RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-006 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:28:53 UTC 2017 s390x Buildd toolchain package versions: launchpad-buildd_145 python-lpbuildd_145 sbuild_0.67.0-2ubuntu7 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.11. Syncing the system clock with the buildd NTP service... 8 Jul 03:59:11 ntpdate[29751]: adjust time server 10.211.37.1 offset 0.000444 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12925704', '/home/buildd/filecache-default/6fa5c2199508da5ee864769667103e5baa50a34d'] Unpacking chroot for build PACKAGEBUILD-12925704 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12925704'] Mounting chroot for build PACKAGEBUILD-12925704 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12925704', 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful main', 'deb http://ftpmaster.internal/ubuntu artful main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-12925704 RUN: /usr/share/launchpad-buildd/slavebin/add-trusted-keys ['add-trusted-keys', 'PACKAGEBUILD-12925704'] Adding trusted keys to build-PACKAGEBUILD-12925704 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12925704', 's390x'] Updating debian chroot for build PACKAGEBUILD-12925704 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful InRelease [15.4 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x Packages [25.2 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main Translation-en [16.6 kB] Get:5 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:6 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main s390x Packages [1073 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main Translation-en [555 kB] Get:9 http://ftpmaster.internal/ubuntu artful/restricted Translation-en [2724 B] Get:10 http://ftpmaster.internal/ubuntu artful/universe s390x Packages [7960 kB] Get:11 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4768 kB] Get:12 http://ftpmaster.internal/ubuntu artful/multiverse s390x Packages [128 kB] Get:13 http://ftpmaster.internal/ubuntu artful/multiverse Translation-en [109 kB] Fetched 15.0 MB in 7s (1977 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp cpp-6 debianutils dmsetup dpkg dpkg-dev findutils g++ g++-6 gcc gcc-6 gcc-6-base libapparmor1 libapt-pkg5.0 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libcc1-0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libip4tc0 libitm1 libkmod2 libkrb5-26-heimdal libldap-2.4-2 libldap-common libmount1 libnpth0 libp11-kit0 libperl5.24 libpng16-16 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount openssl passwd perl perl-base perl-modules-5.24 systemd systemd-sysv tzdata util-linux 80 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 43.4 MB of archives. After this operation, 1507 kB of additional disk space will be used. Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x gcc-7-base s390x 7.1.0-9ubuntu1 [18.8 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main s390x base-files s390x 9.6ubuntu101 [59.1 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libgcc1 s390x 1:7.1.0-9ubuntu1 [25.2 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libstdc++6 s390x 7.1.0-9ubuntu1 [408 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main s390x debianutils s390x 4.8.1.1 [85.8 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main s390x bash s390x 4.4-5ubuntu1 [594 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x binutils s390x 2.28.90.20170704-0ubuntu1 [1105 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main s390x bsdutils s390x 1:2.29-1ubuntu3 [54.8 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main s390x dpkg s390x 1.18.24ubuntu1 [1121 kB] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libgomp1 s390x 7.1.0-9ubuntu1 [69.9 kB] Get:11 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libitm1 s390x 7.1.0-9ubuntu1 [26.9 kB] Get:12 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libatomic1 s390x 7.1.0-9ubuntu1 [8198 B] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x g++-6 s390x 6.4.0-1ubuntu2 [5841 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main s390x findutils s390x 4.6.0+git+20170606-3 [288 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main s390x login s390x 1:4.2-3.2ubuntu2 [302 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main s390x util-linux s390x 2.29-1ubuntu3 [885 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main s390x mount s390x 2.29-1ubuntu3 [126 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main s390x libperl5.24 s390x 5.24.1-4ubuntu1 [3324 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main s390x perl s390x 5.24.1-4ubuntu1 [219 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main s390x perl-base s390x 5.24.1-4ubuntu1 [1272 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main s390x perl-modules-5.24 all 5.24.1-4ubuntu1 [2663 kB] Get:22 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libstdc++-6-dev s390x 6.4.0-1ubuntu2 [1403 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main s390x libapt-pkg5.0 s390x 1.5~beta1 [732 kB] Get:24 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x gcc-6 s390x 6.4.0-1ubuntu2 [5692 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main s390x apt-transport-https s390x 1.5~beta1 [32.1 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main s390x libp11-kit0 s390x 0.23.7-2 [187 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main s390x libtasn1-6 s390x 4.12-2 [33.9 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main s390x libgnutls30 s390x 3.5.8-6ubuntu1 [591 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main s390x apt s390x 1.5~beta1 [1076 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main s390x libip4tc0 s390x 1.6.1-2ubuntu1 [19.4 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main s390x libapparmor1 s390x 2.11.0-2ubuntu8 [29.0 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main s390x libaudit-common all 1:2.7.7-1ubuntu1 [4118 B] Get:33 http://ftpmaster.internal/ubuntu artful/main s390x libaudit1 s390x 1:2.7.7-1ubuntu1 [36.7 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main s390x libselinux1 s390x 2.6-3build1 [64.3 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main s390x libsemanage-common all 2.6-2build1 [6738 B] Get:36 http://ftpmaster.internal/ubuntu artful/main s390x libsemanage1 s390x 2.6-2build1 [76.5 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main s390x passwd s390x 1:4.2-3.2ubuntu2 [770 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main s390x libuuid1 s390x 2.29-1ubuntu3 [14.9 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main s390x libblkid1 s390x 2.29-1ubuntu3 [104 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main s390x libgpg-error0 s390x 1.27-3 [35.2 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main s390x libgcrypt20 s390x 1.7.8-2 [338 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main s390x libkmod2 s390x 24-1ubuntu1 [36.7 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main s390x libmount1 s390x 2.29-1ubuntu3 [111 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main s390x systemd s390x 233-8ubuntu2 [2337 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main s390x libsystemd0 s390x 233-8ubuntu2 [193 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main s390x systemd-sysv s390x 233-8ubuntu2 [12.4 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main s390x libfdisk1 s390x 2.29-1ubuntu3 [134 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main s390x libsmartcols1 s390x 2.29-1ubuntu3 [65.8 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main s390x libudev1 s390x 233-8ubuntu2 [53.5 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main s390x libdevmapper1.02.1 s390x 2:1.02.137-2ubuntu2 [123 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main s390x dmsetup s390x 2:1.02.137-2ubuntu2 [68.8 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main s390x libroken18-heimdal s390x 7.1.0+dfsg-13 [39.1 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main s390x libasn1-8-heimdal s390x 7.1.0+dfsg-13 [150 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main s390x libheimbase1-heimdal s390x 7.1.0+dfsg-13 [27.4 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main s390x libhcrypto4-heimdal s390x 7.1.0+dfsg-13 [83.5 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main s390x libwind0-heimdal s390x 7.1.0+dfsg-13 [47.8 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main s390x libhx509-5-heimdal s390x 7.1.0+dfsg-13 [99.6 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main s390x libsqlite3-0 s390x 3.19.3-2 [463 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main s390x libkrb5-26-heimdal s390x 7.1.0+dfsg-13 [191 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main s390x libheimntlm0-heimdal s390x 7.1.0+dfsg-13 [14.5 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main s390x libgssapi3-heimdal s390x 7.1.0+dfsg-13 [88.5 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main s390x libldap-2.4-2 s390x 2.4.44+dfsg-7ubuntu1 [144 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main s390x libldap-common all 2.4.44+dfsg-7ubuntu1 [16.4 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main s390x libnpth0 s390x 1.5-2 [7448 B] Get:65 http://ftpmaster.internal/ubuntu artful/main s390x libssl1.0.0 s390x 1.0.2g-1ubuntu13 [773 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main s390x tzdata all 2017b-2 [203 