Thu Jun 25 05:38:28 UTC 2020 I: starting to build gbrowse/buster/armhf on jenkins on '2020-06-25 05:38' Thu Jun 25 05:38:28 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_36/680/console.log Thu Jun 25 05:38:28 UTC 2020 I: Downloading source for buster/gbrowse=2.56+dfsg-4 --2020-06-25 05:38:28-- http://deb.debian.org/debian/pool/main/g/gbrowse/gbrowse_2.56+dfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2660 (2.6K) Saving to: ‘gbrowse_2.56+dfsg-4.dsc’ 0K .. 100% 25.4M=0s 2020-06-25 05:38:28 (25.4 MB/s) - ‘gbrowse_2.56+dfsg-4.dsc’ saved [2660/2660] Thu Jun 25 05:38:28 UTC 2020 I: gbrowse_2.56+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: gbrowse Binary: gbrowse, gbrowse-data, gbrowse-calign Architecture: any all Version: 2.56+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Charles Plessy , Aaron M. Ucko , Andreas Tille Homepage: http://www.gbrowse.org/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/gbrowse Vcs-Git: https://salsa.debian.org/med-team/gbrowse.git Testsuite: autopkgtest-pkg-perl Build-Depends: bioperl, debhelper (>= 11~), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl (>= 2.31), libbio-coordinate-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl | perl (<< 5.19), rename Package-List: gbrowse deb science optional arch=all gbrowse-calign deb science optional arch=any gbrowse-data deb science optional arch=all Checksums-Sha1: 269fba6b75112b0a2037350308914f05d4747697 4355977 gbrowse_2.56+dfsg.orig.tar.gz 2e5609c7118e45f2b09df5e3abe6e29b7758f9d3 23552 gbrowse_2.56+dfsg-4.debian.tar.xz Checksums-Sha256: f6da1ff315b17ec260810cf439a54ae7ddd66728015be03f7fbb6ba795676f81 4355977 gbrowse_2.56+dfsg.orig.tar.gz d4ebd45592d21df182e14e6bac9a33c40a903a4b6db5a71ef87f954f33c97634 23552 gbrowse_2.56+dfsg-4.debian.tar.xz Files: 9638dd3e43897548172911706277f177 4355977 gbrowse_2.56+dfsg.orig.tar.gz 911babbfb6363e0692d4901a1075b795 23552 gbrowse_2.56+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlu0xN0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFMMRAAhFko01GfyRDZpKikmSHVekT/XVFtRJgh gS7NeHU22EEX6ToDOblK8Il1uyeObYrM40oRdeYAE/7kFkK06TQ+xKutkGU5rU0c 04n4KEMIsOrJxboTkqZw7Rh6KTVrP8ERn9iBmaEDkIQqmJgcr0A6ANtY2LMG1Kgu K5MgtgZUOeg29oMF9Dud5ddqWKVF2od6T3+zuP8lcy194TrJG6H7R4VpvuqIeAD6 Ul65N9sJrSMptEKEpUcJPEFnZ8gXvV1/An5nq7aTSy0cs07Cq4+zfS6EC3NPvewI rHOHSEmjB32TD4DUK3wvDJ3Z+ngfsXAtxWcbSQXf85twzsx9F3ojl4EzbraELKOM KJO0vDuFpEyankIQWBlKMc5V04X97P2PGhPuddPfiSys8hFYDmd52BZM8GRhPwEP uP58UfGMoysXWqe+2HVhlGYCURE3SjWmnKKfZdkN9x8CLzKMMwTbR94ak5s65Z0l uiKPvnpVxPX9kD+Nve5SvqxBIC1SfGiDoaYFryHXc94zbPaVXFZFKq22hjFUCD7g IUWGzaCfCO5GRk6DZ4f0RquMn6jSTEWu+NrtxaZ54pAXk1C8FX2vm2ihjb6DJDLV 7ggwVImlopVrTi7gGcNh2b3LgA6+irW0oPcm65eAUxEFatPOC+q+4UC1aGXBOUMH w8e4wnWV2Mc= =WWzD -----END PGP SIGNATURE----- Thu Jun 25 05:38:28 UTC 2020 I: Checking whether the package is not for us Thu Jun 25 05:38:28 UTC 2020 I: Starting 1st build on remote node p64c-armhf-rb.debian.net. Thu Jun 25 05:38:28 UTC 2020 I: Preparing to do remote build '1' on p64c-armhf-rb.debian.net. Thu Jun 25 05:57:47 UTC 2020 I: Deleting $TMPDIR on p64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 24 17:38:40 -12 2020 I: pbuilder-time-stamp: 1593063520 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gbrowse_2.56+dfsg-4.dsc] I: copying [./gbrowse_2.56+dfsg.orig.tar.gz] I: copying [./gbrowse_2.56+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Oct 3 01:32:13 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gbrowse_2.56+dfsg-4.dsc dpkg-source: info: extracting gbrowse in gbrowse-2.56+dfsg dpkg-source: info: unpacking gbrowse_2.56+dfsg.orig.tar.gz dpkg-source: info: unpacking gbrowse_2.56+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian-packaging-patch dpkg-source: info: applying gbrowse-slave-fix_defaults_path dpkg-source: info: applying manpages.patch dpkg-source: info: applying fix_pop_url dpkg-source: info: applying skip_check_installed_test.patch dpkg-source: info: applying source_init_functions dpkg-source: info: applying init_script_dependency.patch dpkg-source: info: applying fix_runlevel.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying fix_whatis_entry.patch dpkg-source: info: applying remove_copy_of_LoadHelper.pm.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/18674/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='b9e13fca3ec04031b0f14bce629078ef' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='18674' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.WjUh08ONSq/pbuilderrc_GWxv --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WjUh08ONSq/b1 --logfile b1/build.log gbrowse_2.56+dfsg-4.dsc' SUDO_GID='115' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux p64c 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jun 23 20:30 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/18674/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bioperl, debhelper (>= 11~), dh-apache2, dh-exec, apache2-dev, libbio-graphics-perl (>= 2.31), libbio-coordinate-perl, libcapture-tiny-perl, libcgi-session-perl, libgd-gd2-perl | libgd-gd2-noxpm-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl, sqlite3, libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, libmodule-build-perl, libcgi-pm-perl | perl (<< 5.19), rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on bioperl; however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-apache2; however: Package dh-apache2 is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on apache2-dev; however: Package apache2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbio-graphics-perl (>= 2.31); however: Package libbio-graphics-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-coordinate-perl; however: Package libbio-coordinate-perl is not installed. pbuilder-satisfydepends-dummy depends on libcapture-tiny-perl; however: Package libcapture-tiny-perl is not installed. pbuilder-satisfydepends-dummy depends on libcgi-session-perl; however: Package libcgi-session-perl is not installed. pbuilder-satisfydepends-dummy depends on libgd-gd2-perl | libgd-gd2-noxpm-perl; however: Package libgd-gd2-perl is not installed. Package libgd-gd2-noxpm-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on libjson-perl; however: Package libjson-perl is not installed. pbuilder-satisfydepends-dummy depends on libstatistics-descriptive-perl; however: Package libstatistics-descriptive-perl is not installed. pbuilder-satisfydepends-dummy depends on libwww-perl; however: Package libwww-perl is not installed. pbuilder-satisfydepends-dummy depends on libhttp-daemon-perl; however: Package libhttp-daemon-perl is not installed. pbuilder-satisfydepends-dummy depends on sqlite3; however: Package sqlite3 is not installed. pbuilder-satisfydepends-dummy depends on libdbd-sqlite3-perl; however: Package libdbd-sqlite3-perl is not installed. pbuilder-satisfydepends-dummy depends on libterm-readkey-perl; however: Package libterm-readkey-perl is not installed. pbuilder-satisfydepends-dummy depends on libjs-prototype; however: Package libjs-prototype is not installed. pbuilder-satisfydepends-dummy depends on libjs-scriptaculous; however: Package libjs-scriptaculous is not installed. pbuilder-satisfydepends-dummy depends on libvm-ec2-perl; however: Package libvm-ec2-perl is not installed. pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however: Package libmodule-build-perl is not installed. pbuilder-satisfydepends-dummy depends on libcgi-pm-perl | perl (<< 5.19); however: Package libcgi-pm-perl is not installed. Version of perl on system is 5.28.1-6. