sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | disulfinder 1.2.11-8 (arm64) Fri, 26 Apr 2019 02:32:41 +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-f067add0-4d78-4aef-8fbf-a8806fb2869b' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [247 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 2019-04-25-0811.30.pdiff [1062 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-04-25-1416.16.pdiff [6677 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-04-25-2030.15.pdiff [1976 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-04-25-2030.15.pdiff [1976 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-04-25-0811.30.pdiff [926 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-04-25-1416.16.pdiff [3324 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-04-25-2030.15.pdiff [6252 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-04-25-2030.15.pdiff [6252 B] Get:10 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8101 kB] Fetched 8424 kB in 2s (4339 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libaudit-common libaudit1 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 79.8 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 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.8 kB in 0s (0 B/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 ... 11942 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a2.8.4-3_all.deb ... Unpacking libaudit-common (1:2.8.4-3) over (1:2.8.4-2) ... Setting up libaudit-common (1:2.8.4-3) ... (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 ... 11942 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.8.4-3_amd64.deb ... Unpacking libaudit1:amd64 (1:2.8.4-3) over (1:2.8.4-2) ... Setting up libaudit1:amd64 (1:2.8.4-3) ... Processing triggers for libc-bin (2.28-8) ... +------------------------------------------------------------------------------+ | 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 (42.4 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/disulfinder-ZVxc0i/disulfinder-1.2.11' with '<>' I: NOTICE: Log filtering will replace 'build/disulfinder-ZVxc0i' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-THKVeA/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-THKVeA/apt_archive ./ InRelease Get:2 copy:/<>/resolver-THKVeA/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-THKVeA/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-THKVeA/apt_archive ./ Sources [362 B] Get:5 copy:/<>/resolver-THKVeA/apt_archive ./ Packages [450 B] Fetched 1769 B in 0s (94.8 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: binutils-aarch64-linux-gnu cpp-8-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 dpkg-cross file g++-8-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-8-aarch64-linux-gnu gcc-8-aarch64-linux-gnu-base gcc-8-cross-base gcc-aarch64-linux-gnu libasan5-arm64-cross libatomic1-arm64-cross libc6-arm64-cross libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-arm64-cross libgcc1-arm64-cross libgomp1-arm64-cross libicu63 libio-string-perl libitm1-arm64-cross liblocale-gettext-perl liblsan0-arm64-cross libmagic-mgc libmagic1 libstdc++-8-dev-arm64-cross libstdc++6-arm64-cross libtsan0-arm64-cross libubsan1-arm64-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-arm64-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch gcc-8-doc libstdc++6-8-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 libmpx2-dbg-arm64-cross libquadmath0-dbg-arm64-cross manpages-dev autoconf automake libtool flex bison gdb-aarch64-linux-gnu gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-aarch64-linux-gnu cpp-8-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 dpkg-cross file g++-8-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-8-aarch64-linux-gnu gcc-8-aarch64-linux-gnu-base gcc-8-cross-base gcc-aarch64-linux-gnu libasan5-arm64-cross libatomic1-arm64-cross libc6-arm64-cross libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-arm64-cross libgcc1-arm64-cross libgomp1-arm64-cross libicu63 libio-string-perl libitm1-arm64-cross liblocale-gettext-perl liblsan0-arm64-cross libmagic-mgc libmagic1 libstdc++-8-dev-arm64-cross libstdc++6-arm64-cross libtsan0-arm64-cross libubsan1-arm64-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-arm64-cross sbuild-build-depends-core-dummy:arm64 sensible-utils ucf 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. Need to get 41.8 MB of archives. After this operation, 161 MB of additional disk space will be used. Get:1 copy:/<>/resolver-THKVeA/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [872 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-4 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.31.1-16 [2905 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-aarch64-linux-gnu-base amd64 8.3.0-4cross1 [191 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-aarch64-linux-gnu amd64 8.3.0-4cross1 [6250 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-2 [39.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-4cross1 [186 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.28-7cross1 [1312 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-arm64-cross all 1:8.3.0-4cross1 [34.4 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 8.3.0-4cross1 [66.3 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 8.3.0-4cross1 [23.