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main s390x openssl s390x 1.0.2g-1ubuntu13 [476 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main s390x ca-certificates all 20161130+nmu1 [186 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main s390x libpng16-16 s390x 1.6.29-3 [169 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main s390x advancecomp s390x 2.0-1 [183 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main s390x cpp s390x 4:6.3.0-2ubuntu2 [27.5 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main s390x dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:73 http://ftpmaster.internal/ubuntu artful/main s390x libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main s390x gcc s390x 4:6.3.0-2ubuntu2 [5252 B] Get:75 http://ftpmaster.internal/ubuntu artful/main s390x g++ s390x 4:6.3.0-2ubuntu2 [1488 B] Get:76 http://ftpmaster.internal/ubuntu artful/main s390x libusb-0.1-4 s390x 2:0.1.12-31 [16.4 kB] Get:77 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libgcc-6-dev s390x 6.4.0-1ubuntu2 [269 kB] Get:78 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x libcc1-0 s390x 7.1.0-9ubuntu1 [37.6 kB] Get:79 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x cpp-6 s390x 6.4.0-1ubuntu2 [5058 kB] Get:80 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x gcc-6-base s390x 6.4.0-1ubuntu2 [17.3 kB] Get:81 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu artful/main s390x linux-libc-dev s390x 4.11.0-10.15 [917 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 43.4 MB in 10s (4017 kB/s) (Reading database ... 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Setting up perl-base (5.24.1-4ubuntu1) ... (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 ... 12209 files and directories currently installed.) Preparing to unpack .../perl-modules-5.24_5.24.1-4ubuntu1_all.deb ... Unpacking perl-modules-5.24 (5.24.1-4ubuntu1) over (5.24.1-2ubuntu1) ... Selecting previously unselected package gcc-7-base:s390x. Preparing to unpack .../gcc-7-base_7.1.0-9ubuntu1_s390x.deb ... Unpacking gcc-7-base:s390x (7.1.0-9ubuntu1) ... 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Unpacking libusb-0.1-4:s390x (2:0.1.12-31) over (2:0.1.12-30) ... Preparing to unpack .../38-linux-libc-dev_4.11.0-10.15_s390x.deb ... Unpacking linux-libc-dev:s390x (4.11.0-10.15) over (4.10.0-20.22) ... Setting up libnpth0:s390x (1.5-2) ... Setting up libgomp1:s390x (7.1.0-9ubuntu1) ... Setting up libatomic1:s390x (7.1.0-9ubuntu1) ... Setting up perl-modules-5.24 (5.24.1-4ubuntu1) ... Setting up libperl5.24:s390x (5.24.1-4ubuntu1) ... Setting up libcc1-0:s390x (7.1.0-9ubuntu1) ... Setting up apt-transport-https (1.5~beta1) ... Setting up libssl1.0.0:s390x (1.0.2g-1ubuntu13) ... Setting up libpng16-16:s390x (1.6.29-3) ... Setting up libldap-common (2.4.44+dfsg-7ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jul 8 03:59:45 UTC 2017. Universal Time is now: Sat Jul 8 03:59:45 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (233-8ubuntu2) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12925704', 's390x', 'artful', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=artful', '--purge=never', '--nolog', 'probabel_0.4.5-4.dsc'] Initiating build PACKAGEBUILD-12925704 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:28:53 UTC 2017 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on z13-006.buildd +==============================================================================+ | probabel 0.4.5-4 (s390x) 08 Jul 2017 03:59 | +==============================================================================+ Package: probabel Version: 0.4.5-4 Source Version: 0.4.5-4 Distribution: artful Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/probabel-k5Fp7X/probabel-0.4.5' with '<>' I: NOTICE: Log filtering will replace 'build/probabel-k5Fp7X' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12925704/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- probabel_0.4.5-4.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Y95wJ_/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Y95wJ_/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Y95wJ_/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Y95wJ_/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Y95wJ_/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Y95wJ_/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (0 B/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 NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 780 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Y95wJ_/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [780 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 780 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (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 ... 12251 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), autotools-dev, dh-autoreconf, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended, libeigen3-dev Filtered Build-Depends: debhelper (>= 10), autotools-dev, dh-autoreconf, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended, libeigen3-dev dpkg-deb: building package 'sbuild-build-depends-probabel-dummy' in '/<>/resolver-TtOQPh/apt_archive/sbuild-build-depends-probabel-dummy.deb'. Ign:1 copy:/<>/resolver-TtOQPh/apt_archive ./ InRelease Get:2 copy:/<>/resolver-TtOQPh/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-TtOQPh/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-TtOQPh/apt_archive ./ Sources [268 B] Get:5 copy:/<>/resolver-TtOQPh/apt_archive ./ Packages [588 B] Fetched 2975 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install probabel 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 file fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base groff-base intltool-debian libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libbsd0 libcairo2 libcroco3 libcups2 libcupsimage2 libdbus-1-3 libeigen3-dev libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libharfbuzz-icu0 libharfbuzz0b libice6 libicu57 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblcms2-2 libmagic-mgc libmagic1 libnspr4 libnss3 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpoppler64 libpotrace0 libptexenc1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsm6 libsynctex1 libtexlua52 libtiff5 libtimedate-perl libtool libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 man-db mime-support pkg-config po-debconf poppler-data preview-latex-style python python-minimal python2.7 python2.7-minimal t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ucf x11-common xdg-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff cups-common libeigen3-doc libmrpt-dev liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk python2.7-doc binfmt-support gv | postscript-viewer perl-tk xpdf-reader | pdf-viewer python-pygments libfile-which-perl libspreadsheet-parseexcel-perl texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby gvfs-bin Recommended packages: curl | wget | lynx-cur libcupsfilters1 dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback libltdl-dev xml-core libmail-sendmail-perl lmodern ruby wish tex-gyre texlive-fonts-recommended-doc tipa texlive-latex-base-doc texlive-latex-extra-doc texlive-plain-generic prosper texlive-latex-recommended-doc ruby | ruby-interpreter texlive-pictures-doc tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base groff-base intltool-debian libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libbsd0 libcairo2 libcroco3 libcups2 libcupsimage2 libdbus-1-3 libeigen3-dev libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libharfbuzz-icu0 libharfbuzz0b libice6 libicu57 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblcms2-2 libmagic-mgc libmagic1 libnspr4 libnss3 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpoppler64 libpotrace0 libptexenc1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libsm6 libsynctex1 libtexlua52 libtiff5 libtimedate-perl libtool libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 man-db mime-support pkg-config po-debconf poppler-data preview-latex-style python python-minimal python2.7 python2.7-minimal sbuild-build-depends-probabel-dummy t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ucf x11-common xdg-utils 0 upgraded, 107 newly installed, 1 to remove and 0 not upgraded. Need to get 100 MB of archives. After this operation, 370 MB of additional disk space will be used. Get:1 copy:/<>/resolver-TtOQPh/apt_archive ./ sbuild-build-depends-probabel-dummy 0.invalid.0 [844 B] Get:2 http://ftpmaster.internal/ubuntu artful/main s390x groff-base s390x 1.22.3-9 [1174 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main s390x libbsd0 s390x 0.8.5-1 [41.0 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main s390x bsdmainutils s390x 9.0.12ubuntu1 [179 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main s390x libpipeline1 s390x 1.4.1-2 [24.8 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main s390x man-db s390x 2.7.6.1-2 [887 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main s390x libjpeg-turbo8 s390x 1.5.1-0ubuntu1 [103 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main s390x poppler-data all 0.4.7-8 [1449 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main s390x libpython2.7-minimal s390x 2.7.13-2 [338 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main s390x python2.7-minimal s390x 2.7.13-2 [1209 kB] Get:11 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s390x 1:5.30-1 [66.8 