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: apache2-dev{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bioperl{a} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-diff-perl{a} libanyevent-cachedns-perl{a} libanyevent-http-perl{a} libanyevent-perl{a} libapr1{a} libapr1-dev{a} libaprutil1{a} libaprutil1-dev{a} libarchive-zip-perl{a} libbio-coordinate-perl{a} libbio-graphics-perl{a} libbio-perl-perl{a} libbsd0{a} libcapture-tiny-perl{a} libcgi-pm-perl{a} libcgi-session-perl{a} libclass-data-inheritable-perl{a} libcommon-sense-perl{a} libcroco3{a} libdata-stag-perl{a} libdbd-sqlite3-perl{a} libdbi-perl{a} libdevel-stacktrace-perl{a} libelf1{a} libencode-locale-perl{a} libexception-class-perl{a} libexpat1{a} libexpat1-dev{a} libexporter-tiny-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgd-perl{a} libgd3{a} libglib2.0-0{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-daemon-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu63{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libjbig0{a} libjpeg62-turbo{a} libjs-prototype{a} libjs-scriptaculous{a} libjson-perl{a} libldap-2.4-2{a} libldap-common{a} libldap2-dev{a} liblist-moreutils-perl{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmodule-build-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libpipeline1{a} libpng16-16{a} libreadline7{a} libsasl2-2{a} libsasl2-modules-db{a} libsctp-dev{a} libsctp1{a} libsigsegv2{a} libssl1.1{a} libstatistics-descriptive-perl{a} libstring-approx-perl{a} libsub-uplevel-perl{a} libterm-readkey-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtiff5{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvm-ec2-perl{a} libwebp6{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml2{a} libxpm4{a} m4{a} man-db{a} netbase{a} openssl{a} perl-openssl-defaults{a} po-debconf{a} readline-common{a} rename{a} sensible-utils{a} sqlite3{a} ucf{a} uuid-dev{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl javascript-common libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libasync-interrupt-perl libberkeleydb-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libbio-scf-perl libcache-cache-perl libcgi-fast-perl libclone-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libev-perl libevent-perl libfreezethaw-perl libgd-svg-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libguard-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libjson-xs-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libpod-readme-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libxml-dom-xpath-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-expat-perl libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk shared-mime-info wget xdg-user-dirs 0 packages upgraded, 138 newly installed, 0 to remove and 0 not upgraded. Need to get 40.3 MB of archives. After unpacking 132 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf netbase all 5.6 [19.4 kB] Get: 8 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 9 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 10 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 12 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 13 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 14 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 17 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 18 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 19 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 20 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 25 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 27 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 33 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 34 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 35 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 36 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libapr1 armhf 1.6.5-1+b1 [85.0 kB] Get: 38 http://deb.debian.org/debian buster/main armhf uuid-dev armhf 2.33.1-0.1 [92.6 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libsctp1 armhf 1.0.18+dfsg-1 [27.6 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libsctp-dev armhf 1.0.18+dfsg-1 [81.0 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libapr1-dev armhf 1.6.5-1+b1 [691 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libaprutil1 armhf 1.6.1-4 [84.6 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libldap2-dev armhf 2.4.47+dfsg-3+deb10u2 [314 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libexpat1-dev armhf 2.2.6-2+deb10u1 [126 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libaprutil1-dev armhf 1.6.1-4 [401 kB] Get: 52 http://deb.debian.org/debian buster/main armhf openssl armhf 1.1.1d-0+deb10u3 [818 kB] Get: 53 http://deb.debian.org/debian buster/main armhf apache2-dev armhf 2.4.38-3+deb10u3 [331 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libio-string-perl all 1.08-3 [12.3 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libdata-stag-perl all 0.14-2 [448 kB] Get: 56 http://deb.debian.org/debian buster/main armhf libbio-perl-perl all 1.7.2-3 [4553 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 58 http://deb.debian.org/debian buster/main armhf libdevel-stacktrace-perl all 2.0300-1 [28.0 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libexception-class-perl all 1.44-1 [32.3 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libtest-deep-perl all 1.128-1 [48.8 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libalgorithm-diff-perl all 1.19.03-2 [47.9 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libtext-diff-perl all 1.45-1 [27.7 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libtest-differences-perl all 0.65-1 [18.1 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libsub-uplevel-perl all 0.2800-1 [16.3 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libtest-exception-perl all 0.43-1 [18.7 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libtest-warn-perl all 0.36-1 [16.2 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libtest-most-perl all 0.35-1 [24.5 kB] Get: 69 http://deb.debian.org/debian buster/main armhf bioperl all 1.7.2-3 [418 kB] Get: 70 http://deb.debian.org/debian buster/main armhf ca-certificates all 20190110 [157 kB] Get: 71 http://deb.debian.org/debian buster/main armhf dh-exec armhf 0.23.1 [24.9 kB] Get: 72 http://deb.debian.org/debian buster/main armhf fonts-dejavu-core all 2.37-1 [1068 kB] Get: 73 http://deb.debian.org/debian buster/main armhf fontconfig-config all 2.13.1-2 [280 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libanyevent-perl armhf 7.140-3 [393 kB] Get: 75 http://deb.debian.org/debian buster/main armhf libanyevent-cachedns-perl all 0.08-2 [7150 B] Get: 76 http://deb.debian.org/debian buster/main armhf libcommon-sense-perl armhf 3.74-2+b7 [24.0 kB] Get: 77 http://deb.debian.org/debian buster/main armhf libanyevent-http-perl all 2.24-1 [35.5 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libbio-coordinate-perl all 1.7.1-3 [56.0 kB] Get: 79 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 80 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libfontconfig1 armhf 2.13.1-2 [328 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [112 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libjbig0 armhf 2.1-3.1+b2 [28.4 kB] Get: 84 http://deb.debian.org/debian buster/main armhf libwebp6 armhf 0.6.1-2 [229 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libtiff5 armhf 4.1.0+git191117-2~deb10u1 [252 kB] Get: 86 http://deb.debian.org/debian buster/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB] Get: 87 http://deb.debian.org/debian buster/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libxcb1 armhf 1.13.1-2 [132 kB] Get: 89 http://deb.debian.org/debian buster/main armhf libx11-data all 2:1.6.7-1 [298 kB] Get: 90 http://deb.debian.org/debian buster/main armhf libx11-6 armhf 2:1.6.7-1 [698 kB] Get: 91 http://deb.debian.org/debian buster/main armhf libxpm4 armhf 1:3.5.12-1 [44.0 kB] Get: 92 http://deb.debian.org/debian buster/main armhf libgd3 armhf 2.2.5-5.2 [117 kB] Get: 93 http://deb.debian.org/debian buster/main armhf libgd-perl armhf 2.71-2 [134 kB] Get: 94 http://deb.debian.org/debian buster/main armhf libbio-graphics-perl all 2.40-3 [610 kB] Get: 95 http://deb.debian.org/debian buster/main armhf libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 96 http://deb.debian.org/debian buster/main armhf liburi-perl all 1.76-1 [89.9 kB] Get: 97 http://deb.debian.org/debian buster/main armhf libhtml-parser-perl armhf 3.72-3+b3 [102 kB] Get: 98 http://deb.debian.org/debian buster/main armhf libcgi-pm-perl all 4.40-1 [222 kB] Get: 99 http://deb.debian.org/debian buster/main armhf libcgi-session-perl all 4.48-3 [119 kB] Get: 100 http://deb.debian.org/debian buster/main armhf libdbi-perl armhf 1.642-1+b1 [768 kB] Get: 101 http://deb.debian.org/debian buster/main armhf libdbd-sqlite3-perl armhf 1.62-3 [170 kB] Get: 102 http://deb.debian.org/debian buster/main armhf libencode-locale-perl all 1.05-1 [13.7 kB] Get: 103 http://deb.debian.org/debian buster/main armhf libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get: 104 http://deb.debian.org/debian buster/main armhf libtimedate-perl all 2.3000-2+deb10u1 [38.1 kB] Get: 105 http://deb.debian.org/debian buster/main armhf libhttp-date-perl all 6.02-1 [10.7 kB] Get: 106 http://deb.debian.org/debian buster/main armhf libfile-listing-perl all 6.04-1 [10.3 kB] Get: 107 http://deb.debian.org/debian buster/main armhf libhtml-tree-perl all 5.07-2 [213 kB] Get: 108 http://deb.debian.org/debian