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 8.3.0-4cross1 [8628 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 8.3.0-4cross1 [326 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-arm64-cross all 8.3.0-4cross1 [321 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 8.3.0-4cross1 [117 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 8.3.0-4cross1 [254 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 8.3.0-4cross1 [110 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-arm64-cross all 8.3.0-4cross1 [826 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-aarch64-linux-gnu amd64 8.3.0-4cross1 [6686 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:8.3.0-1 [1456 B] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 4.19.20-1cross1 [1209 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.28-7cross1 [2322 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-arm64-cross all 8.3.0-4cross1 [1484 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-aarch64-linux-gnu amd64 8.3.0-4cross1 [6825 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:8.3.0-1 [1176 B] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.1-6 [8292 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-2 [38.5 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-2 [49.3 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.6 [6572 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.8 MB in 1s (54.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11942 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4_amd64.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package binutils-aarch64-linux-gnu. Preparing to unpack .../06-binutils-aarch64-linux-gnu_2.31.1-16_amd64.deb ... Unpacking binutils-aarch64-linux-gnu (2.31.1-16) ... Selecting previously unselected package gcc-8-aarch64-linux-gnu-base:amd64. Preparing to unpack .../07-gcc-8-aarch64-linux-gnu-base_8.3.0-4cross1_amd64.deb ... Unpacking gcc-8-aarch64-linux-gnu-base:amd64 (8.3.0-4cross1) ... Selecting previously unselected package cpp-8-aarch64-linux-gnu. Preparing to unpack .../08-cpp-8-aarch64-linux-gnu_8.3.0-4cross1_amd64.deb ... Unpacking cpp-8-aarch64-linux-gnu (8.3.0-4cross1) ... Selecting previously unselected package cpp-aarch64-linux-gnu. Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a8.3.0-1_amd64.deb ... Unpacking cpp-aarch64-linux-gnu (4:8.3.0-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../10-cross-config_2.6.15-2_all.deb ... Unpacking cross-config (2.6.15-2) ... 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Preparing to unpack .../31-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../32-libicu63_63.1-6_amd64.deb ... Unpacking libicu63:amd64 (63.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../33-libxml2_2.9.4+dfsg1-7+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../34-libxml-namespacesupport-perl_1.12-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../35-libxml-sax-base-perl_1.09-1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../36-libxml-sax-perl_1.00+dfsg-1_all.deb ... Unpacking libxml-sax-perl (1.00+dfsg-1) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../37-libxml-libxml-perl_2.0134+dfsg-1_amd64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../38-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../39-libyaml-perl_1.27-1_all.deb ... Unpacking libyaml-perl (1.27-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../40-libconfig-auto-perl_0.44-1_all.deb ... Unpacking libconfig-auto-perl (0.44-1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../41-libfile-which-perl_1.23-1_all.deb ... Unpacking libfile-which-perl (1.23-1) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../42-libfile-homedir-perl_1.004-1_all.deb ... Unpacking libfile-homedir-perl (1.004-1) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../43-libdebian-dpkgcross-perl_2.6.15-2_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.15-2) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../44-dpkg-cross_2.6.15-2_all.deb ... Unpacking dpkg-cross (2.6.15-2) ... Selecting previously unselected package crossbuild-essential-arm64. Preparing to unpack .../45-crossbuild-essential-arm64_12.6_all.deb ... Unpacking crossbuild-essential-arm64 (12.6) ... Selecting previously unselected package sbuild-build-depends-core-dummy:arm64. Preparing to unpack .../46-sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy:arm64 (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up gcc-8-cross-base (8.3.0-4cross1) ... Setting up libmagic1:amd64 (1:5.35-4) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up binutils-aarch64-linux-gnu (2.31.1-16) ... Setting up file (1:5.35-4) ... Setting up libyaml-perl (1.27-1) ... Setting up libicu63:amd64 (63.1-6) ... Setting up gcc-8-aarch64-linux-gnu-base:amd64 (8.3.0-4cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-2) ... Setting up libc6-arm64-cross (2.28-7cross1) ... Setting up cpp-8-aarch64-linux-gnu (8.3.0-4cross1) ... Setting up libitm1-arm64-cross (8.3.0-4cross1) ... Setting up linux-libc-dev-arm64-cross (4.19.20-1cross1) ... Setting up sensible-utils (0.0.12) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libatomic1-arm64-cross (8.3.0-4cross1) ... Setting up libgcc1-arm64-cross (1:8.3.0-4cross1) ... Setting up libgomp1-arm64-cross (8.3.0-4cross1) ... Setting up libc6-dev-arm64-cross (2.28-7cross1) ... Setting up libstdc++6-arm64-cross (8.3.0-4cross1) ... Setting up cpp-aarch64-linux-gnu (4:8.3.0-1) ... Setting up ucf (3.0038+nmu1) ... Setting up liblsan0-arm64-cross (8.3.0-4cross1) ... Setting up libubsan1-arm64-cross (8.3.0-4cross1) ... Setting up libtsan0-arm64-cross (8.3.0-4cross1) ... Setting up libxml-sax-perl (1.00+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 libasan5-arm64-cross (8.3.0-4cross1) ... Setting up libgcc-8-dev-arm64-cross (8.3.0-4cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-8-aarch64-linux-gnu (8.3.0-4cross1) ... Setting up libstdc++-8-dev-arm64-cross (8.3.0-4cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-aarch64-linux-gnu (4:8.3.0-1) ... Setting up g++-8-aarch64-linux-gnu (8.3.0-4cross1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up g++-aarch64-linux-gnu (4:8.3.0-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-2) ... Setting up dpkg-cross (2.6.15-2) ... Setting up crossbuild-essential-arm64 (12.6) ... Setting up sbuild-build-depends-core-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.28-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-THKVeA/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-THKVeA/apt_archive ./ InRelease Get:2 copy:/<>/resolver-THKVeA/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-THKVeA/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-THKVeA/apt_archive ./ Sources [484 B] Get:5 copy:/<>/resolver-THKVeA/apt_archive ./ Packages [567 B] Fetched 2014 B in 0s (116 kB/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:arm64 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 840 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-THKVeA/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 840 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:arm64. (Reading database ... 