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main s390x file s390x 1:5.30-1 [21.9 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main s390x libdbus-1-3 s390x 1.10.18-1ubuntu2 [157 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main s390x gettext-base s390x 0.19.8.1-2ubuntu1 [47.7 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main s390x libglib2.0-0 s390x 2.53.3-1 [1073 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main s390x libicu57 s390x 57.1-6 [7484 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main s390x libxau6 s390x 1:1.0.8-1 [7420 B] Get:28 http://ftpmaster.internal/ubuntu artful/main s390x libxdmcp6 s390x 1:1.1.2-3 [10.7 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main s390x libxcb1 s390x 1.11.1-1ubuntu1 [38.8 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main s390x libx11-data all 2:1.6.4-3 [114 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main s390x libx11-6 s390x 2:1.6.4-3 [546 kB] Get:32 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libarchive-zip-perl all 1.59-1 [84.0 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main s390x libfile-stripnondeterminism-perl all 0.035-2 [13.3 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main s390x dh-strip-nondeterminism all 0.035-2 [5018 B] Get:46 http://ftpmaster.internal/ubuntu artful/main s390x libcroco3 s390x 0.6.12-1 [74.7 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main s390x gettext s390x 0.19.8.1-2ubuntu1 [1051 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main s390x po-debconf all 1.0.20 [232 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main s390x debhelper all 10.4ubuntu3 [876 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main s390x fonts-dejavu-core all 2.37-1 [1041 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main s390x fontconfig-config all 2.11.94-0ubuntu2 [49.9 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main s390x fonts-lmodern all 2.004.5-3 [4551 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main s390x libavahi-common-data s390x 0.6.32-1ubuntu1 [22.0 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main s390x libavahi-common3 s390x 0.6.32-1ubuntu1 [20.3 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main s390x libavahi-client3 s390x 0.6.32-1ubuntu1 [22.7 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main s390x libfreetype6 s390x 2.6.3-3.2ubuntu1 [303 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main s390x libfontconfig1 s390x 2.11.94-0ubuntu2 [127 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main s390x libpixman-1-0 s390x 0.34.0-1 [136 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main s390x libxcb-render0 s390x 1.11.1-1ubuntu1 [11.4 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main s390x libxcb-shm0 s390x 1.11.1-1ubuntu1 [5488 B] Get:62 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s390x libxpm4 s390x 1:3.5.12-1 [32.6 kB] Get:93 http://ftpmaster.internal/ubuntu artful/main s390x libxaw7 s390x 2:1.0.13-1 [163 kB] Get:94 http://ftpmaster.internal/ubuntu artful/main s390x libxi6 s390x 2:1.7.9-1 [27.5 kB] Get:95 http://ftpmaster.internal/ubuntu artful/main s390x libzzip-0-13 s390x 0.13.62-3.1 [25.2 kB] Get:96 http://ftpmaster.internal/ubuntu artful/main s390x pkg-config s390x 0.29.1-0ubuntu2 [44.0 kB] Get:97 http://ftpmaster.internal/ubuntu artful/main s390x preview-latex-style all 11.90-1ubuntu1 [184 kB] Get:98 http://ftpmaster.internal/ubuntu artful/main s390x t1utils s390x 1.39-2 [52.3 kB] Get:99 http://ftpmaster.internal/ubuntu artful/main s390x texlive-binaries s390x 2017.20170613.44572-2 [7321 kB] Get:100 http://ftpmaster.internal/ubuntu artful/main s390x xdg-utils all 1.1.1-1ubuntu2 [59.6 kB] Get:101 http://ftpmaster.internal/ubuntu artful/main s390x texlive-base all 2017.20170629-1 [18.6 MB] Get:102 http://ftpmaster.internal/ubuntu artful/universe s390x texlive-fonts-recommended all 2017.20170629-1 [5280 kB] Get:103 http://ftpmaster.internal/ubuntu artful/main s390x texlive-latex-base all 2017.20170629-1 [946 kB] Get:104 http://ftpmaster.internal/ubuntu artful/main s390x texlive-latex-recommended all 2017.20170629-1 [14.8 MB] Get:105 http://ftpmaster.internal/ubuntu artful/main s390x texlive-pictures all 2017.20170629-1 [3953 kB] Get:106 http://ftpmaster.internal/ubuntu artful/universe s390x texlive-latex-extra all 2017.20170629-1 [10.3 MB] Get:107 http://ftpmaster.internal/ubuntu artful/universe s390x libeigen3-dev all 3.3.4-2 [811 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 100 MB in 1min 21s (1232 kB/s) (Reading database ... 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Setting up libsynctex1:s390x (2017.20170613.44572-2) ... Setting up libptexenc1:s390x (2017.20170613.44572-2) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up liblcms2-2:s390x (2.7-1ubuntu1) ... Setting up libjbig0:s390x (2.1-3.1) ... Setting up libsigsegv2:s390x (2.11-1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up poppler-data (0.4.7-8) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:s390x (2.53.3-1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-2ubuntu1) ... Setting up libjpeg-turbo8:s390x (1.5.1-0ubuntu1) ... Setting up libpipeline1:s390x (1.4.1-2) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:s390x (57.1-6) ... Setting up libbsd0:s390x (0.8.5-1) ... Setting up libnspr4:s390x (2:4.13.1-0ubuntu1) ... Setting up ucf (3.0036) ... Setting up libxml2:s390x (2.9.4+dfsg1-2.2ubuntu1) ... Setting up libfreetype6:s390x (2.6.3-3.2ubuntu1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:s390x (1:5.30-1) ... Setting up libgraphite2-3:s390x (1.3.10-2) ... Setting up libcroco3:s390x (0.6.12-1) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Setting up libjbig2dec0:s390x (0.13-4.1) ... Setting up libpixman-1-0:s390x (0.34.0-1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up t1utils (1.39-2) ... Processing triggers for systemd (233-8ubuntu2) ... Setting up libijs-0.35:s390x (0.35-12) ... Setting up libpotrace0 (1.14-2) ... Setting up libxdmcp6:s390x (1:1.1.2-3) ... Setting up bsdmainutils (9.0.12ubuntu1) ... 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 libzzip-0-13:s390x (0.13.62-3.1) ... Setting up x11-common (1:7.7+19ubuntu1) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.1-1ubuntu2) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libpython2.7-stdlib:s390x (2.7.13-2) ... Setting up libxau6:s390x (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up libdbus-1-3:s390x (1.10.18-1ubuntu2) ... Setting up fonts-lmodern (2.004.5-3) ... Setting up libavahi-common-data:s390x (0.6.32-1ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libjpeg8:s390x (8c-2ubuntu8) ... Setting up libpaper1:s390x (1.1.24+nmu5ubuntu1) ... Creating config file /etc/papersize with new version Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ... Setting up fontconfig-config (2.11.94-0ubuntu2) ... Setting up tex-common (6.07) ... update-language: texlive-base not installed and configured, doing nothing! Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up libeigen3-dev (3.3.4-2) ... Setting up python2.7 (2.7.13-2) ... Setting up libnss3:s390x (2:3.28.4-0ubuntu2) ... Setting up libharfbuzz0b:s390x (1.4.2-1) ... Setting up libtiff5:s390x (4.0.8-3) ... Setting up preview-latex-style (11.90-1ubuntu1) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libpython-stdlib:s390x (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:s390x (2:1.0.9-2) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libavahi-common3:s390x (0.6.32-1ubuntu1) ... Setting up libxcb1:s390x (1.11.1-1ubuntu1) ... Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up libfontconfig1:s390x (2.11.94-0ubuntu2) ... Setting up libsm6:s390x (2:1.2.2-1) ... Setting up libxcb-render0:s390x (1.11.1-1ubuntu1) ... Setting up libharfbuzz-icu0:s390x (1.4.2-1) ... Setting up po-debconf (1.0.20) ... Setting up libpoppler64:s390x (0.48.0-2ubuntu2) ... Setting up libx11-6:s390x (2:1.6.4-3) ... Setting up libxcb-shm0:s390x (1.11.1-1ubuntu1) ... Setting up libxpm4:s390x (1:3.5.12-1) ... Setting up libxt6:s390x (1:1.1.5-1) ... Setting up libxrender1:s390x (1:0.9.10-1) ... Setting up libavahi-client3:s390x (0.6.32-1ubuntu1) ... Setting up libcups2:s390x (2.2.3-2) ... Setting up libxext6:s390x (2:1.3.3-1) ... Setting up libxmu6:s390x (2:1.1.2-2) ... Setting up libcupsimage2:s390x (2.2.3-2) ... Setting up libgs9:s390x (9.19~dfsg+1-0ubuntu10) ... Setting up libxi6:s390x (2:1.7.9-1) ... Setting up libxaw7:s390x (2:1.0.13-1) ... Setting up libcairo2:s390x (1.14.8-1) ... Setting up texlive-binaries (2017.20170613.44572-2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2017.20170629-1) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Setting up texlive-fonts-recommended (2017.20170629-1) ... Setting up texlive-latex-base (2017.20170629-1) ... Setting up texlive-latex-recommended (2017.20170629-1) ... Setting up texlive-pictures (2017.20170629-1) ... Setting up texlive-latex-extra (2017.20170629-1) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.4ubuntu3) ... Setting up sbuild-build-depends-probabel-dummy (0.invalid.0) ... (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 ... 