buster/main armhf libio-html-perl all 1.001-1 [17.6 kB] Get: 109 http://deb.debian.org/debian buster/main armhf liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get: 110 http://deb.debian.org/debian buster/main armhf libhttp-message-perl all 6.18-1 [77.8 kB] Get: 111 http://deb.debian.org/debian buster/main armhf libhttp-cookies-perl all 6.04-1 [17.8 kB] Get: 112 http://deb.debian.org/debian buster/main armhf libhttp-daemon-perl all 6.01-3 [16.6 kB] Get: 113 http://deb.debian.org/debian buster/main armhf libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 114 http://deb.debian.org/debian buster/main armhf perl-openssl-defaults armhf 3 [6782 B] Get: 115 http://deb.debian.org/debian buster/main armhf libnet-ssleay-perl armhf 1.85-2+b1 [288 kB] Get: 116 http://deb.debian.org/debian buster/main armhf libio-socket-ssl-perl all 2.060-3 [207 kB] Get: 117 http://deb.debian.org/debian buster/main armhf libjs-prototype all 1.7.1-3 [44.3 kB] Get: 118 http://deb.debian.org/debian buster/main armhf libjs-scriptaculous all 1.9.0-2 [129 kB] Get: 119 http://deb.debian.org/debian buster/main armhf libjson-perl all 4.02000-1 [88.8 kB] Get: 120 http://deb.debian.org/debian buster/main armhf liblist-moreutils-perl armhf 0.416-1+b4 [60.5 kB] Get: 121 http://deb.debian.org/debian buster/main armhf libnet-http-perl all 6.18-1 [24.5 kB] Get: 122 http://deb.debian.org/debian buster/main armhf libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 123 http://deb.debian.org/debian buster/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 124 http://deb.debian.org/debian buster/main armhf libwww-perl all 6.36-2 [188 kB] Get: 125 http://deb.debian.org/debian buster/main armhf liblwp-protocol-https-perl all 6.07-2 [9242 B] Get: 126 http://deb.debian.org/debian buster/main armhf libmodule-build-perl all 0.422400-1 [259 kB] Get: 127 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 128 http://deb.debian.org/debian buster/main armhf libstatistics-descriptive-perl all 3.0702-1 [64.8 kB] Get: 129 http://deb.debian.org/debian buster/main armhf libstring-approx-perl armhf 3.28-1+b1 [38.4 kB] Get: 130 http://deb.debian.org/debian buster/main armhf libterm-readkey-perl armhf 2.38-1 [26.3 kB] Get: 131 http://deb.debian.org/debian buster/main armhf libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get: 132 http://deb.debian.org/debian buster/main armhf libxml-sax-base-perl all 1.09-1 [20.4 kB] Get: 133 http://deb.debian.org/debian buster/main armhf libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get: 134 http://deb.debian.org/debian buster/main armhf libxml-libxml-perl armhf 2.0134+dfsg-1 [326 kB] Get: 135 http://deb.debian.org/debian buster/main armhf libxml-simple-perl all 2.25-1 [72.0 kB] Get: 136 http://deb.debian.org/debian buster/main armhf libvm-ec2-perl all 1.28-2 [768 kB] Get: 137 http://deb.debian.org/debian buster/main armhf rename all 1.10-1 [17.2 kB] Get: 138 http://deb.debian.org/debian buster/main armhf sqlite3 armhf 3.27.2-3 [810 kB] Fetched 40.3 MB in 11s (3652 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../002-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../004-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package netbase. Preparing to unpack .../006-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package readline-common. Preparing to unpack .../007-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../008-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../009-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../010-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../011-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../012-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../013-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../015-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package automake. Preparing to unpack .../018-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../019-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../023-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../024-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../025-libelf1_0.176-1.1_armhf.deb ... Unpacking libelf1:armhf (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../026-dwz_0.12-3_armhf.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../027-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../028-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../029-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../030-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../031-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../032-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../033-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../034-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../035-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libapr1:armhf. Preparing to unpack .../036-libapr1_1.6.5-1+b1_armhf.deb ... Unpacking libapr1:armhf (1.6.5-1+b1) ... Selecting previously unselected package uuid-dev:armhf. Preparing to unpack .../037-uuid-dev_2.33.1-0.1_armhf.deb ... Unpacking uuid-dev:armhf (2.33.1-0.1) ... Selecting previously unselected package libsctp1:armhf. Preparing to unpack .../038-libsctp1_1.0.18+dfsg-1_armhf.deb ... Unpacking libsctp1:armhf (1.0.18+dfsg-1) ... Selecting previously unselected package libsctp-dev:armhf. 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Selecting previously unselected package liblist-moreutils-perl. Preparing to unpack .../119-liblist-moreutils-perl_0.416-1+b4_armhf.deb ... Unpacking liblist-moreutils-perl (0.416-1+b4) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../120-libnet-http-perl_6.18-1_all.deb ... Unpacking libnet-http-perl (6.18-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../121-libtry-tiny-perl_0.30-1_all.deb ... Unpacking libtry-tiny-perl (0.30-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../122-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../123-libwww-perl_6.36-2_all.deb ... Unpacking libwww-perl (6.36-2) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../124-liblwp-protocol-https-perl_6.07-2_all.deb ... Unpacking liblwp-protocol-https-perl (6.07-2) ... Selecting previously unselected package libmodule-build-perl. Preparing to unpack .../125-libmodule-build-perl_0.422400-1_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.422400-1) ... Selecting previously unselected package libreadline7:armhf. Preparing to unpack .../126-libreadline7_7.0-5_armhf.deb ... Unpacking libreadline7:armhf (7.0-5) ... Selecting previously unselected package libstatistics-descriptive-perl. Preparing to unpack .../127-libstatistics-descriptive-perl_3.0702-1_all.deb ... Unpacking libstatistics-descriptive-perl (3.0702-1) ... Selecting previously unselected package libstring-approx-perl. Preparing to unpack .../128-libstring-approx-perl_3.28-1+b1_armhf.deb ... Unpacking libstring-approx-perl (3.28-1+b1) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../129-libterm-readkey-perl_2.38-1_armhf.deb ... Unpacking libterm-readkey-perl (2.38-1) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../130-libxml-namespacesupport-perl_1.12-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../131-libxml-sax-base-perl_1.09-1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../132-libxml-sax-perl_1.00+dfsg-1_all.deb ... Unpacking libxml-sax-perl (1.00+dfsg-1) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../133-libxml-libxml-perl_2.0134+dfsg-1_armhf.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../134-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libvm-ec2-perl. Preparing to unpack .../135-libvm-ec2-perl_1.28-2_all.deb ... Unpacking libvm-ec2-perl (1.28-2) ... Selecting previously unselected package rename. Preparing to unpack .../136-rename_1.10-1_all.deb ... Unpacking rename (1.10-1) ... Selecting previously unselected package sqlite3. Preparing to unpack .../137-sqlite3_3.27.2-3_armhf.deb ... Unpacking sqlite3 (3.27.2-3) ... Setting up libexpat1:armhf (2.2.6-2+deb10u1) ... Setting up libanyevent-perl (7.140-3) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libstring-approx-perl (3.28-1+b1) ... Setting up libxau6:armhf (1:1.0.8-1+b2) ... Setting up libtest-deep-perl (1.128-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libalgorithm-diff-perl (1.19.03-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up libapr1:armhf (1.6.5-1+b1) ... Setting up perl-openssl-defaults:armhf (3) ... Setting up libcommon-sense-perl (3.74-2+b7) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libanyevent-http-perl (2.24-1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up rename (1.10-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libjbig0:armhf (2.1-3.1+b2) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libmodule-build-perl (0.422400-1) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libexpat1-dev:armhf (2.2.6-2+deb10u1) ... Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up uuid-dev:armhf (2.33.1-0.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libanyevent-cachedns-perl (0.08-2) ... Setting up libpng16-16:armhf (1.6.36-6) ... Setting up libio-html-perl (1.001-1) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:armhf (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libjs-prototype (1.7.1-3) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3000-2+deb10u1) ... Setting up libsctp1:armhf (1.0.18+dfsg-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libjson-perl (4.02000-1) ... Setting up libsub-uplevel-perl (0.2800-1) ... Setting up netbase (5.6) ... Setting up libdevel-stacktrace-perl (2.0300-1) ... Setting up libtiff5:armhf (4.1.0+git191117-2~deb10u1) ... Setting up libbio-perl-perl (1.7.2-3) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libterm-readkey-perl (2.38-1) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up liburi-perl (1.76-1) ... Setting up libdbi-perl:armhf (1.642-1+b1) ... Setting up libreadline7:armhf (7.0-5) ... Setting up libaprutil1:armhf (1.6.1-4) ... Setting up libnet-ssleay-perl (1.85-2+b1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libxcb1:armhf (1.13.1-2) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libtool (2.4.6-9) ... Setting up libjs-scriptaculous (1.9.0-2) ... Setting up liblist-moreutils-perl (0.416-1+b4) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libtest-differences-perl (0.65-1) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up libnet-http-perl (6.18-1) ... Setting up m4 (1.4.18-2) ... Setting up libexception-class-perl (1.44-1) ... Setting up libldap2-dev:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libtest-exception-perl (0.43-1) ... Setting up libfreetype6:armhf (2.9.1-3+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up libsctp-dev:armhf (1.0.18+dfsg-1) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up libx11-6:armhf (2:1.6.7-1) ... Setting up libdbd-sqlite3-perl:armhf (1.62-3) ... Setting up sqlite3 (3.27.2-3) ... Setting up libio-socket-ssl-perl (2.060-3) ... Setting up libhttp-message-perl (6.18-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhttp-negotiate-perl (6.01-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libstatistics-descriptive-perl (3.0702-1) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up libhttp-cookies-perl (6.04-1) ... Setting up libtest-most-perl (0.35-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libcgi-pm-perl (4.40-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libcgi-session-perl (4.48-3) ... Setting up libapr1-dev (1.6.5-1+b1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libhttp-daemon-perl (6.01-3) ... Setting up libaprutil1-dev (1.6.1-4) ... Setting up libfontconfig1:armhf (2.13.1-2) ... Setting up bioperl (1.7.2-3) ... Setting up po-debconf (1.0.21) ... Setting up libbio-coordinate-perl (1.7.1-3) ... Setting up libgd3:armhf (2.2.5-5.2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libgd-perl (2.71-2) ... Setting up libbio-graphics-perl (2.40-3) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up libwww-perl (6.36-2) ... Setting up debhelper (12.1.1) ... Setting up dh-exec (0.23.1) ... Setting up apache2-dev (2.4.38-3+deb10u3) ... Setting up libvm-ec2-perl (1.28-2) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/gbrowse-2.56+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package gbrowse dpkg-buildpackage: info: source version 2.56+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with apache2 dh_clean debian/rules build dh build --with apache2 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/gbrowse-2.56+dfsg' dh_auto_configure -- --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse perl Build.PL --installdirs vendor --config "optimize=-g -O2 -ffile-prefix-map=/build/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/build/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now" --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse WARNING: the following files are missing in your kit: contrib/ace2gff.pl contrib/AxtPairwise_convert/axt2phy.pl contrib/blast2gff.pl contrib/conf_files/01.yeast.conf contrib/conf_files/02.wormbase.conf contrib/conf_files/03.fly.conf contrib/conf_files/04.human.conf contrib/conf_files/05.embl_proxy.conf contrib/conf_files/06.biosql.conf contrib/conf_files/07.chado.conf contrib/conf_files/08.genbank.conf contrib/conf_files/09.human_karyotype.conf contrib/conf_files/index.html contrib/conf_files/wormbase.syn contrib/Coverage/INSTALL contrib/Coverage/plugin/Coverage.pm contrib/Coverage/README contrib/gdump.pl contrib/GeneFinder/genefinder/gfcode.c contrib/GeneFinder/genefinder/README contrib/GeneFinder/genefinder/readseq.c contrib/GeneFinder/genefinder/readseq.h contrib/GeneFinder/nematode_gftables/cds.hex contrib/GeneFinder/nematode_gftables/gftables contrib/GeneFinder/nematode_gftables/newnem.atg contrib/GeneFinder/nematode_gftables/newnem.codon contrib/GeneFinder/nematode_gftables/newnem.gene contrib/GeneFinder/nematode_gftables/newnem.intron3 contrib/GeneFinder/nematode_gftables/newnem.intron5 contrib/GeneFinder/nematode_gftables/ref.hist contrib/GeneFinder/nematode_gftables/zk637.atg contrib/GeneFinder/nematode_gftables/zk637.intron3 contrib/GeneFinder/nematode_gftables/zk637.intron5 contrib/GeneFinder/nematode_gftables/zk637.trinuc contrib/import_ncbi_mv_hs.pl contrib/install_macosx/BuildConfig.pm contrib/install_macosx/README.html contrib/install_macosx/README.pod contrib/install_macosx/scripts/build-gbrowse.pl contrib/install_macosx/scripts/build-libraries.pl contrib/README contrib/SynView/cgi-lib/DAS/GUS.pm contrib/SynView/cgi-lib/DAS/GUS/Segment.pm contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm contrib/SynView/gbrowse.conf/plasmodb.conf contrib/SynView/gbrowse.conf/plasmodb.xml contrib/SynView/MAL11/MAL11.conf contrib/SynView/MAL11/MAL11.fa contrib/SynView/MAL11/MAL11.gff3 contrib/SynView/README contrib/TextDumper/README contrib/TextDumper/TextDumper.pm lib/Bio/DB/SeqFeature/Store/LoadHelper.pm Please inform the author. Checking prerequisites... recommends: * Bio::DB::BigFile is not installed * Bio::DB::Sam is not installed * Bio::Das is not installed * Crypt::SSLeay is not installed * DBD::Pg is not installed * DBD::mysql is not installed * DB_File::Lock is not installed * FCGI is not installed * File::NFSLock is not installed * GD::SVG is not installed * Net::OpenID::Consumer is not installed * Net::SMTP::SSL is not installed * Parse::Apache::ServerStatus is not installed * Template is not installed * Do not worry if some "recommended" prerequisites are missing. You can install * * them later if you need the features they provide. Do not proceed with the * * install if any of "REQUIRED" prerequisites are missing. * * * * The optional Safe::World module does not currently run on Perl 5.10 or * * higher, and so cannot be installed. * ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. **** WARNING ***************************************************************************************** If you are upgrading from an earlier version of GBrowse and wish to use named user accounts, please set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run bin/gbrowse_metadb_config.pl to create/update your user account database. See /etc/gbrowse2/GBrowse.conf.new for suggested settings. ****************************************************************************************************** Now run: ./Build test ./Build demo (optional) ./Build install (as superuser/administrator) -or- ./Build install_slave (optional, for slave installations) Other useful targets: ./Build register (to register your copy of GBrowse) ./Build reconfig (to reconfigure install locations) ./Build demostop (to stop the demo) Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'GBrowse' version '2.56' make[1]: Leaving directory '/build/gbrowse-2.56+dfsg' dh_auto_build perl Build NOTE: Run ./Build reconfig to change existing configuration. Building GBrowse arm-linux-gnueabihf-gcc -I/build/gbrowse-2.56+dfsg/libalign -I/usr/lib/arm-linux-gnueabihf/perl/5.28/CORE -DVERSION="2.56" -DXS_VERSION="2.56" -fPIC -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -ffile-prefix-map=/build/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs') arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/build/gbrowse-2.56+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.so lib/Bio/Graphics/Browser2/CAlign.o Performing variable substitutions in blib/conf/aws_balancer.conf Performing variable substitutions in blib/conf/detail_select_menu.conf Performing variable substitutions in blib/conf/enzymes.txt Performing variable substitutions in blib/conf/GBrowse.conf Performing variable substitutions in blib/conf/log4perl.conf Performing variable substitutions in blib/conf/MobyServices/moby.conf Performing variable substitutions in blib/conf/pop_demo.conf Performing variable substitutions in blib/conf/renderfarm.conf Performing variable substitutions in blib/conf/slave_preload.conf Performing variable substitutions in blib/conf/submitter_plugin.conf Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf Performing variable substitutions in blib/conf/synteny/rice_synteny.conf Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf Performing variable substitutions in blib/conf/themes/solid_gray_colors Performing variable substitutions in blib/conf/themes/transparent_colors Performing variable substitutions in blib/conf/themes/warm_colors Performing variable substitutions in blib/conf/volvox.conf Performing variable substitutions in blib/conf/yeast_chr1+2.conf Performing variable substitutions in blib/conf/yeast_renderfarm.conf Performing variable substitutions in blib/conf/yeast_simple.conf Performing variable substitutions in blib/htdocs/annotation_help.html Performing variable substitutions in blib/htdocs/cloud_index.html Performing variable substitutions in blib/htdocs/example_scripts/index.html Performing variable substitutions in blib/htdocs/example_scripts/README Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html Performing variable substitutions in blib/htdocs/general_help.html Performing variable substitutions in blib/htdocs/index.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html Performing variable substitutions in blib/htdocs/vbox_index.html Use of uninitialized value in pattern match (m//) at /build/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. debian/rules override_dh_auto_test make[1]: Entering directory '/build/gbrowse-2.56+dfsg' dh_auto_test -- TEST_FILES="t/02.rearchitecture.t t/05.deferredrendering.t t/00.compile.t t/01.yeast.t t/07.balancer.t t/08.calign.t" perl Build test --verbose 1 "TEST_FILES=t/02.rearchitecture.t t/05.deferredrendering.t t/00.compile.t t/01.yeast.t t/07.balancer.t t/08.calign.t" NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /build/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. t/00.compile.t ............ ok 1 - cgi-bin/das compiled ok ok 2 - cgi-bin/das stderr said "syntax OK" ok 3 - cgi-bin/das nothing on stdout ok 4 - cgi-bin/gbgff compiled ok ok 5 - cgi-bin/gbgff stderr said "syntax OK" ok 6 - cgi-bin/gbgff nothing on stdout ok 7 - cgi-bin/gbrowse compiled ok ok 8 - cgi-bin/gbrowse stderr said "syntax OK" ok 9 - cgi-bin/gbrowse nothing on stdout ok 10 - cgi-bin/gbrowse_details compiled ok ok 11 - cgi-bin/gbrowse_details stderr said "syntax OK" ok 12 - cgi-bin/gbrowse_details nothing on stdout ok 13 # skip explicitly skipping cgi-bin/gbrowse_gmap ok 14 - cgi-bin/gbrowse_img compiled ok ok 15 - cgi-bin/gbrowse_img stderr said "syntax OK" ok 16 - cgi-bin/gbrowse_img nothing on stdout ok 17 - cgi-bin/gbrowse_key_img compiled ok ok 18 - cgi-bin/gbrowse_key_img stderr said "syntax OK" ok 19 - cgi-bin/gbrowse_key_img nothing on stdout ok 20 - cgi-bin/gbrowse_login compiled ok ok 21 - cgi-bin/gbrowse_login stderr said "syntax OK" ok 22 - cgi-bin/gbrowse_login nothing on stdout ok 23 - cgi-bin/gbrowse_syn compiled ok ok 24 - cgi-bin/gbrowse_syn stderr said "syntax OK" ok 25 - cgi-bin/gbrowse_syn nothing on stdout ok 26 - bin/auto_install_databases.pl compiled ok ok 27 - bin/auto_install_databases.pl stderr said "syntax OK" ok 28 - bin/auto_install_databases.pl nothing on stdout ok 29 - bin/bed2gff3.pl compiled ok ok 30 - bin/bed2gff3.pl stderr said "syntax OK" ok 31 - bin/bed2gff3.pl nothing on stdout ok 32 - bin/bp_load_gff.pl compiled ok ok 33 - bin/bp_load_gff.pl stderr said "syntax OK" ok 34 - bin/bp_load_gff.pl nothing on stdout ok 35 # skip explicitly skipping bin/gbrowse_aws_balancer.pl ok 36 - bin/gbrowse_change_passwd.pl compiled ok ok 37 - bin/gbrowse_change_passwd.pl stderr said "syntax OK" ok 38 - bin/gbrowse_change_passwd.pl nothing on stdout ok 39 - bin/gbrowse_clean.pl compiled ok ok 40 - bin/gbrowse_clean.pl stderr said "syntax OK" ok 41 - bin/gbrowse_clean.pl nothing on stdout ok 42 - bin/gbrowse_configure_slaves.pl compiled ok ok 43 - bin/gbrowse_configure_slaves.pl stderr said "syntax OK" ok 44 - bin/gbrowse_configure_slaves.pl nothing on stdout ok 45 - bin/gbrowse_create_account.pl compiled ok ok 46 - bin/gbrowse_create_account.pl stderr said "syntax OK" ok 47 - bin/gbrowse_create_account.pl nothing on stdout ok 48 # skip explicitly skipping bin/gbrowse_grow_cloud_vol.pl ok 49 - bin/gbrowse_import_ucsc_db.pl compiled ok ok 50 - bin/gbrowse_import_ucsc_db.pl stderr said "syntax OK" ok 51 - bin/gbrowse_import_ucsc_db.pl nothing on stdout ok 52 - bin/gbrowse_metadb_config.pl compiled ok ok 53 - bin/gbrowse_metadb_config.pl stderr said "syntax OK" ok 54 - bin/gbrowse_metadb_config.pl nothing on stdout ok 55 # skip explicitly skipping bin/gbrowse_netinstall.pl ok 56 # skip explicitly skipping bin/gbrowse_netinstall2.pl ok 57 - bin/gbrowse_set_admin_passwd.pl compiled ok ok 58 - bin/gbrowse_set_admin_passwd.pl stderr said "syntax OK" ok 59 - bin/gbrowse_set_admin_passwd.pl nothing on stdout ok 60 - bin/gbrowse_slave compiled ok ok 61 - bin/gbrowse_slave stderr said "syntax OK" ok 62 - bin/gbrowse_slave nothing on stdout ok 63 # skip explicitly skipping bin/gbrowse_slave_start_aws.sh ok 64 - bin/gbrowse_syn_load_alignment_database.pl compiled ok ok 65 - bin/gbrowse_syn_load_alignment_database.pl stderr said "syntax OK" ok 66 - bin/gbrowse_syn_load_alignment_database.pl nothing on stdout ok 67 - bin/gbrowse_syn_load_alignments_msa.pl compiled ok ok 68 - bin/gbrowse_syn_load_alignments_msa.pl stderr said "syntax OK" ok 69 - bin/gbrowse_syn_load_alignments_msa.pl nothing on stdout ok 70 # skip explicitly skipping bin/gbrowse_sync_aws_slave.pl ok 71 - bin/gtf2gff3.pl compiled ok ok 72 - bin/gtf2gff3.pl stderr said "syntax OK" ok 73 - bin/gtf2gff3.pl nothing on stdout ok 74 - bin/load_genbank.pl compiled ok ok 75 - bin/load_genbank.pl stderr said "syntax OK" ok 76 - bin/load_genbank.pl nothing on stdout ok 77 # skip explicitly skipping bin/make_das_conf.pl ok 78 - bin/process_bamfiles.pl compiled ok ok 79 - bin/process_bamfiles.pl stderr said "syntax OK" ok 80 - bin/process_bamfiles.pl nothing on stdout ok 81 - bin/process_gadfly.pl compiled ok ok 82 - bin/process_gadfly.pl stderr said "syntax OK" ok 83 - bin/process_gadfly.pl nothing on stdout ok 84 - bin/process_ncbi_human.pl compiled ok ok 85 - bin/process_ncbi_human.pl stderr said "syntax OK" ok 86 - bin/process_ncbi_human.pl nothing on stdout ok 87 - bin/process_sgd.pl compiled ok ok 88 - bin/process_sgd.pl stderr said "syntax OK" ok 89 - bin/process_sgd.pl nothing on stdout ok 90 - bin/report_missing_language_tags.pl compiled ok ok 91 - bin/report_missing_language_tags.pl stderr said "syntax OK" ok 92 - bin/report_missing_language_tags.pl nothing on stdout ok 93 - bin/scan_gbrowse.pl compiled ok ok 94 - bin/scan_gbrowse.pl stderr said "syntax OK" ok 95 - bin/scan_gbrowse.pl nothing on stdout ok 96 - bin/split_wig.pl compiled ok ok 97 - bin/split_wig.pl stderr said "syntax OK" ok 98 - bin/split_wig.pl nothing on stdout ok 99 - bin/ucsc_genes2gff.pl compiled ok ok 100 - bin/ucsc_genes2gff.pl stderr said "syntax OK" ok 101 - bin/ucsc_genes2gff.pl nothing on stdout ok 102 - bin/wiggle2gff3.pl compiled ok ok 103 - bin/wiggle2gff3.pl stderr said "syntax OK" ok 104 - bin/wiggle2gff3.pl nothing on stdout 1..104 ok Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. t/01.yeast.t .............. 1..7 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756. t/02.rearchitecture.t ..... 1..90 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1044, line 2. Use of uninitialized value $_[5] in pack at /usr/share/perl5/Bio/DB/IndexedBase.pm line 1044, line 2. cannot remove directory for /tmp/gbrowse_testing/qhoaBhsg8Q: No such file or directory at /usr/share/perl/5.28/File/Temp.pm line 778. t/03.render.t ............. 