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"
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