32530 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for tex-common (6.07) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Processing triggers for libc-bin (2.24-9ubuntu2) ... Processing triggers for systemd (233-8ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-78-generic s390x (s390x) Toolchain package versions: binutils_2.28.90.20170704-0ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-1ubuntu2 gcc-6_6.4.0-1ubuntu2 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.4.0-1ubuntu2 libstdc++6_7.1.0-9ubuntu1 linux-libc-dev_4.11.0-10.15 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~beta1 apt-transport-https_1.5~beta1 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.28.90.20170704-0ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu2 cpp-6_6.4.0-1ubuntu2 dash_0.5.8-2.3ubuntu1 debconf_1.5.60ubuntu1 debhelper_10.4ubuntu3 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu2 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20170606-3 fontconfig-config_2.11.94-0ubuntu2 fonts-dejavu-core_2.37-1 fonts-lmodern_2.004.5-3 g++_4:6.3.0-2ubuntu2 g++-6_6.4.0-1ubuntu2 gcc_4:6.3.0-2ubuntu2 gcc-6_6.4.0-1ubuntu2 gcc-6-base_6.4.0-1ubuntu2 gcc-7-base_7.1.0-9ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu8 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasn1-8-heimdal_7.1.0+dfsg-13 libassuan0_2.4.3-2 libatomic1_7.1.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu1 libaudit1_1:2.7.7-1ubuntu1 libavahi-client3_0.6.32-1ubuntu1 libavahi-common-data_0.6.32-1ubuntu1 libavahi-common3_0.6.32-1ubuntu1 libblkid1_2.29-1ubuntu3 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9ubuntu2 libc-dev-bin_2.24-9ubuntu2 libc6_2.24-9ubuntu2 libc6-dev_2.24-9ubuntu2 libcairo2_1.14.8-1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9ubuntu1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.2-0ubuntu1 libcups2_2.2.3-2 libcupsimage2_2.2.3-2 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.18-1ubuntu2 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu2 libdpkg-perl_1.18.24ubuntu1 libeigen3-dev_3.3.4-2 libexpat1_2.2.1-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu3 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.035-2 libfontconfig1_2.11.94-0ubuntu2 libfreetype6_2.6.3-3.2ubuntu1 libgcc-6-dev_6.4.0-1ubuntu2 libgcc1_1:7.1.0-9ubuntu1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu1 libgomp1_7.1.0-9ubuntu1 libgpg-error0_1.27-3 libgraphite2-3_1.3.10-2 libgs9_9.19~dfsg+1-0ubuntu10 libgs9-common_9.19~dfsg+1-0ubuntu10 libgssapi-krb5-2_1.15-2 libgssapi3-heimdal_7.1.0+dfsg-13 libharfbuzz-icu0_1.4.2-1 libharfbuzz0b_1.4.2-1 libhcrypto4-heimdal_7.1.0+dfsg-13 libheimbase1-heimdal_7.1.0+dfsg-13 libheimntlm0-heimdal_7.1.0+dfsg-13 libhogweed4_3.3-1 libhx509-5-heimdal_7.1.0+dfsg-13 libice6_2:1.0.9-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libijs-0.35_0.35-12 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libitm1_7.1.0-9ubuntu1 libjbig0_2.1-3.1 libjbig2dec0_0.13-4.1 libjpeg-turbo8_1.5.1-0ubuntu1 libjpeg8_8c-2ubuntu8 libk5crypto3_1.15-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkpathsea6_2017.20170613.44572-2 libkrb5-26-heimdal_7.1.0+dfsg-13 libkrb5-3_1.15-2 libkrb5support0_1.15-2 libksba8_1.3.5-2 liblcms2-2_2.7-1ubuntu1 libldap-2.4-2_2.4.44+dfsg-7ubuntu1 libldap-common_2.4.44+dfsg-7ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.5-2 libnspr4_2:4.13.1-0ubuntu1 libnss3_2:3.28.4-0ubuntu2 libp11-kit0_0.23.7-2 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpaper-utils_1.1.24+nmu5ubuntu1 libpaper1_1.1.24+nmu5ubuntu1 libpcre3_2:8.39-3 libperl5.24_5.24.1-4ubuntu1 libpipeline1_1.4.1-2 libpixman-1-0_0.34.0-1 libpng16-16_1.6.29-3 libpoppler64_0.48.0-2ubuntu2 libpotrace0_1.14-2 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-4 libptexenc1_2017.20170613.44572-2 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libreadline7_7.0-0ubuntu2 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readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-probabel-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_233-8ubuntu2 systemd-sysv_233-8ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 t1utils_1.39-2 tar_1.29b-1.1 tex-common_6.07 texlive-base_2017.20170629-1 texlive-binaries_2017.20170613.44572-2 texlive-fonts-recommended_2017.20170629-1 texlive-latex-base_2017.20170629-1 texlive-latex-extra_2017.20170629-1 texlive-latex-recommended_2017.20170629-1 texlive-pictures_2017.20170629-1 tzdata_2017b-2 ubuntu-keyring_2016.10.27 ucf_3.0036 util-linux_2.29-1ubuntu3 x11-common_1:7.7+19ubuntu1 xdg-utils_1.1.1-1ubuntu2 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Jun 22 13:04:20 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./probabel_0.4.5-4.dsc dpkg-source: info: extracting probabel in probabel-0.4.5 dpkg-source: info: unpacking probabel_0.4.5.orig.tar.gz dpkg-source: info: unpacking probabel_0.4.5-4.debian.tar.xz Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package probabel dpkg-buildpackage: info: source version 0.4.5-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build probabel-0.4.5 dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --with autoreconf dh_testdir -a dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --disable-silent-rules ./configure --build=s390x-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/s390x-linux-gnu --libexecdir=\${prefix}/lib/s390x-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --disable-silent-rules checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /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 whether make supports nested variables... (cached) yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking whether ln -s works... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for inttypes.h... (cached) yes checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking wctype.h usability... yes checking wctype.h presence... yes checking for wctype.h... yes configure: building using the Eigen headers enabled checking Eigen/Dense usability... yes checking Eigen/Dense presence... yes checking for Eigen/Dense... yes checking Eigen/LU usability... yes checking Eigen/LU presence... yes checking for Eigen/LU... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for off_t... yes checking for size_t... (cached) yes checking for error_at_line... yes checking for pow... yes checking for putenv... yes checking for sqrt... yes checking for strdup... yes checking for strncasecmp... yes checking for floor... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for a sed that does not truncate output... /bin/sed checking for gawk... (cached) mawk checking for pdflatex... pdflatex checking for R... no configure: Unable to do tests comparing ProbABEL output against R output configure: building of palinear is enabled configure: building of palogist is enabled configure: building of pacoxph is enabled checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating examples/Makefile config.status: creating checks/Makefile config.status: creating checks/R-tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 make[1]: Entering directory '/<>' Making all in src make[2]: Entering directory '/<>/src' make all-am make[3]: Entering directory '/<>/src' g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-data.o `test -f 'data.cpp' || echo './'`data.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo './'`gendata.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo './'`command_line_settings.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-usage.o `test -f 'usage.cpp' || echo './'`usage.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-main.o `test -f 'main.cpp' || echo './'`main.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-utilities.o `test -f 'utilities.cpp' || echo './'`utilities.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-phedata.o `test -f 'phedata.cpp' || echo './'`phedata.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-cholesky.o `test -f 'cholesky.cpp' || echo './'`cholesky.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-regdata.o `test -f 'regdata.cpp' || echo './'`regdata.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-maskedmatrix.o `test -f 'maskedmatrix.cpp' || echo './'`maskedmatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-reg1.o `test -f 'reg1.cpp' || echo './'`reg1.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-main_functions_dump.o `test -f 'main_functions_dump.cpp' || echo './'`main_functions_dump.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo './'`eigen_mematrix.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-data.o `test -f 'data.cpp' || echo './'`data.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-gendata.o `test -f 'gendata.cpp' || echo './'`gendata.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-command_line_settings.o `test -f 'command_line_settings.cpp' || echo './'`command_line_settings.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-usage.o `test -f 'usage.cpp' || echo './'`usage.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-main.o `test -f 'main.cpp' || echo './'`main.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-utilities.o `test -f 'utilities.cpp' || echo './'`utilities.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-phedata.o `test -f 'phedata.cpp' || echo './'`phedata.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-cholesky.o `test -f 'cholesky.cpp' || echo './'`cholesky.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-regdata.o `test -f 'regdata.cpp' || echo './'`regdata.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-maskedmatrix.o `test -f 'maskedmatrix.cpp' || echo './'`maskedmatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-reg1.o `test -f 'reg1.cpp' || echo './'`reg1.