fPropagateInput(std::vector&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list, boost::property >]’: BRNN/RNNs/RecursiveNN.h:1356:3: required from ‘void RecursiveNN::propagateStructuredInput(std::vector&, const std::pair, boost::property >, boost::adjacency_list, boost::property > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]’ BRNN/rnn_util.cpp:99:47: required from here BRNN/RNNs/RecursiveNN.h:1390:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1390 | require(_n == toNodes[t]->_encodedInput.size(), "Error in input dim!"); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1415:38: warning: comparison of integer expressions of different signedness: ‘const unsigned int’ and ‘int’ [-Wsign-compare] 1415 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { BRNN/RNNs/RecursiveNN.h:1418:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1418 | for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1384:12: warning: variable ‘vertex_id’ set but not used [-Wunused-but-set-variable] 1384 | VertexId vertex_id = boost::get(boost::vertex_index, sdag); | ^~~~~~~~~ BRNN/RNNs/RecursiveNN.h: In instantiation of ‘void RecursiveNN::bPropagateInput(std::vector&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list, boost::property >]’: BRNN/RNNs/RecursiveNN.h:1359:19: required from ‘void RecursiveNN::propagateStructuredInput(std::vector&, const std::pair, boost::property >, boost::adjacency_list, boost::property > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]’ BRNN/rnn_util.cpp:99:47: required from here BRNN/RNNs/RecursiveNN.h:1470:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1470 | for(int t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1471 | require(_n == toNodes[t]->_encodedInput.size(), "Error!"); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1492:38: warning: comparison of integer expressions of different signedness: ‘const unsigned int’ and ‘int’ [-Wsign-compare] 1492 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { BRNN/RNNs/RecursiveNN.h:1495:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1495 | for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1465:12: warning: variable ‘vertex_id’ set but not used [-Wunused-but-set-variable] 1465 | VertexId vertex_id = boost::get(boost::vertex_index, sdag); | ^~~~~~~~~ In file included from BRNN/rnn_util.cpp:6: BRNN/RNNs/StructureSearch.h: In instantiation of ‘float StructureSearch::RNNMeasure(const DPAG&, RNN*, std::vector&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN; DPAG = boost::adjacency_list, boost::property >]’: BRNN/RNNs/StructureSearch.h:989:11: required from ‘std::vector, boost::property > > StructureSearch::ConnectivityPatternSearch(RNN*, const std::vector, boost::property > >&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]’ BRNN/rnn_util.cpp:396:65: required from here BRNN/RNNs/StructureSearch.h:186:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 186 | for(int i=0; i>/disulfind/src/Common' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Vector.cpp -o Vector.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Util.cpp -o Util.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c CommonMethods.cpp -o CommonMethods.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c ConfusionMatrix.cpp -o ConfusionMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Exception.cpp -o Exception.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Statistics.cpp -o Statistics.o aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balanc.o eig/balanc.c aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balbak.o eig/balbak.c aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/cdiv.o eig/cdiv.c aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/elmhes.o eig/elmhes.c aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/eltran.o eig/eltran.c aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr.o eig/hqr.c aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr2.o eig/hqr2.c aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/rg.o eig/rg.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c coords.cpp -o coords.o aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/d_sign.o eig/d_sign.c ar rvs libCommon.a Vector.o Util.o CommonMethods.o ConfusionMatrix.o Exception.o Statistics.o eig/balanc.o eig/balbak.o eig/cdiv.o eig/elmhes.o eig/eltran.o eig/hqr.o eig/hqr2.o eig/rg.o coords.o eig/d_sign.o ar: creating libCommon.a a - Vector.o a - Util.o a - CommonMethods.o a - ConfusionMatrix.o a - Exception.o a - Statistics.o a - eig/balanc.o a - eig/balbak.o a - eig/cdiv.o a - eig/elmhes.o a - eig/eltran.o a - eig/hqr.o a - eig/hqr2.o a - eig/rg.o a - coords.o a - eig/d_sign.o make[4]: Leaving directory '/<>/disulfind/src/Common' aarch64-linux-gnu-g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c disulfinder.cpp -o disulfinder.o In file included from Input/utils.h:2, from disulfinder.cpp:8: Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ Input/Protein.h:16:20: warning: ‘aa_codes’ defined but not used [-Wunused-variable] 16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files | ^~~~~~~~ aarch64-linux-gnu-g++ -o disulfinder disulfinder.o Input/GlobalDescriptor.o Input/createBRNNDataset.o Input/createKernelDataset.o Input/makeWindow.o Input/makeSparseVector.o Input/Protein.o Input/buildXfolds.o SVM/SVMClassifier.o Output/makeHTMLOutput.o Output/utils.o Output/makeASCIIOutput.o FSA-Alignment/fsa.o FSA-Alignment/viterbi_aligner.o NN/multi-array.o NN/array.o NN/brnn-model.o NN/brnn-test.o BRNN/RNNs/Node.o BRNN/RNNs/StructureSearch.o BRNN/RNNs/DataSet.o BRNN/RNNs/DPAG.o BRNN/RNNs/Options.o BRNN/protein_util.o BRNN/blast_util.o BRNN/rnn_util.o -Wl,-z,relro -Wl,-z,now -LCommon/ -lCommon /usr/lib/gcc-cross/aarch64-linux-gnu/9/../../../../aarch64-linux-gnu/bin/ld: skipping incompatible Common//libCommon.a when searching for -lCommon /usr/lib/gcc-cross/aarch64-linux-gnu/9/../../../../aarch64-linux-gnu/bin/ld: cannot find -lCommon collect2: error: ld returned 1 exit status make[3]: *** [Makefile:53: disulfinder] Error 1 make[3]: Leaving directory '/<>/disulfind/src' make[2]: *** [Makefile:24: disulfinder] Error 2 make[2]: Leaving directory '/<>' dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc returned exit code 2 make[1]: *** [debian/rules:16: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:13: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-05-16T04:24:14Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 63360 Build-Time: 86 Distribution: unstable Fail-Stage: build Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 21 Job: disulfinder_1.2.11-8 Machine Architecture: amd64 Package: disulfinder Package-Time: 117 Source-Version: 1.2.11-8 Space: 63360 Status: attempted Version: 1.2.11-8 -------------------------------------------------------------------------------- Finished at 2020-05-16T04:24:14Z Build needed 00:01:57, 63360k disk space