Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 420061 - dev-python/rpy-2.2.6 fails tests
Summary: dev-python/rpy-2.2.6 fails tests
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Development (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Python Gentoo Team
URL:
Whiteboard:
Keywords: TESTFAILURE
: 442500 (view as bug list)
Depends on:
Blocks: 418919
  Show dependency tree
 
Reported: 2012-06-07 09:38 UTC by Paweł Hajdan, Jr. (RETIRED)
Modified: 2012-11-09 20:40 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---

Attachments
build.log.gz (dev-python:rpy-2.2.6:20120606-173312.log.gz,9.67 KB, application/gzip)
2012-06-07 09:38 UTC, Paweł Hajdan, Jr. (RETIRED) 		Details
View All Add an attachment (proposed patch, testcase, etc.)

Note You need to log in before you can comment on or make changes to this bug.
Description Paweł Hajdan, Jr. (RETIRED) gentoo-dev 2012-06-07 09:38:35 UTC 
Created attachment 314515 [details]
build.log.gz

>>> Source compiled.
 * Testing of dev-python/rpy-2.2.6 with CPython 2.7...
...............................................................................................................................................
......................................................................................................................EE.......................
.........................................
======================================================================
ERROR: testRS4Auto_Type (rpy2.robjects.tests.testMethods.MethodsTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6/build-2.7/lib.linux-i686-2.7/rpy2/robjects/tests/testMethods.py", line 69, in tes
tRS4Auto_Type
    class MLE(robjects.methods.RS4):
  File "/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6/build-2.7/lib.linux-i686-2.7/rpy2/robjects/methods.py", line 191, in __new__
    for name, meth in itertools.izip(all_methods.do_slot("names"), all_methods):
LookupError: The object has no such attribute.

======================================================================
ERROR: testRS4Auto_Type_nopackname (rpy2.robjects.tests.testMethods.MethodsTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6/build-2.7/lib.linux-i686-2.7/rpy2/robjects/tests/testMethods.py", line 76, in tes
tRS4Auto_Type_nopackname
    class MLE(robjects.methods.RS4):
  File "/var/tmp/portage/dev-python/rpy-2.2.6/work/rpy2-2.2.6/build-2.7/lib.linux-i686-2.7/rpy2/robjects/methods.py", line 191, in __new__
    for name, meth in itertools.izip(all_methods.do_slot("names"), all_methods):
LookupError: The object has no such attribute.

----------------------------------------------------------------------
Ran 327 tests in 5.324s

FAILED (errors=2)
 * ERROR: dev-python/rpy-2.2.6 failed (test phase):
 *   Testing failed with CPython 2.7 in testing() function


Portage 2.1.10.49 (default/linux/x86/10.0/developer, gcc-4.5.3, glibc-2.14.1-r3, 3.1.6-gentoo i686)
=================================================================
System uname: Linux-3.1.6-gentoo-i686-Intel-R-_Core-TM-2_Duo_CPU_P8700_@_2.53GHz-with-gentoo-2.1
Timestamp of tree: Mon, 04 Jun 2012 09:00:01 +0000
app-shells/bash:          4.2_p20
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.3-r1, 3.2.3
dev-util/cmake:           2.8.7-r5
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.9.8.4
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.10.3, 1.11.1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            4.5.3-r2
sys-devel/gcc-config:     1.6
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 3.1 (virtual/os-headers)
sys-libs/glibc:           2.14.1-r3
Repositories: gentoo x-portage
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="*"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=i686 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /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 -march=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs collision-protect compress-build-logs distlocks ebuild-locks fixlafiles multilib-strict news parallel-fetch protect-owned sandbox sfperms sign splitdebug strict test test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j3"
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="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa berkdb bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus device-mapper dri dts dvd dvdr emacs emboss encode exif fam firefox flac fortran gdbm gif git gnutls gtk iconv icu jpeg lcms libkms libnotify mad mbox mercurial mmx mng modules mp3 mp4 mpeg mudflap ncurses nls nptl nss objc ogg opengl openmp pam pango pcre pdf perl png policykit ppds pppd python qt3support readline sdl secure-delete session snmp spell sqlite sse ssl startup-notification subversion svg tcb tcpd threads tiff tk toolkit-scroll-bars truetype udev udisks unicode upower usb vorbis wxwidgets x264 x86 xcb xft xinerama xml xorg xulrunner xv xvfb xvid zlib" ALSA_CARDS="ens1371" 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" INPUT_DEVICES="evdev keyboard vmmouse" 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 ruby19" USERLAND="GNU" VIDEO_CARDS="vmware vesa vga" 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, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