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-main_functions_dump.o `test -f 'main_functions_dump.cpp' || echo './'`main_functions_dump.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-AbstractMatrix.o `test -f 'fvlib/AbstractMatrix.cpp' || echo './'`fvlib/AbstractMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo './'`eigen_mematrix.cpp gcc -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-coxfit2.o `test -f 'coxfit2.c' || echo './'`coxfit2.c gcc -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-chinv2.o `test -f 'chinv2.c' || echo './'`chinv2.c gcc -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-cholesky2.o `test -f 'cholesky2.c' || echo './'`cholesky2.c gcc -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-chsolve2.o `test -f 'chsolve2.c' || echo './'`chsolve2.c gcc -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-dmatrix.o `test -f 'dmatrix.c' || echo './'`dmatrix.c g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-data.o `test -f 'data.cpp' || echo './'`data.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-gendata.o `test -f 'gendata.cpp' || echo './'`gendata.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-command_line_settings.o `test -f 'command_line_settings.cpp' || echo './'`command_line_settings.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-usage.o `test -f 'usage.cpp' || echo './'`usage.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-main.o `test -f 'main.cpp' || echo './'`main.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-utilities.o `test -f 'utilities.cpp' || echo './'`utilities.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-phedata.o `test -f 'phedata.cpp' || echo './'`phedata.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-cholesky.o `test -f 'cholesky.cpp' || echo './'`cholesky.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-regdata.o `test -f 'regdata.cpp' || echo './'`regdata.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-maskedmatrix.o `test -f 'maskedmatrix.cpp' || echo './'`maskedmatrix.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-reg1.o `test -f 'reg1.cpp' || echo './'`reg1.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-main_functions_dump.o `test -f 'main_functions_dump.cpp' || echo './'`main_functions_dump.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-AbstractMatrix.o `test -f 'fvlib/AbstractMatrix.cpp' || echo './'`fvlib/AbstractMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -I ../src/include -g -O2 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-c -o fvlib/palinear-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -DEIGEN -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I/usr/include/eigen3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o palogist palogist-data.o palogist-gendata.o palogist-command_line_settings.o palogist-usage.o palogist-main.o palogist-utilities.o palogist-phedata.o palogist-cholesky.o palogist-regdata.o palogist-maskedmatrix.o palogist-reg1.o palogist-main_functions_dump.o fvlib/palogist-AbstractMatrix.o fvlib/palogist-CastUtils.o fvlib/palogist-convert_util.o fvlib/palogist-FileVector.o fvlib/palogist-FilteredMatrix.o fvlib/palogist-frutil.o fvlib/palogist-Logger.o fvlib/palogist-RealHandlerWrapper.o fvlib/palogist-ReusableFileHandle.o fvlib/palogist-Transposer.o palogist-eigen_mematrix.o g++ -I ../src/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o pacoxph pacoxph-coxfit2.o pacoxph-chinv2.o pacoxph-cholesky2.o pacoxph-chsolve2.o pacoxph-dmatrix.o pacoxph-data.o pacoxph-gendata.o pacoxph-command_line_settings.o pacoxph-usage.o pacoxph-main.o pacoxph-utilities.o pacoxph-phedata.o pacoxph-cholesky.o pacoxph-regdata.o pacoxph-maskedmatrix.o pacoxph-reg1.o pacoxph-main_functions_dump.o fvlib/pacoxph-AbstractMatrix.o fvlib/pacoxph-CastUtils.o fvlib/pacoxph-convert_util.o fvlib/pacoxph-FileVector.o fvlib/pacoxph-FilteredMatrix.o fvlib/pacoxph-frutil.o fvlib/pacoxph-Logger.o fvlib/pacoxph-RealHandlerWrapper.o fvlib/pacoxph-ReusableFileHandle.o fvlib/pacoxph-Transposer.o pacoxph-coxph_data.o pacoxph-eigen_mematrix.o g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o palinear palinear-data.o palinear-gendata.o palinear-command_line_settings.o palinear-usage.o palinear-main.o palinear-utilities.o palinear-phedata.o palinear-cholesky.o palinear-regdata.o palinear-maskedmatrix.o palinear-reg1.o palinear-main_functions_dump.o fvlib/palinear-AbstractMatrix.o fvlib/palinear-CastUtils.o fvlib/palinear-convert_util.o fvlib/palinear-FileVector.o fvlib/palinear-FilteredMatrix.o fvlib/palinear-frutil.o fvlib/palinear-Logger.o fvlib/palinear-RealHandlerWrapper.o fvlib/palinear-ReusableFileHandle.o fvlib/palinear-Transposer.o palinear-eigen_mematrix.o make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making all in doc make[2]: Entering directory '/<>/doc' === Making ProbABEL_manual.aux file === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ProbABEL_manual.tex LaTeX2e <2017-04-15> Babel <3.11> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/svgnam.def)) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) (/usr/share/texlive/texmf-dist/tex/latex/titleref/titleref.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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LaTeX Warning: Reference `sec:obtain' on page 3 undefined on input line 176. [3] [4] Overfull \hbox (4.73831pt too wide) in paragraph at lines 275--279 []\T1/cmr/m/n/12 If all went well you will find the ex-e-cutable pro-grams (\T1 /cmtt/m/n/12 palinear\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/12 , Overfull \hbox (1.38382pt too wide) in paragraph at lines 281--286 \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 takes three files as in-put: a file con -tain-ing SNP in-for-ma-tion (e.g. the [5] [6] LaTeX Warning: Reference `sec:runanalysis' on page 7 undefined on input line 36 0. Overfull \hbox (12.56972pt too wide) in paragraph at lines 384--391 []\T1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \ T1/cmtt/m/n/12 palinear \T1/cmr/m/n/12 and \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/ 12 , Overfull \hbox (14.44846pt too wide) in paragraph at lines 384--391 \T1/cmr/m/n/12 lin-ear re-gres-sion anal-y-sis fol-low here (also to be found i n \T1/cmtt/m/n/12 examples/height.txt\T1/cmr/m/n/12 ) [7] [8] [9] Overfull \hbox (5.0841pt too wide) in paragraph at lines 461--465 []\T1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-ify to the \T1/cmtt/m/n/12 ProbABEL Overfull \hbox (5.10352pt too wide) in paragraph at lines 468--468 []\T1/cmtt/m/n/12 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, E MCR[] Overfull \hbox (23.624pt too wide) in paragraph at lines 479--479 [] \T1/cmtt/m/n/12 --chrom : [optional] chromosome (to be passed to o utput)[] Overfull \hbox (103.8794pt too wide) in paragraph at lines 480--480 [] \T1/cmtt/m/n/12 --out : [optional] output file name (default is regression.out.txt)[] Overfull \hbox (60.66495pt too wide) in paragraph at lines 481--481 [] \T1/cmtt/m/n/12 --skipd : [optional] how many columns to skip in t he predictor[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 483--483 [] \T1/cmtt/m/n/12 --ntraits : [optional] how many traits are analysed (default 1)[] Overfull \hbox (35.97098pt too wide) in paragraph at lines 484--484 [] \T1/cmtt/m/n/12 --ngpreds : [optional] how many predictor columns pe r marker[] Overfull \hbox (11.27701pt too wide) in paragraph at lines 485--485 [] \T1/cmtt/m/n/12 (default 1 = MLDOSE; else use 2 for MLP ROB)[] Overfull \hbox (97.7059pt too wide) in paragraph at lines 486--486 [] \T1/cmtt/m/n/12 --separat : [optional] character to separate fields (default is space)[] Overfull \hbox (60.66495pt too wide) in paragraph at lines 489--489 [] \T1/cmtt/m/n/12 --allcov : report estimates for all covariates (lar ge outputs!)[] Overfull \hbox (295.25766pt too wide) in paragraph at lines 490--490 [] \T1/cmtt/m/n/12 --interaction: Which covariate to use for interactio n with SNP analysis (default is no interaction, 0)[] Overfull \hbox (387.86005pt too wide) in paragraph at lines 491--491 [] \T1/cmtt/m/n/12 --interaction_only: like previous but without covari ate acting in interaction with SNP (default is no interaction, 0)[] Overfull \hbox (758.26959pt too wide) in paragraph at lines 492--492 [] \T1/cmtt/m/n/12 --mmscore : score test in samples of related individ uals. File with inverse of variance-covariance matrix (for palinear) or inverse correlation (for palogist) as input parameter[] Overfull \hbox (122.39987pt too wide) in paragraph at lines 493--493 [] \T1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert- White) standard errors[] [10] LaTeX Warning: Reference `ssec:dosein' on page 11 undefined on input line 510. LaTeX Warning: Reference `ssec:phenoin' on page 11 undefined on input line 512. LaTeX Warning: Reference `ssec:infoin' on page 11 undefined on input line 514. Overfull \hbox (17.4505pt too wide) in paragraph at lines 519--519 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mldose -i gtdata/test.m linfo[] Overfull \hbox (29.79749pt too wide) in paragraph at lines 542--542 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob -i gtdata/test.m linfo \[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 552--552 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob.fvi -i gtdata/te st.mlinfo \[] [11] LaTeX Warning: Reference `sec:methodology' on page 12 undefined on input line 5 69. Overfull \hbox (42.14447pt too wide) in paragraph at lines 588--588 [] \T1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$e stimate)][] [12] [13] Overfull \hbox (4.6171pt too wide) in paragraph at lines 686--690 \T1/cmr/m/n/12 After in-stalling \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 you ca n find the \T1/cmtt/m/n/12 prepare_data.R \T1/cmr/m/n/12 file in the \T1/cmtt/m /n/12 scripts [14] [15] Overfull \hbox (8.33644pt too wide) in paragraph at lines 788--790 []\T1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse var iance-covariance [16] [17] LaTeX Warning: Reference `eq:expectation' on page 18 undefined on input line 88 4. LaTeX Warning: Reference `kinship' on page 18 undefined on input line 896. [18] [19] [20] No file ProbABEL_manual.ind. 