1..150 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. cannot remove directory for /tmp/gbrowse_testing: Directory not empty at t/04.remoteserver.t line 170. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Could not open database: Can't call method "seq" on an undefined value at /usr/share/perl5/Bio/DB/SeqFeature/Store/LoadHelper.pm line 173, line 21. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. t/04.remoteserver.t ....... 1..43 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. t/05.deferredrendering.t .. 1..19 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, <> line 132. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. Use of uninitialized value in subtraction (-) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 817. Use of uninitialized value $curr_line in pattern match (m//) at /usr/share/perl5/Bio/DB/IndexedBase.pm line 820. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/DB/GFF.pm line 2000. t/06.featuresearch.t ...... 1..26 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok t/07.balancer.t ........... skipped: Optional module Parse::Apache::ServerStatus not installed File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/share/perl5/Bio/Graphics/FeatureFile.pm line 756. t/07.karyotype.t .......... 1..3 ok 1 ok 2 ok 3 ok t/08.calign.t ............. 1..6 # Running under perl version 5.028001 for linux # Current time local: Wed Jun 24 17:52:36 2020 # Current time GMT: Thu Jun 25 05:52:36 2020 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok All tests successful. Files=10, Tests=448, 283 wallclock secs ( 0.76 usr 0.18 sys + 168.48 cusr 24.04 csys = 193.46 CPU) Result: PASS make[1]: Leaving directory '/build/gbrowse-2.56+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with apache2 dh_testroot dh_prep debian/rules override_dh_installdirs make[1]: Entering directory '/build/gbrowse-2.56+dfsg' # svn(-buildpackage) seems to ignore the x bit chmod +x debian/gbrowse-calign.dirs dh_installdirs make[1]: Leaving directory '/build/gbrowse-2.56+dfsg' debian/rules override_dh_auto_install make[1]: Entering directory '/build/gbrowse-2.56+dfsg' ./Build --install_base=debian/gbrowse debianinstall NOTE: Run ./Build reconfig to change existing configuration. Use of uninitialized value in pattern match (m//) at /build/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 778. Building GBrowse Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.so Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs Installing debian/gbrowse/man/man1/gbrowse_sync_aws_slave.pl.1p Installing debian/gbrowse/man/man1/load_genbank.pl.1p Installing debian/gbrowse/man/man1/gbrowse_clean.pl.1p Installing debian/gbrowse/man/man1/ucsc_genes2gff.pl.1p Installing debian/gbrowse/man/man1/wiggle2gff3.pl.1p Installing debian/gbrowse/man/man1/make_das_conf.pl.1p Installing debian/gbrowse/man/man1/bed2gff3.pl.1p Installing debian/gbrowse/man/man1/gbrowse_aws_balancer.pl.1p Installing debian/gbrowse/man/man1/gbrowse_grow_cloud_vol.pl.1p Installing debian/gbrowse/man/man1/gtf2gff3.pl.1p Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_details Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/das Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_gmap Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_key_img Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_login Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse_syn Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbgff Installing debian/gbrowse/usr/lib/cgi-bin/gbrowse/gbrowse Installing debian/gbrowse/etc/gbrowse/GBrowse.conf Installing debian/gbrowse/etc/gbrowse/volvox.conf Installing debian/gbrowse/etc/gbrowse/aws_balancer.conf Installing debian/gbrowse/etc/gbrowse/yeast_chr1+2.conf Installing debian/gbrowse/etc/gbrowse/submitter_plugin.conf Installing debian/gbrowse/etc/gbrowse/yeast_simple.conf Installing debian/gbrowse/etc/gbrowse/detail_select_menu.conf Installing debian/gbrowse/etc/gbrowse/log4perl.conf Installing debian/gbrowse/etc/gbrowse/pop_demo.conf Installing debian/gbrowse/etc/gbrowse/enzymes.txt Installing debian/gbrowse/etc/gbrowse/renderfarm.conf Installing debian/gbrowse/etc/gbrowse/yeast_renderfarm.conf Installing debian/gbrowse/etc/gbrowse/slave_preload.conf Installing debian/gbrowse/etc/gbrowse/languages/ja.pm Installing debian/gbrowse/etc/gbrowse/languages/zh_cn.pm Installing debian/gbrowse/etc/gbrowse/languages/ru.pm Installing debian/gbrowse/etc/gbrowse/languages/POSIX.pm Installing debian/gbrowse/etc/gbrowse/languages/en.pm Installing debian/gbrowse/etc/gbrowse/languages/is.pm Installing debian/gbrowse/etc/gbrowse/languages/fr.pm Installing debian/gbrowse/etc/gbrowse/languages/zh.pm Installing debian/gbrowse/etc/gbrowse/languages/pl.pm Installing debian/gbrowse/etc/gbrowse/languages/es.pm Installing debian/gbrowse/etc/gbrowse/languages/it.pm Installing debian/gbrowse/etc/gbrowse/languages/ko.pm Installing debian/gbrowse/etc/gbrowse/languages/de.pm Installing debian/gbrowse/etc/gbrowse/languages/nl.pm Installing debian/gbrowse/etc/gbrowse/themes/warm_colors Installing debian/gbrowse/etc/gbrowse/themes/solid_gray_colors Installing debian/gbrowse/etc/gbrowse/themes/transparent_colors Installing debian/gbrowse/etc/gbrowse/plugins/LDAPAuthenticate.pm Installing debian/gbrowse/etc/gbrowse/plugins/test.pm Installing debian/gbrowse/etc/gbrowse/plugins/GeneFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/Blat.pm Installing debian/gbrowse/etc/gbrowse/plugins/AttributeHiliter.pm Installing debian/gbrowse/etc/gbrowse/plugins/Submitter.pm Installing debian/gbrowse/etc/gbrowse/plugins/OligoFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/TestAuthenticator.pm Installing debian/gbrowse/etc/gbrowse/plugins/SimpleTrackFinder.pm Installing debian/gbrowse/etc/gbrowse/plugins/RandomGene.pm Installing debian/gbrowse/etc/gbrowse/plugins/BatchDumper.pm Installing debian/gbrowse/etc/gbrowse/plugins/SinWave.pm Installing debian/gbrowse/etc/gbrowse/plugins/CMapDumper.pm Installing 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debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave/Status.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML/TrackListing.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/SeqFeature/Store/Alias.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/SeqFeature/Store/BedLoader.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/waba_alignment.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/match_gap.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/wormbase_gene.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/GFF/Aggregator/reftranscript.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger/mysql.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Bio/DB/Tagger/Tag.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/GBrowse/ConfigData.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/CGI/Toggle.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/I18n.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/PageSettings.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/Util.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/Graphics/Browser/Synteny.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/DB/SyntenyBlock.pm Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/Legacy/DB/SyntenyIO.pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Markup.3pm Installing debian/gbrowse/man/man3/Legacy::Graphics::Browser.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render.3pm Installing debian/gbrowse/man/man3/GBrowse::ConfigData.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PadAlignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Plugin::AuthPlugin.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataBase.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RemoteSet.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Region.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataSource.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::AWS_Balancer.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RenderPanels.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::AuthorizedFeatureFile.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::archive.3pm Installing debian/gbrowse/man/man3/CGI::Toggle.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::DataLoader::useq.3pm Installing debian/gbrowse/man/man3/Bio::DB::Tagger::Tag.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::PluginSet.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Render::Slave::Status.