| Summary: | sci-biology/bioruby-1.4.3.0001: test failed at "test_new(Bio::TestPhyloXML_class_methods)" | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Linlin Yan <yanlinlin82> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | myckel |
| Priority: | Normal | Keywords: | PATCH, TESTFAILURE |
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| URL: | https://github.com/bioruby/bioruby/commit/edda65b8fb32c2eee6b0652074981c31aa68b0eb | ||
| See Also: | https://github.com/bioruby/bioruby/issues/84 | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
# emerge --info Portage 2.2.7 (default/linux/amd64/13.0, gcc-4.7.3, glibc-2.15-r3, 3.10.7-gentoo-r1 x86_64) ================================================================= System uname: Linux-3.10.7-gentoo-r1-x86_64-Six-Core_AMD_Opteron-tm-_Processor_8439_SE-with-gentoo-2.2 KiB Mem: 529440284 total, 367331228 free KiB Swap: 33557996 total, 33557996 free Timestamp of tree: Mon, 28 Oct 2013 16:30:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 app-shells/bash: 4.2_p45 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.5-r3, 3.2.5-r3 dev-util/cmake: 2.8.11.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.69 sys-devel/automake: 1.11.6, 1.12.6, 1.13.4 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.7.3-r1 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.9 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo gcpan biology science ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -march=native" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe -march=native" FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe -march=native" GENTOO_MIRRORS="ftp://ftp3.tsinghua.edu.cn/mirror/gentoo http://mirrors.xmu.edu.cn/gentoo http://distfiles.gentoo.org ftp://distro.ibiblio.org/pub/linux/distributions/gentoo/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/gcpan /usr/local/portage /var/lib/layman/science" SYNC="rsync://162.105.250.143/gentoo-portage" USE="acl amd64 berkdb bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx modules mudflap multilib ncurses nls nptl openmp pam pcre readline session sse sse2 ssl tcpd test threads unicode zlib" ABI_X86="64" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 author" 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" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="fglrx radeon" 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON Got hit by this while doing bug 488414 for x86, confirming this bug. Bug is triggered by ruby19, not ruby18. *bioruby-1.4.3.0001-r1 (25 Nov 2013) 25 Nov 2013; Manuel Rüger <mrueg@gentoo.org> +bioruby-1.4.3.0001-r1.ebuild, +files/bioruby-1.4.3.0001-fix-tests.patch, bioruby-9999.ebuild: NMU: Add missing dependency on libxml and ruby20 support. Fix tests see bug #489712 |
Emerge failed at test phase when update sci-biology/bioruby from 1.3.1 to 1.4.3.0001 Reproducible: Always Steps to Reproduce: When update sci-biology/bioruby from 1.3.1 to 1.4.3.0001, I got the test failure message as: Finished tests in 20.125546s, 192.1439 tests/s, 1069.2877 assertions/s. 1) Error: test_new(Bio::TestPhyloXML_class_methods): ArgumentError: invalid byte sequence in US-ASCII /var/tmp/portage/sci-biology/bioruby-1.4.3.0001/work/ruby19/bioruby-1.4.3.0001/lib/bio/db/phyloxml/phyloxml_parser.rb:326:in `=~' /var/tmp/portage/sci-biology/bioruby-1.4.3.0001/work/ruby19/bioruby-1.4.3.0001/lib/bio/db/phyloxml/phyloxml_parser.rb:326:in `!~' /var/tmp/portage/sci-biology/bioruby-1.4.3.0001/work/ruby19/bioruby-1.4.3.0001/lib/bio/db/phyloxml/phyloxml_parser.rb:326:in `initialize' /var/tmp/portage/sci-biology/bioruby-1.4.3.0001/work/ruby19/bioruby-1.4.3.0001/test/unit/bio/db/test_phyloxml.rb:105:in `new' /var/tmp/portage/sci-biology/bioruby-1.4.3.0001/work/ruby19/bioruby-1.4.3.0001/test/unit/bio/db/test_phyloxml.rb:105:in `test_new' 3867 tests, 21520 assertions, 0 failures, 1 errors, 0 skips Here goes my configure: # emerge -Oqvp =sci-biology/bioruby-1.4.3.0001 [ebuild U ] sci-biology/bioruby-1.4.3.0001 [1.3.1] USE="{test%*} -doc%" RUBY_TARGETS="ruby18%* ruby19%*" I think this should be a bug of bioruby-1.4.3.0001 package itself. Here is a discussion thread about this bug: https://github.com/bioruby/bioruby/issues/84 And there is a commit for it: https://github.com/bioruby/bioruby/commit/edda65b8fb32c2eee6b0652074981c31aa68b0eb