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Rerun to get cross-references right. ) (see the transcript file for additional information) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1095.tfm. Output written on ectt1095.600gf (256 characters, 47796 bytes). Transcript written on ectt1095.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ectt1095.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1440.tfm. Output written on ectt1440.600gf (256 characters, 61024 bytes). Transcript written on ectt1440.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ectt1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1200 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) Font metrics written on ecbx1200.tfm. Output written on ecbx1200.600gf (256 characters, 59220 bytes). Transcript written on ecbx1200.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecbx1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1000 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1000.tfm. Output written on ectt1000.600gf (256 characters, 43832 bytes). Transcript written on ectt1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ectt1000.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1000 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.06586pt) Font metrics written on ecrm1000.tfm. Output written on ecrm1000.600gf (256 characters, 51184 bytes). Transcript written on ecrm1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecrm1000.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm0700 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm0700 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm0700.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) Font metrics written on ecrm0700.tfm. Output written on ecrm0700.600gf (256 characters, 37344 bytes). Transcript written on ecrm0700.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecrm0700.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm0800 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm0800 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm0800.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.06445pt) Font metrics written on ecrm0800.tfm. Output written on ecrm0800.600gf (256 characters, 41732 bytes). Transcript written on ecrm0800.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecrm0800.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1440 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.10997pt) Font metrics written on ecbx1440.tfm. Output written on ecbx1440.600gf (256 characters, 70764 bytes). Transcript written on ecbx1440.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecbx1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1728 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1728 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1728.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1728.tfm. Output written on ectt1728.600gf (256 characters, 72884 bytes). Transcript written on ectt1728.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ectt1728.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1200 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1200.tfm. Output written on ectt1200.600gf (256 characters, 51736 bytes). Transcript written on ectt1200.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ectt1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1200 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07143pt) Font metrics written on ecrm1200.tfm. Output written on ecrm1200.600gf (256 characters, 60320 bytes). Transcript written on ecrm1200.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecrm1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1728 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1728 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1728.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.13197pt) Font metrics written on ecbx1728.tfm. Output written on ecbx1728.600gf (256 characters, 84848 bytes). Transcript written on ecbx1728.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecbx1728.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1095 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1095 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07599pt) Font metrics written on ecrm1095.tfm. Output written on ecrm1095.600gf (256 characters, 55424 bytes). Transcript written on ecrm1095.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecrm1095.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1440 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.08084pt) Font metrics written on ecrm1440.tfm. Output written on ecrm1440.600gf (256 characters, 71064 bytes). Transcript written on ecrm1440.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecrm1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecti1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecti1440 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecti1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecti.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/extextit.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exileast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilig.mf Ok [25] [26] [27] [28] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exitalp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exillett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exidigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exiligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07997pt) Font metrics written on ecti1440.tfm. Output written on ecti1440.600gf (256 characters, 74296 bytes). Transcript written on ecti1440.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecti1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm2074 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm2074 This is METAFONT, Version 2.7182818 (TeX Live 2017/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm2074.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.1171pt) Font metrics written on ecrm2074.tfm. Output written on ecrm2074.600gf (256 characters, 101464 bytes). Transcript written on ecrm2074.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/ecrm2074.600pk: successfully generated. Output written on ProbABEL_manual.pdf (21 pages, 372483 bytes). Transcript written on ProbABEL_manual.log. diff: .btmp: No such file or directory === Making PDF === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ProbABEL_manual.tex LaTeX2e <2017-04-15> Babel <3.11> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/svgnam.def)) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) (/usr/share/texlive/texmf-dist/tex/latex/titleref/titleref.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (./ProbABEL_manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd ) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./ProbABEL_manual.out) (./ProbABEL_manual.out) Overfull \hbox (7.08261pt too wide) in paragraph at lines 82--82 [][] (./ProbABEL_manual.toc (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (7.36137pt too wide) in paragraph at lines 166--169 \T1/cmr/m/n/12 Prob-A-BEL web page ([][]$\T1/cmtt/m/n/12 http : / / www . genab el . org / packages / ProbABEL$[][]\T1/cmr/m/n/12 ). [3] [4] [5] Overfull \hbox (4.73831pt too wide) in paragraph at lines 275--279 []\T1/cmr/m/n/12 If all went well you will find the ex-e-cutable pro-grams (\T1 /cmtt/m/n/12 palinear\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/12 , Overfull \hbox (1.38382pt too wide) in paragraph at lines 281--286 \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 takes three files as in-put: a file con -tain-ing SNP in-for-ma-tion (e.g. the [6] [7] Overfull \hbox (12.56972pt too wide) in paragraph at lines 384--391 []\T1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \ T1/cmtt/m/n/12 palinear \T1/cmr/m/n/12 and \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/ 12 , Overfull \hbox (14.44846pt too wide) in paragraph at lines 384--391 \T1/cmr/m/n/12 lin-ear re-gres-sion anal-y-sis fol-low here (also to be found i n \T1/cmtt/m/n/12 examples/height.txt\T1/cmr/m/n/12 ) [8] [9] [10] Overfull \hbox (5.0841pt too wide) in paragraph at lines 461--465 []\T1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-ify to the \T1/cmtt/m/n/12 ProbABEL Overfull \hbox (5.10352pt too wide) in paragraph at lines 468--468 []\T1/cmtt/m/n/12 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, E MCR[] Overfull \hbox (23.624pt too wide) in paragraph at lines 479--479 [] \T1/cmtt/m/n/12 --chrom : [optional] chromosome (to be passed to o utput)[] Overfull \hbox (103.8794pt too wide) in paragraph at lines 480--480 [] \T1/cmtt/m/n/12 --out : [optional] output file name (default is regression.out.txt)[] Overfull \hbox (60.66495pt too wide) in paragraph at lines 481--481 [] \T1/cmtt/m/n/12 --skipd : [optional] how many columns to skip in t he predictor[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 483--483 [] \T1/cmtt/m/n/12 --ntraits : [optional] how many traits are analysed (default 1)[] Overfull \hbox (35.97098pt too wide) in paragraph at lines 484--484 [] \T1/cmtt/m/n/12 --ngpreds : [optional] how many predictor columns pe r marker[] Overfull \hbox (11.27701pt too wide) in paragraph at lines 485--485 [] \T1/cmtt/m/n/12 (default 1 = MLDOSE; else use 2 for MLP ROB)[] Overfull \hbox (97.7059pt too wide) in paragraph at lines 486--486 [] \T1/cmtt/m/n/12 --separat : [optional] character to separate fields (default is space)[] Overfull \hbox (60.66495pt too wide) in paragraph at lines 489--489 [] \T1/cmtt/m/n/12 --allcov : report estimates for all covariates (lar ge outputs!)