I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 22 06:42:39 +14 2019 I: pbuilder-time-stamp: 1561135359 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [voronota_1.19.2352-1.dsc] I: copying [./voronota_1.19.2352.orig.tar.gz] I: copying [./voronota_1.19.2352-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Nov 2 21:04:03 2018 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "andrius.merkys@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./voronota_1.19.2352-1.dsc dpkg-source: info: extracting voronota in voronota-1.19.2352 dpkg-source: info: unpacking voronota_1.19.2352.orig.tar.gz dpkg-source: info: unpacking voronota_1.19.2352-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29933/tmp/hooks/D01_modify_environment starting disorder-fs debug: Running on profitbricks-build12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/29933/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19231 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB of archives. After unpacking 70.3 MB will be used. Writing extended state information... Get: 1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://cdn-fastly.deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://cdn-fastly.deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://cdn-fastly.deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://cdn-fastly.deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://cdn-fastly.deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4 [242 kB] Get: 9 http://cdn-fastly.deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4 [124 kB] Get: 10 http://cdn-fastly.deb.debian.org/debian buster/main i386 file i386 1:5.35-4 [66.3 kB] Get: 11 http://cdn-fastly.deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://cdn-fastly.deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://cdn-fastly.deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://cdn-fastly.deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://cdn-fastly.deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://cdn-fastly.deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://cdn-fastly.deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://cdn-fastly.deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://cdn-fastly.deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://cdn-fastly.deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://cdn-fastly.deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://cdn-fastly.deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://cdn-fastly.deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2 [1333 kB] Get: 26 http://cdn-fastly.deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 27 http://cdn-fastly.deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://cdn-fastly.deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://cdn-fastly.deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2 [109 kB] Get: 30 http://cdn-fastly.deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://cdn-fastly.deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://cdn-fastly.deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://cdn-fastly.deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Fetched 19.3 MB in 13s (1535 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4_i386.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4_i386.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... 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Preparing to unpack .../28-libncurses6_6.1+20181013-2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_i386.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:i386 (2.58.3-2) ... No schema files found: doing nothing. Setting up libmagic1:i386 (1:5.35-4) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4) ... Setting up libicu63:i386 (63.1-6) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:i386 (6.1+20181013-2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... 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 gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 182 kB of additional disk space will be used. Get:1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libnumber-compare-perl all 0.03-1 [7642 B] Get:2 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtext-glob-perl all 0.10-1 [8362 B] Get:3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://cdn-fastly.deb.debian.org/debian buster/main i386 usrmerge all 21 [12.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 1s (117 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 21275 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1_all.deb ... Unpacking libnumber-compare-perl (0.03-1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.10-1_all.deb ... Unpacking libtext-glob-perl (0.10-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_21_all.deb ... Unpacking usrmerge (21) ... Setting up libtext-glob-perl (0.10-1) ... Setting up libnumber-compare-perl (0.03-1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (21) ... The system has been successfully converted. Processing triggers for man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package I: Running cd /build/voronota-1.19.2352/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package voronota dpkg-buildpackage: info: source version 1.19.2352-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf Makefile.am:2: warning: source file 'src/mode_draw_values_bitmap.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. Makefile.am:2: warning: source file 'src/mode_run_script.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_simulate_potential_for_membrane_proteins.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_rotational_optimization_demo.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_plot_contacts.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_score_scores.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_query_contacts_solvation_values.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_compare_contacts.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_score_contacts_potential.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_score_contacts_potentials_stats.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_query_contacts.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_query_contacts_depth_values.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_expand_descriptors.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_calculate_vertices.