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::RegionSearch.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Realign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::OptionPick.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::GFFhelper.3pm Installing debian/gbrowse/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm Installing debian/gbrowse/man/man3/Bio::Graphics::Browser2::Util.3pm Installing debian/gbrowse/man/man3/Bio::DB::SeqFeature::Store::Alias.3pm Installing debian/gbrowse/bin/gbrowse_aws_balancer.pl Installing debian/gbrowse/bin/gbrowse_clean.pl Installing debian/gbrowse/bin/gtf2gff3.pl Installing debian/gbrowse/bin/gbrowse_metadb_config.pl Installing debian/gbrowse/bin/gbrowse_slave Installing debian/gbrowse/bin/bed2gff3.pl Installing debian/gbrowse/bin/gbrowse_create_account.pl Installing debian/gbrowse/bin/gbrowse_configure_slaves.pl Installing debian/gbrowse/bin/make_das_conf.pl Installing debian/gbrowse/bin/gbrowse_change_passwd.pl Installing debian/gbrowse/bin/gbrowse_sync_aws_slave.pl Installing debian/gbrowse/bin/gbrowse_import_ucsc_db.pl Installing debian/gbrowse/bin/wiggle2gff3.pl Installing debian/gbrowse/bin/gbrowse_set_admin_passwd.pl Installing debian/gbrowse/bin/ucsc_genes2gff.pl Installing debian/gbrowse/bin/scan_gbrowse.pl Installing debian/gbrowse/bin/gbrowse_grow_cloud_vol.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignments_msa.pl Installing debian/gbrowse/bin/gbrowse_syn_load_alignment_database.pl Installing debian/gbrowse/bin/load_genbank.pl #./Build apache_conf > debian/gbrowse/etc/gbrowse/gbrowse_apache2.conf perl Build.PL --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1 --persistent=/var/lib/gbrowse --installetc=y WARNING: the following files are missing in your kit: contrib/ace2gff.pl contrib/AxtPairwise_convert/axt2phy.pl contrib/blast2gff.pl contrib/conf_files/01.yeast.conf contrib/conf_files/02.wormbase.conf contrib/conf_files/03.fly.conf contrib/conf_files/04.human.conf contrib/conf_files/05.embl_proxy.conf contrib/conf_files/06.biosql.conf contrib/conf_files/07.chado.conf contrib/conf_files/08.genbank.conf contrib/conf_files/09.human_karyotype.conf contrib/conf_files/index.html contrib/conf_files/wormbase.syn contrib/Coverage/INSTALL contrib/Coverage/plugin/Coverage.pm contrib/Coverage/README contrib/gdump.pl contrib/GeneFinder/genefinder/gfcode.c contrib/GeneFinder/genefinder/README contrib/GeneFinder/genefinder/readseq.c contrib/GeneFinder/genefinder/readseq.h contrib/GeneFinder/nematode_gftables/cds.hex contrib/GeneFinder/nematode_gftables/gftables contrib/GeneFinder/nematode_gftables/newnem.atg contrib/GeneFinder/nematode_gftables/newnem.codon contrib/GeneFinder/nematode_gftables/newnem.gene contrib/GeneFinder/nematode_gftables/newnem.intron3 contrib/GeneFinder/nematode_gftables/newnem.intron5 contrib/GeneFinder/nematode_gftables/ref.hist contrib/GeneFinder/nematode_gftables/zk637.atg contrib/GeneFinder/nematode_gftables/zk637.intron3 contrib/GeneFinder/nematode_gftables/zk637.intron5 contrib/GeneFinder/nematode_gftables/zk637.trinuc contrib/import_ncbi_mv_hs.pl contrib/install_macosx/BuildConfig.pm contrib/install_macosx/README.html contrib/install_macosx/README.pod contrib/install_macosx/scripts/build-gbrowse.pl contrib/install_macosx/scripts/build-libraries.pl contrib/README contrib/SynView/cgi-lib/DAS/GUS.pm contrib/SynView/cgi-lib/DAS/GUS/Segment.pm contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm contrib/SynView/gbrowse.conf/plasmodb.conf contrib/SynView/gbrowse.conf/plasmodb.xml contrib/SynView/MAL11/MAL11.conf contrib/SynView/MAL11/MAL11.fa contrib/SynView/MAL11/MAL11.gff3 contrib/SynView/README contrib/TextDumper/README contrib/TextDumper/TextDumper.pm lib/Bio/DB/SeqFeature/Store/LoadHelper.pm Please inform the author. Checking prerequisites... recommends: * Bio::DB::BigFile is not installed * Bio::DB::Sam is not installed * Bio::Das is not installed * Crypt::SSLeay is not installed * DBD::Pg is not installed * DBD::mysql is not installed * DB_File::Lock is not installed * FCGI is not installed * File::NFSLock is not installed * GD::SVG is not installed * Net::OpenID::Consumer is not installed * Net::SMTP::SSL is not installed * Parse::Apache::ServerStatus is not installed * Template is not installed * Do not worry if some "recommended" prerequisites are missing. You can install * * them later if you need the features they provide. Do not proceed with the * * install if any of "REQUIRED" prerequisites are missing. * * * * The optional Safe::World module does not currently run on Perl 5.10 or * * higher, and so cannot be installed. * ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. **** WARNING ***************************************************************************************** If you are upgrading from an earlier version of GBrowse and wish to use named user accounts, please set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run bin/gbrowse_metadb_config.pl to create/update your user account database. See /etc/gbrowse2/GBrowse.conf.new for suggested settings. ****************************************************************************************************** NOTE: Run ./Build reconfig to change existing configuration. Now run: ./Build test ./Build demo (optional) ./Build install (as superuser/administrator) -or- ./Build install_slave (optional, for slave installations) Other useful targets: ./Build register (to register your copy of GBrowse) ./Build reconfig (to reconfigure install locations) ./Build demostop (to stop the demo) Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'GBrowse' version '2.56' ./Build --install_base=debian/gbrowse install_slave NOTE: Run ./Build reconfig to change existing configuration. Performing variable substitutions in blib/conf/aws_balancer.conf Performing variable substitutions in blib/conf/detail_select_menu.conf Performing variable substitutions in blib/conf/enzymes.txt Performing variable substitutions in blib/conf/GBrowse.conf Performing variable substitutions in blib/conf/log4perl.conf Performing variable substitutions in blib/conf/MobyServices/moby.conf Performing variable substitutions in blib/conf/pop_demo.conf Performing variable substitutions in blib/conf/renderfarm.conf Performing variable substitutions in blib/conf/slave_preload.conf Performing variable substitutions in blib/conf/submitter_plugin.conf Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf Performing variable substitutions in blib/conf/synteny/rice_synteny.conf Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf Performing variable substitutions in blib/conf/themes/solid_gray_colors Performing variable substitutions in blib/conf/themes/transparent_colors Performing variable substitutions in blib/conf/themes/warm_colors Performing variable substitutions in blib/conf/volvox.conf Performing variable substitutions in blib/conf/yeast_chr1+2.conf Performing variable substitutions in blib/conf/yeast_renderfarm.conf Performing variable substitutions in blib/conf/yeast_simple.conf Performing variable substitutions in blib/htdocs/annotation_help.html Performing variable substitutions in blib/htdocs/cloud_index.html Performing variable substitutions in blib/htdocs/example_scripts/index.html Performing variable substitutions in blib/htdocs/example_scripts/README Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html Performing variable substitutions in blib/htdocs/general_help.html Performing variable substitutions in blib/htdocs/index.