[] Overfull \hbox (295.25766pt too wide) in paragraph at lines 490--490 [] \T1/cmtt/m/n/12 --interaction: Which covariate to use for interactio n with SNP analysis (default is no interaction, 0)[] Overfull \hbox (387.86005pt too wide) in paragraph at lines 491--491 [] \T1/cmtt/m/n/12 --interaction_only: like previous but without covari ate acting in interaction with SNP (default is no interaction, 0)[] Overfull \hbox (758.26959pt too wide) in paragraph at lines 492--492 [] \T1/cmtt/m/n/12 --mmscore : score test in samples of related individ uals. File with inverse of variance-covariance matrix (for palinear) or inverse correlation (for palogist) as input parameter[] Overfull \hbox (122.39987pt too wide) in paragraph at lines 493--493 [] \T1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert- White) standard errors[] [11] Overfull \hbox (17.4505pt too wide) in paragraph at lines 519--519 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mldose -i gtdata/test.m linfo[] Overfull \hbox (29.79749pt too wide) in paragraph at lines 542--542 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob -i gtdata/test.m linfo \[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 552--552 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob.fvi -i gtdata/te st.mlinfo \[] [12] Overfull \hbox (42.14447pt too wide) in paragraph at lines 588--588 [] \T1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$e stimate)][] [13] [14] Overfull \hbox (4.6171pt too wide) in paragraph at lines 686--690 \T1/cmr/m/n/12 After in-stalling \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 you ca n find the \T1/cmtt/m/n/12 prepare_data.R \T1/cmr/m/n/12 file in the \T1/cmtt/m /n/12 scripts [15] [16] Overfull \hbox (8.33644pt too wide) in paragraph at lines 788--790 []\T1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse var iance-covariance [17] [18] [19] [20] [21] No file ProbABEL_manual.ind. [22] (./ProbABEL_manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (22 pages, 378320 bytes). Transcript written on ProbABEL_manual.log. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ** Re-running LaTeX ** This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ProbABEL_manual.tex LaTeX2e <2017-04-15> Babel <3.11> and hyphenation patterns for 3 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (./ProbABEL_manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd ) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./ProbABEL_manual.out) (./ProbABEL_manual.out) Overfull \hbox (7.08261pt too wide) in paragraph at lines 82--82 [][] (./ProbABEL_manual.toc (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (7.36137pt too wide) in paragraph at lines 166--169 \T1/cmr/m/n/12 Prob-A-BEL web page ([][]$\T1/cmtt/m/n/12 http : / / www . genab el . org / packages / ProbABEL$[][]\T1/cmr/m/n/12 ). [3] [4] [5] Overfull \hbox (4.73831pt too wide) in paragraph at lines 275--279 []\T1/cmr/m/n/12 If all went well you will find the ex-e-cutable pro-grams (\T1 /cmtt/m/n/12 palinear\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/12 , Overfull \hbox (1.38382pt too wide) in paragraph at lines 281--286 \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 takes three files as in-put: a file con -tain-ing SNP in-for-ma-tion (e.g. the [6] [7] Overfull \hbox (12.56972pt too wide) in paragraph at lines 384--391 []\T1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \ T1/cmtt/m/n/12 palinear \T1/cmr/m/n/12 and \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/ 12 , Overfull \hbox (14.44846pt too wide) in paragraph at lines 384--391 \T1/cmr/m/n/12 lin-ear re-gres-sion anal-y-sis fol-low here (also to be found i n \T1/cmtt/m/n/12 examples/height.txt\T1/cmr/m/n/12 ) [8] [9] [10] Overfull \hbox (5.0841pt too wide) in paragraph at lines 461--465 []\T1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-ify to the \T1/cmtt/m/n/12 ProbABEL Overfull \hbox (5.10352pt too wide) in paragraph at lines 468--468 []\T1/cmtt/m/n/12 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, E MCR[] Overfull \hbox (23.624pt too wide) in paragraph at lines 479--479 [] \T1/cmtt/m/n/12 --chrom : [optional] chromosome (to be passed to o utput)[] Overfull \hbox (103.8794pt too wide) in paragraph at lines 480--480 [] \T1/cmtt/m/n/12 --out : [optional] output file name (default is regression.out.txt)[] Overfull \hbox (60.66495pt too wide) in paragraph at lines 481--481 [] \T1/cmtt/m/n/12 --skipd : [optional] how many columns to skip in t he predictor[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 483--483 [] \T1/cmtt/m/n/12 --ntraits : [optional] how many traits are analysed (default 1)[] Overfull \hbox (35.97098pt too wide) in paragraph at lines 484--484 [] \T1/cmtt/m/n/12 --ngpreds : [optional] how many predictor columns pe r marker[] Overfull \hbox (11.27701pt too wide) in paragraph at lines 485--485 [] \T1/cmtt/m/n/12 (default 1 = MLDOSE; else use 2 for MLP ROB)[] Overfull \hbox (97.7059pt too wide) in paragraph at lines 486--486 [] \T1/cmtt/m/n/12 --separat : [optional] character to separate fields (default is space)[] Overfull \hbox (60.66495pt too wide) in paragraph at lines 489--489 [] \T1/cmtt/m/n/12 --allcov : report estimates for all covariates (lar ge outputs!)[] Overfull \hbox (295.25766pt too wide) in paragraph at lines 490--490 [] \T1/cmtt/m/n/12 --interaction: Which covariate to use for interactio n with SNP analysis (default is no interaction, 0)[] Overfull \hbox (387.86005pt too wide) in paragraph at lines 491--491 [] \T1/cmtt/m/n/12 --interaction_only: like previous but without covari ate acting in interaction with SNP (default is no interaction, 0)[] Overfull \hbox (758.26959pt too wide) in paragraph at lines 492--492 [] \T1/cmtt/m/n/12 --mmscore : score test in samples of related individ uals. File with inverse of variance-covariance matrix (for palinear) or inverse correlation (for palogist) as input parameter[] Overfull \hbox (122.39987pt too wide) in paragraph at lines 493--493 [] \T1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert- White) standard errors[] [11] Overfull \hbox (17.4505pt too wide) in paragraph at lines 519--519 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mldose -i gtdata/test.m linfo[] Overfull \hbox (29.79749pt too wide) in paragraph at lines 542--542 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob -i gtdata/test.m linfo \[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 552--552 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob.fvi -i gtdata/te st.mlinfo \[] [12] Overfull \hbox (42.14447pt too wide) in paragraph at lines 588--588 [] \T1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$e stimate)][] [13] [14] Overfull \hbox (4.6171pt too wide) in paragraph at lines 686--690 \T1/cmr/m/n/12 After in-stalling \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 you ca n find the \T1/cmtt/m/n/12 prepare_data.R \T1/cmr/m/n/12 file in the \T1/cmtt/m /n/12 scripts [15] [16] Overfull \hbox (8.33644pt too wide) in paragraph at lines 788--790 []\T1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse var iance-covariance [17] [18] [19] [20] [21] No file ProbABEL_manual.ind. [22] (./ProbABEL_manual.aux) ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (22 pages, 378344 bytes). Transcript written on ProbABEL_manual.log. === Making index === makeindex ProbABEL_manual This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning input file ProbABEL_manual.idx....done (3 entries accepted, 0 rejected). Sorting entries....done (4 comparisons). Generating output file ProbABEL_manual.ind....done (14 lines written, 0 warnings). Output written in ProbABEL_manual.ind. Transcript written in ProbABEL_manual.ilg. === Making final PDF === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ProbABEL_manual.tex LaTeX2e <2017-04-15> Babel <3.11> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/svgnam.def)) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) (/usr/share/texlive/texmf-dist/tex/latex/titleref/titleref.