Bug 25079

Summary:	bioperl-1.2 some pm's not installed where bioperl expects them
Product:	Gentoo Linux	Reporter:	Dick Repasky <rrepasky>
Component:	Current packages	Assignee:	Gentoo Perl team <perl>
Status:	RESOLVED WONTFIX
Severity:	normal	CC:	sediener
Priority:	High
Version:	unspecified
Hardware:	x86
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

Description Dick Repasky 2003-07-22 13:42:04 UTC

I just emerged app-sci/bioperl-1.2.  Two modules that I needed were not installed
where bioperl expects them SeqFeatureI.pm and FeatureHolderI.pm are expected in
Bio/Seq (because they are Bio::Seq modules).  They were installed in the parent
directory (Bio).  I haven't checked all modules in the Bio directory.  These two
modules were modules that I needed.

Reproducible: Always
Steps to Reproduce:
1. emerge bioperl
2. look for SeqFeatureI.pm and FeatureHolderI.pm in
/usr/lib/perl5/site_perl/5.8.0/Bio
Actual Results:  
The modules were in the wrong directory. My script failed with the message from
perl that the modules could not be found in @INC.

Expected Results:  
The modules should be  in /usr/lib/perl5/site_perl/5.8.0/Bio/Seq. My script should
run without error. Note that I've side-stepped the problem by creating symbolic 
links.

Portage 2.0.48-r5 (default-x86-1.4, gcc-3.2.3, glibc-2.3.2-r1)
=================================================================
System uname: 2.4.21-rc2-ac3 i686 Intel(R) Pentium(R) 4 CPU 3.06GHz
GENTOO_MIRRORS=" http://distfiles.gento.org/ ftp://ftp.ussg.iu.edu/pub/linux/gen 
too/ ftp://csociety-ftp.ecn.purdue.edu/pub/gentoo/ http://gentoo.oregonstate.edu 
/ http://www.ibiblio.org/pub/Linux/distributions/gentoo"
CONFIG_PROTECT="/etc /var/qmail/control /usr/kde/2/share/config /usr/kde/3/share 
/config /usr/X11R6/lib/X11/xkb /usr/kde/3.1/share/config /usr/share/config"
CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d"
PORTDIR="/usr/portage"
DISTDIR="/usr/portage/distfiles"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR_OVERLAY=""
USE="x86 3dnow apm avi foomaticdb libg++ mad mmx mpeg nls pdflib quicktime truet 
ype xml2 xmms xv zlib gdbm berkdb slang arts svga tcltk java mysql sdl pam libww 
w perl python esd imlib oggvorbis gtk qt kde opengl ldap -alsa cdr dvd crypt cup 
s dga encode gif -gpm -gnome -gtkhtml jpeg mbox mikmod motif mozilla ncurses oss 
 png readline -scanner spell -snmp ssl tcpd tetex tiff X"
COMPILER="gcc3"
CHOST="i686-pc-linux-gnu"
CFLAGS="-march=pentium3 -O3 -pipe"
CXXFLAGS="-march=pentium3 -O3 -pipe"
ACCEPT_KEYWORDS="x86"
MAKEOPTS="-j2"
AUTOCLEAN="yes"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
FEATURES="sandbox ccache"

Comment 1 Stephen Diener (RETIRED) gentoo-dev

2003-08-01 23:02:27 UTC

That was a change that the bioperl people made.  It is the same in 1.2.2 . I know it doesn't make any sense but I don't think that we should change how bioperl has their tree set up.  Who knows what that could end up messing up?

- Steve