15222 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-essential-dummy:arm64 (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:arm64 (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev dpkg-deb: building package 'sbuild-build-depends-disulfinder-dummy' in '/<>/resolver-THKVeA/apt_archive/sbuild-build-depends-disulfinder-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-disulfinder-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-THKVeA/apt_archive ./ InRelease Get:2 copy:/<>/resolver-THKVeA/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-THKVeA/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-THKVeA/apt_archive ./ Sources [657 B] Get:5 copy:/<>/resolver-THKVeA/apt_archive ./ Packages [734 B] Fetched 2354 B in 0s (141 kB/s) Reading package lists... Reading package lists... Install disulfinder 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 bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:arm64 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:arm64 libatomic1:arm64 libboost-chrono1.67.0:arm64 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-system1.67.0:arm64 libboost-test1.67-dev:arm64 libboost-test1.67.0:arm64 libboost-timer1.67.0:arm64 libboost1.67-dev:arm64 libbsd0 libc6:arm64 libc6-dev:arm64 libcroco3 libelf1 libf2c2:arm64 libf2c2-dev:arm64 libfile-stripnondeterminism-perl libgcc-8-dev:arm64 libgcc1:arm64 libglib2.0-0 libgomp1:arm64 libicu63:arm64 libitm1:arm64 liblsan0:arm64 libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:arm64 libstdc++6:arm64 libtool libtsan0:arm64 libubsan1:arm64 libuchardet0 linux-libc-dev:arm64 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make 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-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 manpages-dev:arm64 libstdc++-8-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk 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 libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:arm64 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:arm64 libatomic1:arm64 libboost-chrono1.67.0:arm64 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-system1.67.0:arm64 libboost-test1.67-dev:arm64 libboost-test1.67.0:arm64 libboost-timer1.67.0:arm64 libboost1.67-dev:arm64 libbsd0 libc6:arm64 libc6-dev:arm64 libcroco3 libelf1 libf2c2:arm64 libf2c2-dev:arm64 libfile-stripnondeterminism-perl libgcc-8-dev:arm64 libgcc1:arm64 libglib2.0-0 libgomp1:arm64 libicu63:arm64 libitm1:arm64 liblsan0:arm64 libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:arm64 libstdc++6:arm64 libtool libtsan0:arm64 libubsan1:arm64 libuchardet0 linux-libc-dev:arm64 m4 man-db po-debconf sbuild-build-depends-disulfinder-dummy:arm64 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 39.6 MB of archives. After this operation, 288 MB of additional disk space will be used. Get:1 copy:/<>/resolver-THKVeA/apt_archive ./ sbuild-build-depends-disulfinder-dummy 0.invalid.0 [900 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 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 2.8.5-2 [1274 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1 [160 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-1 [1258 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-8-base arm64 8.3.0-6 [191 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc1 arm64 1:8.3.0-6 [34.4 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.28-8 [2522 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 8.3.0-6 [363 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main arm64 libasan5 arm64 8.3.0-6 [327 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 8.3.0-6 [8820 B] Get:35 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-system1.67.0 arm64 1.67.0-13 [229 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-chrono1.67.0 arm64 1.67.0-13 [233 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 8.3.0-6 [67.8 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 8.3.0-6 [24.0 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 8.3.0-6 [118 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 8.3.0-6 [262 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 8.3.0-6 [111 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-8-dev arm64 8.3.0-6 [835 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 4.19.28-2 [1137 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.28-8 [2325 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-8-dev arm64 8.3.0-6 [1502 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main arm64 libboost1.67-dev arm64 1.67.0-13 [8386 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-dev arm64 1.67.0.1 [3864 B] Get:48 http://debian.oregonstate.edu/debian unstable/main arm64 libicu63 arm64 63.1-6 [8153 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-regex1.67.0 arm64 1.67.0-13 [457 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-graph1.67.0 arm64 1.67.0-13 [310 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-serialization1.67.0 arm64 1.67.0-13 [312 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-serialization1.67-dev arm64 1.67.0-13 [358 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-timer1.67.0 arm64 1.67.0-13 [231 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-test1.67.0 arm64 1.67.0-13 [435 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-test1.67-dev arm64 1.67.0-13 [504 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-graph1.67-dev arm64 1.67.0-13 [325 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-graph-dev arm64 1.67.0.1 [3752 B] Get:58 http://debian.oregonstate.edu/debian unstable/main arm64 libf2c2 arm64 20130926-3 [110 kB] Get:59 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 39.6 MB in 1s (58.2 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15222 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... 