Portage 2.2.0_alpha110 (default/linux/amd64/10.0, gcc-4.7.1, glibc-2.15-r2, 3.4.2-hardened x86_64) ================================================================= System uname: Linux-3.4.2-hardened-x86_64-AMD_Opteron-TM-_Processor_6272-with-gentoo-2.1 Timestamp of tree: Sat, 16 Jun 2012 07:30:01 +0000 app-shells/bash: 4.2_p29 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.3-r2, 3.2.3-r1 dev-util/cmake: 2.8.8-r3 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.10.3 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.11.5, 1.12.1 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.5.3-r2, 4.7.1 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.4 (virtual/os-headers) sys-libs/glibc: 2.15-r2 Repositories: gentoo Installed sets: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -ggdb -march=native -ftracer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -ggdb -march=native -ftracer" DISTDIR="/var/cache/portage/distfiles" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict test test-fail-continue unknown-features-warn unmerge-orphans userfetch userpriv usersandbox" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j24" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/tmp" PORTDIR="/var/cache/portage/tree" PORTDIR_OVERLAY="" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowex acl amd64 berkdb bzip2 cli cracklib crypt cups cxx dri ffmpeg fortran gdbm gpm iconv ipv6 mmx modules mudflap multilib ncurses nls nptl openmp pam pcre pppd qt3support readline session sse sse2 sse3 sse4 ssl ssse3 tcpd unicode vhosts xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 jruby ruby19 ree18" USERLAND="GNU" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
t/15cluster.t ..... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 155/162 subtests t/16obda.t ........ 1/16 ------------- EXCEPTION ------------- MSG: failed to open connection: Can't connect to MySQL server on '127.0.0.1' (111) STACK Bio::DB::DBI::base::new_connection /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/DBI/base.pm:267 STACK Bio::DB::DBI::base::get_connection /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/DBI/base.pm:227 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1498 STACK Bio::DB::BioSQL::BaseDriver::prepare_findbyuk_sth /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BaseDriver.pm:528 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:945 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:873 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:195 STACK Bio::DB::Persistent::PersistentObject::create /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/Persistent/PersistentObject.pm:257 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264 STACK Bio::DB::Persistent::PersistentObject::store /var/tmp/portage/sci-biology/bioperl-db-1.6.9/work/BioPerl-DB-1.006900/blib/lib/Bio/DB/Persistent/PersistentObject.pm:284 STACK toplevel t/16obda.t:36 ------------------------------------- # Looks like you planned 16 tests but ran 6. # Looks like your test exited with 255 just after 6. t/16obda.t ........ Dubious, test returned 255 (wstat 65280, 0xff00) Failed 10/16 subtests Test Summary Report ------------------- t/01dbadaptor.t (Wstat: 65280 Tests: 8 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 23 tests but ran 8. t/02species.t (Wstat: 65280 Tests: 7 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 67 tests but ran 7. t/03simpleseq.t (Wstat: 65280 Tests: 8 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 70 tests but ran 8. t/04swiss.t (Wstat: 512 Tests: 4 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 55 tests but ran 4. t/05seqfeature.t (Wstat: 65280 Tests: 6 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 52 tests but ran 6. t/06comment.t (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 14 tests but ran 5. t/07dblink.t (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 21 tests but ran 5. t/08genbank.t (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 23 tests but ran 5. t/09fuzzy2.t (Wstat: 65280 Tests: 4 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 23 tests but ran 4. t/10ensembl.t (Wstat: 65280 Tests: 5 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 18 tests but ran 5. t/11locuslink.t (Wstat: 65280 Tests: 7 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 113 tests but ran 7. t/12ontology.t (Wstat: 65280 Tests: 6 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 740 tests but ran 6. t/13remove.t (Wstat: 65280 Tests: 3 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 61 tests but ran 3. t/15cluster.t (Wstat: 65280 Tests: 7 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 162 tests but ran 7. t/16obda.t (Wstat: 65280 Tests: 6 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 16 tests but ran 6. Files=16, Tests=109, 5 wallclock secs ( 0.10 usr 0.04 sys + 3.81 cusr 0.46 csys = 4.41 CPU) Result: FAIL Failed 15/16 test programs. 0/109 subtests failed. * ERROR: sci-biology/bioperl-db-1.6.9::gentoo failed (test phase): * test failed
After spending a day trying to get these tests passing, I got as far as convincing them to talk to mysql, and then barfing, so I gave up and instead threw a RESTRICT at it. Closing as "resolved", even though its resolved only from a usability perspective. commit: 5ee7db5997fa620007d8d66a1a6dd0cead89a272 author: 2017-07-18 16:37:22 +1200 Kent Fredric <kentnl@gentoo.org> commit: 2017-07-18 16:38:42 +1200 Kent Fredric <kentnl@gentoo.org> gpg-key: E854324B1366A820 sci-biology/bioperl-db: Restrict tests re bug #421701 I've tried an excessive amount to get tests working here. But they still need a lot of love. The work I've done so far only gets a mysql test instance up, ( and then, only tested with mariadb ) Somebody needs to work out what's missing to provision the databases that the tests use. Somebody needs to add support for initializing the other kinds of database. Any help here encouraged, but disabling non-functioning tests is the best we can do for now. Package-Manager: Portage-2.3.6, Repoman-2.3.2 sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild | 51 ++-- sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild | 1 + sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch | 52 ++--- 3 files changed, 58 insertions(+), 46 deletions(-)