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Bug 458700 - dev-python/rpy test failure with py3
Summary: dev-python/rpy test failure with py3
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Python Gentoo Team
URL: https://bitbucket.org/lgautier/rpy2/i...
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2013-02-22 07:45 UTC by Patrick Lauer
Modified: 2013-03-07 07:26 UTC (History)
1 user (show)

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


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Description Patrick Lauer gentoo-dev 2013-02-22 07:45:52 UTC
>>> Source compiled.
 * Testing of dev-python/rpy-2.3.2 with CPython 2.7...
rpy2 version: 2.3.2
built against R version: 2-15.2--140152037694506
..............................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 334 tests in 3.897s

OK
 * Testing of dev-python/rpy-2.3.2 with CPython 3.2...
rpy2 version: 2.3.2
built against R version: 2-15.2--140066131836580
.......................................................................................................................................................................................................................................................................................F......................................................
======================================================================
FAIL: testVectorCharacter (rpy2.robjects.tests.testNumpyConversions.NumpyConversionsTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/var/tmp/portage/dev-python/rpy-2.3.2/work/rpy2-2.3.2/build-3.2/lib.linux-x86_64-3.2/rpy2/robjects/tests/testNumpyConversions.py", line 53, in testVectorCharacter
    self.checkHomogeneous(s, "character", "character")
  File "/var/tmp/portage/dev-python/rpy-2.3.2/work/rpy2-2.3.2/build-3.2/lib.linux-x86_64-3.2/rpy2/robjects/tests/testNumpyConversions.py", line 32, in checkHomogeneous
    self.assertEqual(list(obj), list(converted))
AssertionError: Lists differ: [b'a', b'b', b'c'] != [NA_character_, NA_character_,...

First differing element 0:
b'a'
NA

- [b'a', b'b', b'c']
+ [NA_character_, NA_character_, NA_character_]

----------------------------------------------------------------------
Ran 334 tests in 3.929s

FAILED (failures=1)
 * ERROR: dev-python/rpy-2.3.2 failed (test phase):
 *   Testing failed with CPython 3.2 in testing() function

Portage 2.1.11.52 (default/linux/amd64/13.0, gcc-4.6.3, glibc-2.16.0, 3.7.9-vs2.3.5.6 x86_64)
=================================================================
System uname: Linux-3.7.9-vs2.3.5.6-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2
KiB Mem:     7921088 total,   2101036 free
KiB Swap:   29360100 total,  29279192 free
Timestamp of tree: Unknown
ld GNU ld (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p42
dev-lang/python:          2.7.3-r3, 3.2.3-r2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.6
sys-devel/autoconf:       2.69
sys-devel/automake:       1.12.6, 1.13.1
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.7 (virtual/os-headers)
sys-libs/glibc:           2.16.0
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb"
CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
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=""
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="acl amd64 berkdb bzip2 cli cracklib crypt cxx dri egl fortran gdbm gpm iconv ipv6 mmx modules mudflap multilib ncurses nls nptl openmp openvg pam pcre readline session sqlite sse sse2 ssl tcpd unicode xa xvfb 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" 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="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" 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" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19" USERLAND="GNU" VIDEO_CARDS="vesa" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Justin Lecher (RETIRED) gentoo-dev 2013-02-22 09:17:22 UTC
+*rpy-2.3.2 (22 Feb 2013)
+
+  22 Feb 2013; Justin Lecher <jlec@gentoo.org> +rpy-2.3.2.ebuild, metadata.xml:
+  Version Bump, #458700; move to new python eclasses
+
Comment 2 Ian Delaney (RETIRED) gentoo-dev 2013-03-07 05:47:46 UTC
    changed status to resolved

Fixed in branches version_2.3.x (next release will be 2.3.4) and default (next release will be 2.4.0).

Note: with the 2.3.x series for rpy2, only Python 3.3 is supported.

jlec, does this mean we should go for 

PYTHON_COMPAT=( python{2_7,3_3} ) ?
Comment 3 Justin Lecher (RETIRED) gentoo-dev 2013-03-07 07:18:21 UTC
The changelog says

Release 2.2.0
=============

New Features
------------

- Support for Python 3, and for some of its features ported to Python 2.7


They are quite in consistent in what works and what is written.

I will have a closer look on it now
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2013-03-07 07:23:26 UTC
there is no support of py3 yet.
Comment 5 Justin Lecher (RETIRED) gentoo-dev 2013-03-07 07:26:56 UTC
+*rpy-2.3.3 (07 Mar 2013)
+
+  07 Mar 2013; Justin Lecher <jlec@gentoo.org> rpy-2.3.2.ebuild,
+  +rpy-2.3.3.ebuild:
+  Version Bump; drop py support to version 2.7, #458700
+