$ qlist -ICv dev-python
dev-python/PyQt4-4.9.1
dev-python/argparse-1.2.1
dev-python/astng-0.21.1
dev-python/authres-0.401
dev-python/beautifulsoup-3.2.0
dev-python/bpython-0.10.1
dev-python/chardet-2.0.1
dev-python/coverage-3.5.1
dev-python/cython-0.14.1
dev-python/dbus-python-1.0.0
dev-python/decorator-3.3.2
dev-python/docutils-0.8.1
dev-python/dulwich-0.8.1
dev-python/egenix-mx-base-3.1.3
dev-python/enthoughtbase-3.1.0
dev-python/etsdevtools-3.1.1
dev-python/feedparser-5.1.2
dev-python/genshi-0.6
dev-python/html2text-3.200.3
dev-python/imaging-1.1.7-r1
dev-python/jaxml-3.02
dev-python/jinja-2.6
dev-python/logilab-common-0.55.2
dev-python/lxml-2.3.4
dev-python/markupsafe-0.15
dev-python/matplotlib-1.1.0
dev-python/mechanize-0.2.5
dev-python/nose-1.1.2
dev-python/notify-python-0.1.1-r2
dev-python/numpy-1.6.1-r1
dev-python/paramiko-1.7.7.1
dev-python/pexpect-2.4
dev-python/ply-3.4
dev-python/py-1.4.7
dev-python/py-gnupg-0.3.2
dev-python/pyPdf-1.13
dev-python/pycairo-1.10.0-r2
dev-python/pychecker-0.8.19
dev-python/pycrypto-2.6
dev-python/pycxx-6.2.4-r1
dev-python/pydns-2.3.4
dev-python/pyftpdlib-0.7.0
dev-python/pygments-1.5
dev-python/pygobject-2.28.6-r51
dev-python/pygobject-3.0.4
dev-python/pygtk-2.24.0-r2
dev-python/pygtksourceview-2.10.1
dev-python/pylint-0.23.0
dev-python/pyopengl-3.0.1
dev-python/pyopenssl-0.12
dev-python/pyparsing-1.5.6
dev-python/pyparted-3.8-r1
dev-python/pyro-3.16
dev-python/pyro-4.11
dev-python/pyside-1.1.1
dev-python/pyside-tools-0.2.13-r2
dev-python/pyspf-2.0.5
dev-python/pysqlite-2.6.3
dev-python/pysvn-1.7.5
dev-python/pytest-2.0.3
dev-python/python-dateutil-1.5
dev-python/python-poppler-0.12.1-r3
dev-python/pytz-2012c
dev-python/pyudev-0.15
dev-python/pyxdg-0.19
dev-python/rpy-2.2.6
dev-python/scientificpython-2.9.1
dev-python/setuptools-0.6.21
dev-python/shiboken-1.1.1
dev-python/simplejson-2.5.0
dev-python/sip-4.13.2-r1
dev-python/sphinx-1.1.2
dev-python/traits-4.1.0
dev-python/traitsbackendqt-3.6.0
dev-python/traitsbackendwx-3.6.0
dev-python/traitsgui-3.6.0-r1
dev-python/twisted-11.0.0
dev-python/unittest2-0.5.1
dev-python/wxpython-2.8.12.1
Comment 1 Ian Delaney (RETIRED) gentoo-dev 2012-06-08 16:19:10 UTC 
archtester rpy # USE_PYTHON="2.6 2.7" ebuild rpy-2.2.6.ebuild clean test

