Bug 365579 – dev-python/cython-0.14.1 fails test_all during python-updater, until it is itself installed, if the old python is removed before python-updater is run.

• Product: Gentoo Linux
• Status: RESOLVED NEEDINFO

[Description Kevin F. Quinn 2011-05-01 15:53:27 UTC]

I depclean'ed my system recently, which uninstalled python2.6. Ran python-updater to sort out resultant breakage, however cython failed to pass its tests as it couldn't find libpython2.6.  The relevant lines from the build log are:

----
test_all (Cython.Debugger.Tests.TestLibCython.TestAll) ... gdb: error while loading shared libraries: libpython2.6.so.1.0: cannot open shared object file: No such file or directory
ERROR
----

I then skipped the tests and allowed the package to install:

 touch /var/tmp/portage/dev-python/cython-0.14.1/.tested
 ebuild /usr/portage/dev-python/cython/cython-0.14.1.ebuild install qmerge

then re-ran the test phase:

 rm /var/tmp/portage/dev-python/cython-0.14.1/.tested
 ebuild /usr/portage/dev-python/cython/cython-0.14.1.ebuild test

and the same tests shows a different result, which is non-fatal:

----
test_all (Cython.Debugger.Tests.TestLibCython.TestAll) ... Python was not compiled with debug symbols (or it was stripped). Some functionality may not work (properly).
/var/tmp/portage/dev-python/cython-0.14.1/work/Cython-0.14.1/Cython/Debugger/Tests/test_libcython_in_gdb.py:430: UserWarning: Unable to run tests, Python was not compiled with debugging information. Either compile python with -g or get a debug build (configure with --with-pydebug).
  warnings.warn(msg)
ok
----

This implies to me that this particular test case is using cython from the live system, not from the build area, and during the update of course the live system version referred to libpython2.6.so.  Following installation, the live system version now refers to libpython2.7.so, and the test proceeds in an orderly fashion.

Given that the test requires python itself to be built with debug information in order to work and is therefore effectively not run anyway,  it may be simplest just to exclude this one test case.


Reproducible: Always

Steps to Reproduce:
1.Start with a system that has python 2.6, and no python 2.7
2.Upgrade to python 2.7
3.emerge --depclean
4.python-updater
Actual Results:  
cython fails to update, as its tests depend on the live system installation

Expected Results:  
cython tests should use the cython from the build area not the live system, whereupon it would complete its test phase successfully.

Steps to reproduce I've just guessed :)  It may be the case that running python-updated _before_ doing depclean might work, as it may leave python2.6 in place until the stuff that depends on 2.6 has been updated to depend instead on 2.7, in which case the test case in question would still find libpython2.6 in place.  However the fact it uses its own package stuff from the live system is wrong.

# emerge --info
FEATURES variable contains unknown value(s): pax
Portage 2.1.9.42 (default/linux/x86/10.0, gcc-4.4.5, libc-0-r0, 2.6.38-gentoo-r1 i686)
=================================================================
System uname: Linux-2.6.38-gentoo-r1-i686-AMD_Athlon-tm-_XP_2500+-with-gentoo-1.12.14
Timestamp of tree: Thu, 28 Apr 2011 20:30:01 +0000
app-shells/bash:     4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.7.1-r1, 3.1.3-r1
dev-util/cmake:      2.8.1-r2
sys-apps/baselayout: 1.12.14-r1
sys-apps/sandbox:    2.4
sys-devel/autoconf:  2.13, 2.65-r1
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.5
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
sys-devel/make:      3.81-r2
sys-kernel/linux-headers: 2.6.36.1
virtual/os-headers:  0
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm AdobeFlash-10.1"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=athlon-xp -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /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=athlon-xp -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs collision-protect distlocks fixlafiles fixpackages news parallel-fetch pax protect-owned sandbox sfperms sign strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv"
FFLAGS=""
GENTOO_MIRRORS="http://www.mirrorservice.org/sites/www.ibiblio.org/gentoo/ http://gentoo.virginmedia.com/ http://mirror.qubenet.net/mirror/gentoo/"
LANG="en_GB"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-O1"
LINGUAS="en_GB en it de es fr"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/overlays/tree"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow X a52 aac acl acpi alsa apache2 arts audiofile berkdb bluetooth bzip2 cairo caps cdparanoia cdr cli cracklib crypt cups cvs cxx dbus dri dts dv dvb dvd dvdr encode fam ffmpeg firefox flac fontconfig foomaticdb fortran gcj gcrypt gdbm gif gnutls gpm gstreamer gtk iconv imagemagick imap imlib ipod ipv6 jack jadetex java javascript jbig jpeg jpeg2k kde ldap mad mime mmap mmx mng modules mp3 mpeg mplayer mudflap nas ncurses nls nptl nptlonly nsplugin offensive ogg opengl openmp pam pcre pda pdf perl png pppd python qt3 qt4 quicktime readline ruby samba sdl semantic-desktop session sip speex spell sse ssl subversion svg sysfs tcl tcpd test theora threads tidy tiff tk truetype unicode usb v4l v4l2 vcd vim-syntax vorbis wav wifi win32codecs wmf x264 x86 xcomposite xine xinerama xml xmlrpc xorg xulrunner xv xvid 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 auth_digest authn_anon authn_dbd 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 dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" 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 mouse keyboard" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en_GB en it de es fr" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon vesa vga radeonhd" 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

[Comment 1 Kevin F. Quinn 2011-05-01 16:03:29 UTC]

Created attachment 271767 [details]
Build log - shows initial emerge, also includes forced install/qmerge and partial retry of test phase

[Comment 2 Arfrever Frehtes Taifersar Arahesis 2011-11-09 15:49:44 UTC]

I think that your /usr/bin/gdb was still linked against libpython2.6.so.1.0.

[Comment 3 Mike Gilbert 2012-05-31 15:19:55 UTC]

(In reply to comment #2)

That seems likely. Please reopen if you find evidence to the contrary.