Bugzilla Bug 38169

Upon trying to emerge bioperl-1.4, the emerge fails after the various tests are
performed.

Reproducible: Always
Steps to Reproduce:
1. ACCEPT_KEYWORDS="~x86" emerge bioperl


Actual Results:  
Emerge fails with:

...
Failed Test Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/GFF.t        9  2304    32   24  75.00%  21-32
121 subtests skipped.
Failed 1/179 test scripts, 99.44% okay. 12/8273 subtests failed, 99.85% okay.
make: *** [test_dynamic] Error 255

!!! ERROR: app-sci/bioperl-1.4 failed.
!!! Function src_compile, Line 45, Exitcode 2
!!! Test Failed


Expected Results:  
A successful upgrade from bioperl-1.2.3

Portage 2.0.49-r20 (default-x86-1.4, gcc-3.2.3, glibc-2.3.2-r3,
2.6.1-rc3-gentoo)
=================================================================
System uname: 2.6.1-rc3-gentoo i686 AMD Athlon(tm) MP 2000+
Gentoo Base System version 1.4.3.10p1
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CFLAGS="-march=athlon-mp -Os -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
COMPILER="gcc3"
CONFIG_PROTECT="/etc /usr/X11R6/lib/X11/xkb /usr/kde/2/share/config
/usr/kde/3.1/share/config /usr/kde/3/share/config /usr/share/config
/usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/
/var/qmail/control"CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d"
CXXFLAGS="-march=athlon-mp -Os -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs ccache sandbox"
GENTOO_MIRRORS="http://www.mirror.ac.uk/sites/www.ibiblio.org/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X aalib apm arts avi berkdb bonobo cdr crypt cups directfb encode esd
fbcon
foomaticdb gdbm ggi gif gnome gpm gtk gtk2 gtkhtml guile imap imlib jpeg ldap
libg++ libwww mad mikmod motif mozilla mpeg ncurses nls oggvorbis opengl oss
pam
pdflib perl png postgres python quicktime readline sdl slang spell sse ssl svga
tcltk tcpd tetex truetype x86 xml2 xmms xv zlib"

N.B. this also fails with -O2 in CFLAGS instead of -Os

The bioperl tests have always been a beast (meaning some usually fail). This
release though,  I ran through the tests without a failure and thought that
they had managed to clean up their act.  

Short term fix,  comment out line 45 in the ebuild.
'perl-module_src_test || die "Test Failed" '

That should get it installed.  

I think that the problem may be that the tests they are running reference a
bioperl-run module by accident.  And you don't have bioperl-run installed it
will fail.  You could also try that.  I'll look into it more but one of those
two should get you installed.  

- Steve

Deleting line 45 did the trick, thanks. I had installed bioperl-run, and
upgrading it before upgrading bioperl didn't make any difference.

Added a src_test() function to the ebuild, so you can enable the tests if you
want using FEATURES=maketest. I guess this fixes the issue.