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_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../07-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../09-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../10-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../11-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../12-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-10_all.deb ... Unpacking libtool (2.4.6-10) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../16-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../17-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../18-libelf1_0.176-1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1) ... 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Preparing to unpack .../58-sbuild-build-depends-disulfinder-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-disulfinder-dummy:arm64 (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-1) ... No schema files found: doing nothing. Setting up linux-libc-dev:arm64 (4.19.28-2) ... Setting up gettext-base (0.19.8.1-9) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up gcc-8-base:arm64 (8.3.0-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... 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 autoconf (2.69-11) ... Setting up dwz (0.12-3) ... 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 po-debconf (1.0.21) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libc6:arm64 (2.28-8) ... Setting up libc6-dev:arm64 (2.28-8) ... Setting up libf2c2:arm64 (20130926-3) ... Setting up libf2c2-dev:arm64 (20130926-3) ... Setting up libitm1:arm64 (8.3.0-6) ... Setting up libgcc1:arm64 (1:8.3.0-6) ... Setting up debhelper (12.1.1) ... Setting up libgomp1:arm64 (8.3.0-6) ... Setting up dh-autoreconf (19) ... Setting up libatomic1:arm64 (8.3.0-6) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up libstdc++6:arm64 (8.3.0-6) ... Setting up liblsan0:arm64 (8.3.0-6) ... Setting up libtsan0:arm64 (8.3.0-6) ... Setting up libicu63:arm64 (63.1-6) ... Setting up libasan5:arm64 (8.3.0-6) ... Setting up libubsan1:arm64 (8.3.0-6) ... Setting up libboost-system1.67.0:arm64 (1.67.0-13) ... Setting up libboost-serialization1.67.0:arm64 (1.67.0-13) ... Setting up libboost-regex1.67.0:arm64 (1.67.0-13) ... Setting up libboost-chrono1.67.0:arm64 (1.67.0-13) ... Setting up libboost-graph1.67.0:arm64 (1.67.0-13) ... Setting up libgcc-8-dev:arm64 (8.3.0-6) ... Setting up libboost-timer1.67.0:arm64 (1.67.0-13) ... Setting up libstdc++-8-dev:arm64 (8.3.0-6) ... Setting up libboost1.67-dev:arm64 (1.67.0-13) ... Setting up libboost-serialization1.67-dev:arm64 (1.67.0-13) ... Setting up libboost-test1.67.0:arm64 (1.67.0-13) ... Setting up libboost-test1.67-dev:arm64 (1.67.0-13) ... Setting up libboost-graph1.67-dev:arm64 (1.67.0-13) ... Setting up libboost-dev:arm64 (1.67.0.1) ... Setting up libboost-graph-dev:arm64 (1.67.0.1) ... Setting up sbuild-build-depends-disulfinder-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.28-8) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.6 g++-8_8.3.0-6 gcc-8_8.3.0-6 libc6-dev_2.28-8 libstdc++-8-dev_8.3.0-6 libstdc++-8-dev-arm64-cross_8.3.0-4cross1 libstdc++6_8.3.0-6 libstdc++6-arm64-cross_8.3.0-4cross1 linux-libc-dev_4.19.28-2 Package versions: adduser_3.118 apt_1.8.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.2 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16 binutils-aarch64-linux-gnu_2.31.1-16 binutils-common_2.31.1-16 binutils-x86-64-linux-gnu_2.31.1-16 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-8_8.3.0-6 cpp-8-aarch64-linux-gnu_8.3.0-4cross1 cpp-aarch64-linux-gnu_4:8.3.0-1 cross-config_2.6.15-2 crossbuild-essential-arm64_12.6 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.1.1 debian-archive-keyring_2019.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dpkg_1.19.6 dpkg-cross_2.6.15-2 dpkg-dev_1.19.6 dwz_0.12-3 e2fsprogs_1.45.0-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1 g++-8_8.3.0-6 g++-8-aarch64-linux-gnu_8.3.0-4cross1 g++-aarch64-linux-gnu_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-6 gcc-8-aarch64-linux-gnu_8.3.0-4cross1 gcc-8-aarch64-linux-gnu-base_8.3.0-4cross1 gcc-8-base_8.3.0-6 gcc-8-cross-base_8.3.0-4cross1 gcc-aarch64-linux-gnu_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.13-1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.0 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6 libasan5-arm64-cross_8.3.0-4cross1 libatomic1_8.3.0-6 libatomic1-arm64-cross_8.3.0-4cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16 libblkid1_2.33.1-0.1 libboost-chrono1.67.0_1.67.0-13 libboost-dev_1.67.0.1 libboost-graph-dev_1.67.0.1 libboost-graph1.67-dev_1.67.0-13 libboost-graph1.67.0_1.67.0-13 libboost-regex1.67.0_1.67.0-13 libboost-serialization1.67-dev_1.67.0-13 libboost-serialization1.67.0_1.67.0-13 libboost-system1.67.0_1.67.0-13 libboost-test1.67-dev_1.67.0-13 libboost-test1.67.0_1.67.0-13 libboost-timer1.67.0_1.67.0-13 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9 libc-bin_2.28-8 libc-dev-bin_2.28-8 libc6_2.28-8 libc6-arm64-cross_2.28-7cross1 libc6-dev_2.28-8 