>>> Source compiled.
 * Testing of dev-python/rpy-2.2.6 with CPython 2.6...
.......................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 327 tests in 3.326s

OK
 * Testing of dev-python/rpy-2.2.6 with CPython 2.7...
.......................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 327 tests in 3.332s

OK

couldn't replicate.  only minor diffs in python version, main diff is $ARCH
Comment 2 Sébastien Fabbro (RETIRED) gentoo-dev 2012-06-19 16:44:54 UTC 
can't reproduce here either. please confirm.
Comment 3 Myckel Habets 2012-07-21 15:45:14 UTC 
I get the same on x86.

emerge --info
Portage 2.1.10.65 (default/linux/x86/10.0, gcc-4.5.3, glibc-2.14.1-r3, 3.2.21-gentoo i686)
=================================================================
System uname: Linux-3.2.21-gentoo-i686-Intel-R-_Celeron-R-_CPU_2.40GHz-with-gentoo-2.1
Timestamp of tree: Sat, 21 Jul 2012 07:00:01 +0000
distcc 3.1 i686-pc-linux-gnu [enabled]
app-shells/bash:          4.2_p20
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.3-r2, 3.2.3
dev-util/cmake:           2.8.6-r4
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.9.8.4
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.11.1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            4.5.3-r2
sys-devel/gcc-config:     1.6
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 3.1 (virtual/os-headers)
sys-libs/glibc:           2.14.1-r3
Repositories: gentoo x-portage
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="* -@EULA -dlj-1.1"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=pentium4 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /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/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /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 -march=pentium4 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -march=i686 -pipe"
FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distcc distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv"
FFLAGS="-O2 -march=i686 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="nl"
MAKEOPTS="-j2"
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="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X accessibility acl alsa apng avahi bash-completion berkdb bluetooth bzip2 cairo cli consolekit corefonts cracklib crypt cups curl cxx dbus deprecated devil dri examples expat extensions extras fam fbcon fontconfig fortran fts3 gdbm gdu gif glib gmp gnutls gpm gtk gtk3 gudev hwdb iconv ipv6 java jpeg lapack libnotify libssh2 md5sum midi mikmod minizip mmx mod modules mp3 mudflap ncurses nls nptl nsplugin objc ogg opengl openmp pam pcre php pic png policykit pppd python readline sdl session smpeg sockets sqlite3 sse sse2 ssl startup-notification svg tcpd threads thunar tiff timidity tk tordns truetype udev unicode v4l2 vorbis webdav x86 xcb xml xorg xvfb zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="nl" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19 jruby ree18" USERLAND="GNU" VIDEO_CARDS="vesa intel" 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
Comment 4 Andreas Schürch gentoo-dev 2012-08-13 10:46:23 UTC 
The same thing happen for me on x86.

See https://bitbucket.org/lgautier/rpy2/issue/79/errors-when-running-python-m-rpy2tests

Seems like we would need a newer dev-lang/R!
Comment 5 Ian Delaney (RETIRED) gentoo-dev 2012-11-06 05:10:45 UTC 
rpy # USE_PYTHON="2.6 2.7 2.7-pypy-1.9 " ebuild rpy-2.2.6.ebuild clean test

fixed with new versionns of dev-lang/R

 * Testing of dev-python/rpy-2.2.6 with CPython 2.6...
Ran 327 tests in 3.429s

OK
 * Testing of dev-python/rpy-2.2.6 with CPython 2.7...
Ran 327 tests in 3.421s

OK
Comment 6 Myckel Habets 2012-11-09 20:40:11 UTC 
*** Bug 442500 has been marked as a duplicate of this bug. ***