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_write_qa_scores_in_casp_format.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_vectorize_points.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_score_contacts_quality.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_score_contacts_global_energy_by_cuts.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_vectorize_contact_environments.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_query_balls_sequences_pairings_stats.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_query_contacts_simulating_unfolding.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_score_contacts_energy.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_vectorize_contacts.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_write_balls_to_atoms_file.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_score_contacts_energy_stats.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_query_balls.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_query_balls_clashes.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_calculate_vertices_in_parallel.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_demo_ses.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_demo_polygon_triangulation.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_place_membrane.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_draw_contacts.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_get_balls_from_atoms_file.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_draw_balls.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_calculate_mock_solvent.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_calculate_contacts.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_demo_hypercut.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_query_balls_distances.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_reprint_hbp.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_calculate_path_centralities.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/main.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_compare_files_as_sets.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled Makefile.am:2: warning: source file 'src/mode_split_atoms_file.cpp' is in a subdirectory, Makefile.am:2: but option 'subdir-objects' is disabled dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make -j10 make[1]: Entering directory '/build/voronota-1.19.2352' g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_draw_values_bitmap.o `test -f 'src/mode_draw_values_bitmap.cpp' || echo './'`src/mode_draw_values_bitmap.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_run_script.o `test -f 'src/mode_run_script.cpp' || echo './'`src/mode_run_script.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_simulate_potential_for_membrane_proteins.o `test -f 'src/mode_simulate_potential_for_membrane_proteins.cpp' || echo './'`src/mode_simulate_potential_for_membrane_proteins.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_rotational_optimization_demo.o `test -f 'src/mode_rotational_optimization_demo.cpp' || echo './'`src/mode_rotational_optimization_demo.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_plot_contacts.o `test -f 'src/mode_plot_contacts.cpp' || echo './'`src/mode_plot_contacts.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_score_scores.o `test -f 'src/mode_score_scores.cpp' || echo './'`src/mode_score_scores.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_query_contacts_solvation_values.o `test -f 'src/mode_query_contacts_solvation_values.cpp' || echo './'`src/mode_query_contacts_solvation_values.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_compare_contacts.o `test -f 'src/mode_compare_contacts.cpp' || echo './'`src/mode_compare_contacts.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_score_contacts_potential.o `test -f 'src/mode_score_contacts_potential.cpp' || echo './'`src/mode_score_contacts_potential.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_score_contacts_potentials_stats.o `test -f 'src/mode_score_contacts_potentials_stats.cpp' || echo './'`src/mode_score_contacts_potentials_stats.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_query_contacts.o `test -f 'src/mode_query_contacts.cpp' || echo './'`src/mode_query_contacts.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_query_contacts_depth_values.o `test -f 'src/mode_query_contacts_depth_values.cpp' || echo './'`src/mode_query_contacts_depth_values.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_expand_descriptors.o `test -f 'src/mode_expand_descriptors.cpp' || echo './'`src/mode_expand_descriptors.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_calculate_vertices.o `test -f 'src/mode_calculate_vertices.cpp' || echo './'`src/mode_calculate_vertices.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_write_qa_scores_in_casp_format.o `test -f 'src/mode_write_qa_scores_in_casp_format.cpp' || echo './'`src/mode_write_qa_scores_in_casp_format.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_vectorize_points.o `test -f 'src/mode_vectorize_points.cpp' || echo './'`src/mode_vectorize_points.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_score_contacts_quality.o `test -f 'src/mode_score_contacts_quality.cpp' || echo './'`src/mode_score_contacts_quality.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_score_contacts_global_energy_by_cuts.o `test -f 'src/mode_score_contacts_global_energy_by_cuts.cpp' || echo './'`src/mode_score_contacts_global_energy_by_cuts.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_vectorize_contact_environments.o `test -f 'src/mode_vectorize_contact_environments.cpp' || echo './'`src/mode_vectorize_contact_environments.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_query_balls_sequences_pairings_stats.o `test -f 'src/mode_query_balls_sequences_pairings_stats.cpp' || echo './'`src/mode_query_balls_sequences_pairings_stats.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_query_contacts_simulating_unfolding.o `test -f 'src/mode_query_contacts_simulating_unfolding.cpp' || echo './'`src/mode_query_contacts_simulating_unfolding.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_score_contacts_energy.o `test -f 'src/mode_score_contacts_energy.cpp' || echo './'`src/mode_score_contacts_energy.