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.html Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html Performing variable substitutions in blib/htdocs/vbox_index.html Performing variable substitutions in blib/etc/default/gbrowse-aws-balancer Use of uninitialized value $wwwuser in substitution (s///) at /build/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 871, line 10. Performing variable substitutions in blib/etc/default/gbrowse-slave Performing variable substitutions in blib/etc/init.d/gbrowse-aws-balancer Performing variable substitutions in blib/etc/init.d/gbrowse-slave Use of uninitialized value $wwwuser in substitution (s///) at /build/gbrowse-2.56+dfsg/install_util/GBrowseInstall.pm line 871, line 20. Building GBrowse Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing debian/gbrowse/etc/default/gbrowse-aws-balancer Installing debian/gbrowse/etc/default/gbrowse-slave Installing debian/gbrowse/etc/init.d/gbrowse-aws-balancer Installing debian/gbrowse/etc/init.d/gbrowse-slave Installing debian/gbrowse/lib/perl5/arm-linux-gnueabihf-thread-multi-64int/GBrowse/ConfigData.pm mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5 # Remove arch dependant data mkdir -p debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.28/auto/Bio/Graphics/Browser2/CAlign/ mkdir -p debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.28/Bio/Graphics/Browser2/ mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.28/auto/Bio/Graphics/Browser2/CAlign/ mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/arm-linux-gnueabihf/perl5/5.28/Bio/Graphics/Browser2/CAlign.pm rm -rf debian/gbrowse/lib rm -f debian/gbrowse/usr/share/doc/gbrowse/INSTALL rm -f debian/gbrowse/usr/share/perl5/auto/GBrowse/.packlist rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/prototype.js rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/scriptaculous.js chmod 644 debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled.conf #Remove database (kept as separate package) rm -rf debian/gbrowse/var/lib/gbrowse/databases/* #Rename pl scripts in bin file-rename 's/\.pl//' debian/gbrowse/bin/*.pl mv debian/gbrowse/bin debian/gbrowse/usr/bin # Activate configuration files. find /build/gbrowse-2.56+dfsg/debian/gbrowse/etc -name '*.new' | xargs file-rename 's/.new//' rm -rf /build/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/auto # Update conf files sed -i 's/gbrowse2/gbrowse/g' /build/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/yeast*.conf sed -i 's/gbrowse2/gbrowse/g' /build/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/slave*.conf # move OpenID constumer secret to /etc/gbrowse to make it system admin configurable mv /build/gbrowse-2.56+dfsg/debian/gbrowse/usr/share/perl5/GBrowse/ConfigData.pm /build/gbrowse-2.56+dfsg/debian/gbrowse/etc/gbrowse/ConfigData.pm make[1]: Leaving directory '/build/gbrowse-2.56+dfsg' dh_install dh_apache2 dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/gbrowse-2.56+dfsg' #Rename due to perl extension seen as polish file-rename 's/\.pl\.1p/\.1p/' debian/gbrowse/man/man1/*.pl.1p mkdir -p debian/gbrowse-calign/man/man3/ mv debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm debian/gbrowse-calign/man/man3/Bio::Graphics::Browser2::CAlign.3pm dh_installman rm -rf debian/gbrowse/man rm -rf debian/gbrowse-calign/man make[1]: Leaving directory '/build/gbrowse-2.56+dfsg' dh_lintian dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/gbrowse-2.56+dfsg' dh_link # Fix broken link ... even if I habe no idea what a link to a not existing dir should serve for ln -sf /var/cache/gbrowse/images debian/gbrowse/usr/share/gbrowse/htdocs/i make[1]: Leaving directory '/build/gbrowse-2.56+dfsg' dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gbrowse-calign' in '../gbrowse-calign_2.56+dfsg-4_armhf.deb'. dpkg-deb: building package 'gbrowse' in '../gbrowse_2.56+dfsg-4_all.deb'. dpkg-deb: building package 'gbrowse-calign-dbgsym' in '../gbrowse-calign-dbgsym_2.56+dfsg-4_armhf.deb'. dpkg-deb: building package 'gbrowse-data' in '../gbrowse-data_2.56+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gbrowse_2.56+dfsg-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/18674 and its subdirectories I: Current time: Wed Jun 24 17:57:34 -12 2020 I: pbuilder-time-stamp: 1593064654 Thu Jun 25 05:57:52 UTC 2020 I: 1st build successful. Starting 2nd build on remote node ff2b-armhf-rb.debian.net. Thu Jun 25 05:57:52 UTC 2020 I: Preparing to do remote build '2' on ff2b-armhf-rb.debian.net. Thu Jun 25 06:01:27 UTC 2020 I: Deleting $TMPDIR on ff2b-armhf-rb.debian.net. Thu Jun 25 06:01:30 UTC 2020 I: gbrowse_2.56+dfsg-4_armhf.changes: Format: 1.8 Date: Wed, 03 Oct 2018 15:07:54 +0200 Source: gbrowse Binary: gbrowse gbrowse-calign gbrowse-calign-dbgsym gbrowse-data Architecture: armhf all Version: 2.56+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gbrowse - GMOD Generic Genome Browser gbrowse-calign - CAlign helper gbrowse-data - Sample data to use GBrowse Changes: gbrowse (2.56+dfsg-4) unstable; urgency=medium . * Update URL in watch file * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: a3806d98845094a704facfaedfc4730999483f04 30256 gbrowse-calign-dbgsym_2.56+dfsg-4_armhf.deb 32ce513a7c04e12e8a7176be5a15ab5b3a45b600 35620 gbrowse-calign_2.56+dfsg-4_armhf.deb fd7980453d83c71039c6b8e9239cc237731888c5 1234844 gbrowse-data_2.56+dfsg-4_all.deb 5f0a08faca496b9331f0f3ee5cceb02f8902f945 2375092 gbrowse_2.56+dfsg-4_all.deb 66024d226b60930dcfdfb911ce095a4be3c94857 8710 gbrowse_2.56+dfsg-4_armhf.buildinfo Checksums-Sha256: d85c651033591f89a57f8dc73a93053d99507cf258a7976f69560c98bd2b2911 30256 gbrowse-calign-dbgsym_2.56+dfsg-4_armhf.deb b7929a54cdf5f61a21e6e7c66032a9033de67064c7be0da457191f00278b8358 35620 gbrowse-calign_2.56+dfsg-4_armhf.deb e9824b9cc33e9aefe6fa45d368f3c4ac913f0f14b471ba36c58e45a3ca8294b1 1234844 gbrowse-data_2.56+dfsg-4_all.deb 02f4319adb84342f5d7839b351c072880035b6162d0e0699a08f27de2836c7a7 2375092 gbrowse_2.56+dfsg-4_all.deb 6b8091bace7f26366c4eac0fbaa1dd24725730114553fae751c05cdae058ded6 8710 gbrowse_2.56+dfsg-4_armhf.buildinfo Files: 585c006aa4a09d88ecb390016236a3ef 30256 debug optional gbrowse-calign-dbgsym_2.56+dfsg-4_armhf.deb 45aa3f1280070b39376ac8169179e0d6 35620 science optional gbrowse-calign_2.56+dfsg-4_armhf.deb 6687aa1812fc565c32408c0ee67f5bc1 1234844 science optional gbrowse-data_2.56+dfsg-4_all.deb 536fef58f52f0115aed8ce0bc483b5e2 2375092 science optional gbrowse_2.56+dfsg-4_all.deb 2e868cb206d5def6c4b8fe612a19d725 8710 science optional gbrowse_2.56+dfsg-4_armhf.buildinfo Thu Jun 25 06:01:31 UTC 2020 I: diffoscope 148 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.WjUh08ONSq/gbrowse_2.56+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.WjUh08ONSq/gbrowse_2.56+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.WjUh08ONSq/gbrowse_2.56+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.WjUh08ONSq/b1/gbrowse_2.56+dfsg-4_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.WjUh08ONSq/b2/gbrowse_2.56+dfsg-4_armhf.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 2.184s) 1.038s 10 calls xz 1.021s 42 calls diff 0.093s 7 calls cmp 0.024s 10 calls xxd 0.007s 93 calls cmp (internal) 0.001s 10 calls db_dump ## compare_files (cumulative) (total time: 16.779s) 5.191s 1 call abc.DotChangesFile 4.492s 2 calls abc.DebFile 4.018s 3 calls abc.XzFile 2.637s 2 calls abc.DebDataTarFile 0.224s 1 call abc.BerkeleyDBFile 0.128s 1 call abc.TarFile 0.077s 1 call abc.TextFile 0.012s 1 call abc.Md5sumsFile ## container_extract (total time: 1.451s) 1.040s 10 calls diffoscope.comparators.xz.XzContainer 0.351s 1220 calls diffoscope.comparators.deb.DebTarContainer 0.052s 16 calls diffoscope.comparators.deb.DebContainer 0.009s 10 calls diffoscope.comparators.tar.TarContainer ## has_same_content_as (total time: 0.111s) 0.039s 4 calls abc.DebFile 0.032s 2 calls abc.DebDataTarFile 0.021s 79 calls abc.TextFile 0.017s 4 calls abc.XzFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 2 calls abc.JSONFile 0.000s 2 calls abc.Md5sumsFile 0.000s 1 call abc.TarFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.BerkeleyDBFile ## main (total time: 5.698s) 5.642s 2 calls outputs 0.056s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 10 calls diffoscope.comparators.xz.XzContainer 0.000s 6 calls diffoscope.comparators.tar.TarContainer 0.000s 4 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.131s) 0.129s 1 call html 0.001s 1 call json 0.001s 1 call text ## recognizes (total time: 1.613s) 1.204s 3734 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.193s 168 calls diffoscope.comparators.debian.DebControlMember 0.137s 348 calls diffoscope.comparators.utils.archive.ArchiveMember 0.078s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile 0.000s 14 calls abc.Md5sumsFile 0.000s 16 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink Thu Jun 25 06:01:40 UTC 2020 E: gbrowse failed to build reproducibly in buster on armhf. Thu Jun 25 06:01:43 UTC 2020 I: Submitting .buildinfo files to external archives: Thu Jun 25 06:01:43 UTC 2020 I: Submitting 12K b1/gbrowse_2.56+dfsg-4_armhf.buildinfo.asc Thu Jun 25 06:01:44 UTC 2020 I: Submitting 12K b2/gbrowse_2.56+dfsg-4_armhf.buildinfo.asc Thu Jun 25 06:01:46 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jun 25 06:01:46 UTC 2020 I: Done submitting .buildinfo files. Thu Jun 25 06:01:46 UTC 2020 I: Removing signed gbrowse_2.56+dfsg-4_armhf.buildinfo.asc files: removed './b1/gbrowse_2.56+dfsg-4_armhf.buildinfo.asc' removed './b2/gbrowse_2.56+dfsg-4_armhf.buildinfo.asc'