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (./ProbABEL_manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd ) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./ProbABEL_manual.out) (./ProbABEL_manual.out) Overfull \hbox (7.08261pt too wide) in paragraph at lines 82--82 [][] (./ProbABEL_manual.toc (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (7.36137pt too wide) in paragraph at lines 166--169 \T1/cmr/m/n/12 Prob-A-BEL web page ([][]$\T1/cmtt/m/n/12 http : / / www . genab el . org / packages / ProbABEL$[][]\T1/cmr/m/n/12 ). [3] [4] [5] Overfull \hbox (4.73831pt too wide) in paragraph at lines 275--279 []\T1/cmr/m/n/12 If all went well you will find the ex-e-cutable pro-grams (\T1 /cmtt/m/n/12 palinear\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/12 , Overfull \hbox (1.38382pt too wide) in paragraph at lines 281--286 \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 takes three files as in-put: a file con -tain-ing SNP in-for-ma-tion (e.g. the [6] [7] Overfull \hbox (12.56972pt too wide) in paragraph at lines 384--391 []\T1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \ T1/cmtt/m/n/12 palinear \T1/cmr/m/n/12 and \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/ 12 , Overfull \hbox (14.44846pt too wide) in paragraph at lines 384--391 \T1/cmr/m/n/12 lin-ear re-gres-sion anal-y-sis fol-low here (also to be found i n \T1/cmtt/m/n/12 examples/height.txt\T1/cmr/m/n/12 ) [8] [9] [10] Overfull \hbox (5.0841pt too wide) in paragraph at lines 461--465 []\T1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-ify to the \T1/cmtt/m/n/12 ProbABEL Overfull \hbox (5.10352pt too wide) in paragraph at lines 468--468 []\T1/cmtt/m/n/12 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, E MCR[] Overfull \hbox (23.624pt too wide) in paragraph at lines 479--479 [] \T1/cmtt/m/n/12 --chrom : [optional] chromosome (to be passed to o utput)[] Overfull \hbox (103.8794pt too wide) in paragraph at lines 480--480 [] \T1/cmtt/m/n/12 --out : [optional] output file name (default is regression.out.txt)[] Overfull \hbox (60.66495pt too wide) in paragraph at lines 481--481 [] \T1/cmtt/m/n/12 --skipd : [optional] how many columns to skip in t he predictor[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 483--483 [] \T1/cmtt/m/n/12 --ntraits : [optional] how many traits are analysed (default 1)[] Overfull \hbox (35.97098pt too wide) in paragraph at lines 484--484 [] \T1/cmtt/m/n/12 --ngpreds : [optional] how many predictor columns pe r marker[] Overfull \hbox (11.27701pt too wide) in paragraph at lines 485--485 [] \T1/cmtt/m/n/12 (default 1 = MLDOSE; else use 2 for MLP ROB)[] Overfull \hbox (97.7059pt too wide) in paragraph at lines 486--486 [] \T1/cmtt/m/n/12 --separat : [optional] character to separate fields (default is space)[] Overfull \hbox (60.66495pt too wide) in paragraph at lines 489--489 [] \T1/cmtt/m/n/12 --allcov : report estimates for all covariates (lar ge outputs!)[] Overfull \hbox (295.25766pt too wide) in paragraph at lines 490--490 [] \T1/cmtt/m/n/12 --interaction: Which covariate to use for interactio n with SNP analysis (default is no interaction, 0)[] Overfull \hbox (387.86005pt too wide) in paragraph at lines 491--491 [] \T1/cmtt/m/n/12 --interaction_only: like previous but without covari ate acting in interaction with SNP (default is no interaction, 0)[] Overfull \hbox (758.26959pt too wide) in paragraph at lines 492--492 [] \T1/cmtt/m/n/12 --mmscore : score test in samples of related individ uals. File with inverse of variance-covariance matrix (for palinear) or inverse correlation (for palogist) as input parameter[] Overfull \hbox (122.39987pt too wide) in paragraph at lines 493--493 [] \T1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert- White) standard errors[] [11] Overfull \hbox (17.4505pt too wide) in paragraph at lines 519--519 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mldose -i gtdata/test.m linfo[] Overfull \hbox (29.79749pt too wide) in paragraph at lines 542--542 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob -i gtdata/test.m linfo \[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 552--552 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob.fvi -i gtdata/te st.mlinfo \[] [12] Overfull \hbox (42.14447pt too wide) in paragraph at lines 588--588 [] \T1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$e stimate)][] [13] [14] Overfull \hbox (4.6171pt too wide) in paragraph at lines 686--690 \T1/cmr/m/n/12 After in-stalling \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 you ca n find the \T1/cmtt/m/n/12 prepare_data.R \T1/cmr/m/n/12 file in the \T1/cmtt/m /n/12 scripts [15] [16] Overfull \hbox (8.33644pt too wide) in paragraph at lines 788--790 []\T1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse var iance-covariance [17] [18] [19] [20] [21] (./ProbABEL_manual.ind [22] [23]) (./ProbABEL_manual.aux) ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (23 pages, 379489 bytes). Transcript written on ProbABEL_manual.log. rm ProbABEL_manual.aux make[2]: Leaving directory '/<>/doc' Making all in checks make[2]: Entering directory '/<>/checks' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/checks' Making all in examples make[2]: Entering directory '/<>/examples' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/examples' Making all in checks/R-tests make[2]: Entering directory '/<>/checks/R-tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/checks/R-tests' make[2]: Entering directory '/<>' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/<>' Making check in src make[2]: Entering directory '/<>/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/src' Making check in doc make[2]: Entering directory '/<>/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/doc' Making check in checks make[2]: Entering directory '/<>/checks' make check_probabel_chunk.sh check_dose_input.sh test_qt.sh test_mms.sh test_bt.sh test_cox.sh test_cox_nocovar.sh make[3]: Entering directory '/<>/checks' make[3]: Nothing to be done for 'check_probabel_chunk.sh'. make[3]: Nothing to be done for 'check_dose_input.sh'. make[3]: Nothing to be done for 'test_qt.sh'. make[3]: Nothing to be done for 'test_mms.sh'. make[3]: Nothing to be done for 'test_bt.sh'. make[3]: Nothing to be done for 'test_cox.sh'. make[3]: Nothing to be done for 'test_cox_nocovar.sh'. make[3]: Leaving directory '/<>/checks' make check-TESTS make[3]: Entering directory '/<>/checks' make[4]: Entering directory '/<>/checks' FAIL: test_qt.sh PASS: check_dose_input.sh FAIL: test_bt.sh FAIL: test_cox.sh FAIL: test_cox_nocovar.sh PASS: check_probabel_chunk.sh FAIL: test_mms.sh =========================================== ProbABEL 0.4.5: checks/test-suite.log =========================================== # TOTAL: 7 # PASS: 2 # SKIP: 0 # XFAIL: 0 # FAIL: 5 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 FAIL: test_qt.sh ================ Analysing QT... base analysis file contains data of unknown type 1280 diff: linear_base_fv_add.out.txt: No such file or directory QT check: dose vs. dose_fv FAILED FAIL test_qt.sh (exit status: 1) FAIL: test_mms.sh ================= Analysis using MMScore... file contains data of unknown type 1280 diff: mmscore_dose_fv_add.out.txt: No such file or directory mmscore check: dose vs. dose_fv FAILED FAIL test_mms.sh (exit status: 1) FAIL: test_bt.sh ================ Analysing BT... file contains data of unknown type 1280 diff: logist_fv_add.out.txt: No such file or directory BT check: dose vs. dose_fv FAILED FAIL test_bt.sh (exit status: 1) FAIL: test_cox.sh ================= Analysing Cox model... Warning for rs3174230: beta may be infinite, setting beta and se to 'NaN' file contains data of unknown type 1280 diff: coxph_dose_fv_add.out.txt: No such file or directory pacoxph check: dose vs. dose_fv FAILED FAIL test_cox.sh (exit status: 1) FAIL: test_cox_nocovar.sh ========================= Analysing Cox model without covariates... Warning for rs3174230: beta may be infinite, setting beta and se to 'NaN' file contains data of unknown type 1280 diff: coxph_dose_nocovar_fv_add.out.txt: No such file or directory pacoxph check: dose vs. dose_fv FAILED FAIL test_cox_nocovar.sh (exit status: 1) ============================================================================ Testsuite summary for ProbABEL 0.4.5 ============================================================================ # TOTAL: 7 # PASS: 2 # SKIP: 0 # XFAIL: 0 # FAIL: 5 # XPASS: 0 # ERROR: 0 ============================================================================ See checks/test-suite.log Please report to genabel-devel@r-forge.wu-wien.ac.at ============================================================================ Makefile:623: recipe for target 'test-suite.log' failed make[4]: *** [test-suite.log] Error 1 make[4]: Leaving directory '/<>/checks' Makefile:729: recipe for target 'check-TESTS' failed make[3]: *** [check-TESTS] Error 2 make[3]: Leaving directory '/<>/checks' Makefile:844: recipe for target 'check-am' failed make[2]: *** [check-am] Error 2 make[2]: Leaving directory '/<>/checks' Makefile:345: recipe for target 'check-recursive' failed make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: make -j4 check VERBOSE=1 returned exit code 2 debian/rules:20: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20170708-0402 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 97060 Build-Time: 36 Distribution: artful Fail-Stage: build Host Architecture: s390x Install-Time: 103 Job: probabel_0.4.5-4.dsc Machine Architecture: s390x Package: probabel Package-Time: 140 Source-Version: 0.4.5-4 Space: 97060 Status: attempted Version: 0.4.5-4 -------------------------------------------------------------------------------- Finished at 20170708-0402 Build needed 00:02:20, 97060k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12925704'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12925704/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12925704'] Unmounting chroot for build PACKAGEBUILD-12925704... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12925704'] Removing build PACKAGEBUILD-12925704