libc6-dev-arm64-cross_2.28-7cross1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6 libcom-err2_1.45.0-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-2 libdpkg-perl_1.19.6 libelf1_0.176-1 libext2fs2_1.45.0-1 libf2c2_20130926-3 libf2c2-dev_20130926-3 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.1.2-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-6 libgcc-8-dev-arm64-cross_8.3.0-4cross1 libgcc1_1:8.3.0-6 libgcc1-arm64-cross_1:8.3.0-4cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-2 libgomp1_8.3.0-6 libgomp1-arm64-cross_8.3.0-4cross1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libicu63_63.1-6 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.3.0-6 libitm1-arm64-cross_8.3.0-4cross1 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.3.0-6 liblsan0-arm64-cross_8.3.0-4cross1 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-6 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libquadmath0_8.3.0-6 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libss2_1.45.0-1 libstdc++-8-dev_8.3.0-6 libstdc++-8-dev-arm64-cross_8.3.0-4cross1 libstdc++6_8.3.0-6 libstdc++6-arm64-cross_8.3.0-4cross1 libsystemd0_241-3 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-6 libtsan0-arm64-cross_8.3.0-4cross1 libubsan1_8.3.0-6 libubsan1-arm64-cross_8.3.0-4cross1 libuchardet0_0.0.6-3 libudev1_241-3 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.28-2 linux-libc-dev-arm64-cross_4.19.20-1cross1 login_1:4.5-1.1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-disulfinder-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Sep 23 15:44:56 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./disulfinder_1.2.11-8.dsc dpkg-source: info: extracting disulfinder in /<> dpkg-source: info: unpacking 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=POSIX 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-f067add0-4d78-4aef-8fbf-a8806fb2869b SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- 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] static const char *aa_three_codes[23] = { ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 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] 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] static const char *aa_three_codes[23] = { ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 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] 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] static const char *aa_three_codes[23] = { ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 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::__cxx11::string, const char*, int, std::__cxx11::string, std::ostream&)': Output/makeHTMLOutput.cpp:162:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char * altname[2] = {"Second","Third"}; ^ Output/makeHTMLOutput.cpp:162:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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::__cxx11::string, const char*, int, std::__cxx11::string, std::ostream&)': Output/makeASCIIOutput.cpp:144:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char * altname[2] = {"SECOND","THIRD"}; ^ Output/makeASCIIOutput.cpp:144:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 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 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] 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] 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] 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 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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] 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] int global_predicted_positives = boost::num_edges(g), ^~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:49:5: warning: unused variable 'global_actual_positives' [-Wunused-variable] global_actual_positives = boost::num_edges(gtarget), ^~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:52:12: warning: unused variable 'graphNode' [-Wunused-variable] 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] 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] 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] require(true_positives + true_negatives + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ false_positives + false_negatives == ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ boost::num_vertices(gpred) * (boost::num_vertices(gpred)-1) / 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:471:9: warning: unused variable 'weight' [-Wunused-variable] 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] 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] 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] 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] 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] 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] 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] for(int i=0; i<(*it).second.size(); i++) ~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:813:12: warning: unused variable 'node' [-Wunused-variable] 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] 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 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:36:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:42:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:47:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:61:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:79:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:85:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:90:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:144:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:150:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:155:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:169:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:187:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:193:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:198:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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] Coordinate3D _coord; // residue representative coordinates ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 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] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^~~~~~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 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] Coordinate3D _coord; // residue representative coordinates ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^~~~~~~ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^~~~~~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^~~~~~~ BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder] int _bp1, _bp2; // bridge partners ^~~~ BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder] int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner ^~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 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] Coordinate3D _baricentre; // baricentrum of C_alpha atoms set ^~~~~~~~~~~ BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder] Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment ^~~~~ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] SSegment(char symbol): ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/8/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] 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] if(r_i >= resHydrScales.size()) r_i = resHydrScales.size()-1; ~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/8/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] 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] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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 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] 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] 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] 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] Coordinate3D _coord; // residue representative coordinates ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 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] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^~~~~~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 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] Coordinate3D _coord; // residue representative coordinates ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^~~~~~~ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^~~~~~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^~~~~~~ BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder] int _bp1, _bp2; // bridge partners ^~~~ BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder] int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner ^~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 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] Coordinate3D _baricentre; // baricentrum of C_alpha atoms set ^~~~~~~~~~~ BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder] Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment ^~~~~ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] 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] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] require(B == boost::num_edges(candidate) && ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:348:16: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] 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] 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] 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] B == boost::num_vertices(bestPatterns[j]) / 2, ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:378:18: warning: unused variable 'nodes' [-Wunused-variable] 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] 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] std::pair indexes = Options::instance()->getLayersIndexes(); ^~~~~~~ BRNN/RNNs/RecursiveNN.h:1047:7: warning: unused variable 'default_precision' [-Wunused-variable] 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] 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] 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] 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] 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] 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] 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] for(int t=0; t::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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] 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] 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] 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] static const char *aa_three_codes[23] = { ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 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] 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/8/../../../../aarch64-linux-gnu/bin/ld: skipping incompatible Common//libCommon.a when searching for -lCommon /usr/lib/gcc-cross/aarch64-linux-gnu/8/../../../../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: 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 2 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 2019-04-26T02:34:51Z 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: 62028 Build-Time: 90 Distribution: unstable Fail-Stage: build Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 29 Job: disulfinder_1.2.11-8 Machine Architecture: amd64 Package: disulfinder Package-Time: 130 Source-Version: 1.2.11-8 Space: 62028 Status: attempted Version: 1.2.11-8 -------------------------------------------------------------------------------- Finished at 2019-04-26T02:34:51Z Build needed 00:02:10, 62028k disk space