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_vectorize_contacts.o `test -f 'src/mode_vectorize_contacts.cpp' || echo './'`src/mode_vectorize_contacts.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_write_balls_to_atoms_file.o `test -f 'src/mode_write_balls_to_atoms_file.cpp' || echo './'`src/mode_write_balls_to_atoms_file.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_score_contacts_energy_stats.o `test -f 'src/mode_score_contacts_energy_stats.cpp' || echo './'`src/mode_score_contacts_energy_stats.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_query_balls.o `test -f 'src/mode_query_balls.cpp' || echo './'`src/mode_query_balls.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_query_balls_clashes.o `test -f 'src/mode_query_balls_clashes.cpp' || echo './'`src/mode_query_balls_clashes.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_calculate_vertices_in_parallel.o `test -f 'src/mode_calculate_vertices_in_parallel.cpp' || echo './'`src/mode_calculate_vertices_in_parallel.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_demo_ses.o `test -f 'src/mode_demo_ses.cpp' || echo './'`src/mode_demo_ses.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_demo_polygon_triangulation.o `test -f 'src/mode_demo_polygon_triangulation.cpp' || echo './'`src/mode_demo_polygon_triangulation.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_place_membrane.o `test -f 'src/mode_place_membrane.cpp' || echo './'`src/mode_place_membrane.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_draw_contacts.o `test -f 'src/mode_draw_contacts.cpp' || echo './'`src/mode_draw_contacts.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_get_balls_from_atoms_file.o `test -f 'src/mode_get_balls_from_atoms_file.cpp' || echo './'`src/mode_get_balls_from_atoms_file.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_draw_balls.o `test -f 'src/mode_draw_balls.cpp' || echo './'`src/mode_draw_balls.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_calculate_mock_solvent.o `test -f 'src/mode_calculate_mock_solvent.cpp' || echo './'`src/mode_calculate_mock_solvent.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_calculate_contacts.o `test -f 'src/mode_calculate_contacts.cpp' || echo './'`src/mode_calculate_contacts.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_demo_hypercut.o `test -f 'src/mode_demo_hypercut.cpp' || echo './'`src/mode_demo_hypercut.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_query_balls_distances.o `test -f 'src/mode_query_balls_distances.cpp' || echo './'`src/mode_query_balls_distances.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_reprint_hbp.o `test -f 'src/mode_reprint_hbp.cpp' || echo './'`src/mode_reprint_hbp.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_calculate_path_centralities.o `test -f 'src/mode_calculate_path_centralities.cpp' || echo './'`src/mode_calculate_path_centralities.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o `test -f 'src/main.cpp' || echo './'`src/main.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_compare_files_as_sets.o `test -f 'src/mode_compare_files_as_sets.cpp' || echo './'`src/mode_compare_files_as_sets.cpp g++ -DPACKAGE_NAME=\"voronota\" -DPACKAGE_TARNAME=\"voronota\" -DPACKAGE_VERSION=\"1.19.2352\" -DPACKAGE_STRING=\"voronota\ 1.19.2352\" -DPACKAGE_BUGREPORT=\"kliment@ibt.lt\" -DPACKAGE_URL=\"\" -DPACKAGE=\"voronota\" -DVERSION=\"1.19.2352\" -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mode_split_atoms_file.o `test -f 'src/mode_split_atoms_file.cpp' || echo './'`src/mode_split_atoms_file.cpp g++ -g -O2 -ffile-prefix-map=/build/voronota-1.19.2352=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o voronota mode_draw_values_bitmap.o mode_run_script.o mode_simulate_potential_for_membrane_proteins.o mode_rotational_optimization_demo.o mode_plot_contacts.o mode_score_scores.o mode_query_contacts_solvation_values.o mode_compare_contacts.o mode_score_contacts_potential.o mode_score_contacts_potentials_stats.o mode_query_contacts.o mode_query_contacts_depth_values.o mode_expand_descriptors.o mode_calculate_vertices.o mode_write_qa_scores_in_casp_format.o mode_vectorize_points.o mode_score_contacts_quality.o mode_score_contacts_global_energy_by_cuts.o mode_vectorize_contact_environments.o mode_query_balls_sequences_pairings_stats.o mode_query_contacts_simulating_unfolding.o mode_score_contacts_energy.o mode_vectorize_contacts.o mode_write_balls_to_atoms_file.o mode_score_contacts_energy_stats.o mode_query_balls.o mode_query_balls_clashes.o mode_calculate_vertices_in_parallel.o mode_demo_ses.o mode_demo_polygon_triangulation.o mode_place_membrane.o mode_draw_contacts.o mode_get_balls_from_atoms_file.o mode_draw_balls.o mode_calculate_mock_solvent.o mode_calculate_contacts.o mode_demo_hypercut.o mode_query_balls_distances.o mode_reprint_hbp.o mode_calculate_path_centralities.o main.o mode_compare_files_as_sets.o mode_split_atoms_file.o make[1]: Leaving directory '/build/voronota-1.19.2352' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j10 install DESTDIR=/build/voronota-1.19.2352/debian/voronota AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/voronota-1.19.2352' make[2]: Entering directory '/build/voronota-1.19.2352' /usr/bin/mkdir -p '/build/voronota-1.19.2352/debian/voronota/usr/bin' /usr/bin/mkdir -p '/build/voronota-1.19.2352/debian/voronota/usr/bin' /usr/bin/mkdir -p '/build/voronota-1.19.2352/debian/voronota/usr/share/man/man1' /usr/bin/install -c voronota '/build/voronota-1.19.2352/debian/voronota/usr/bin' /usr/bin/install -c voronota-resources voronota-voromqa voronota-contacts voronota-cadscore voronota-volumes '/build/voronota-1.19.2352/debian/voronota/usr/bin' /usr/bin/install -c -m 644 'voronota.man' '/build/voronota-1.19.2352/debian/voronota/usr/share/man/man1/voronota.1' make[2]: Leaving directory '/build/voronota-1.19.2352' make[1]: Leaving directory '/build/voronota-1.19.2352' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'voronota-dbgsym' in '../voronota-dbgsym_1.19.2352-1_i386.deb'. dpkg-deb: building package 'voronota' in '../voronota_1.19.2352-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../voronota_1.19.2352-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/29933/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/29933/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/29933 and its subdirectories I: Current time: Sat Jun 22 06:54:54 +14 2019 I: pbuilder-time-stamp: 1561136094