I only tested a hmmer and blast search and instantiated a few sequences for fun. Reproducible: Always Steps to Reproduce: 1. 2. 3. Portage 2.0.53_rc4 (default-linux/amd64/2005.0, gcc-3.4.4, glibc-2.3.5-r2, 2.6.13-gentoo-r2 x86_64) ================================================================= System uname: 2.6.13-gentoo-r2 x86_64 AMD Athlon(tm) 64 Processor 3500+ Gentoo Base System version 1.12.0_pre8 distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] dev-lang/python: 2.3.5-r2, 2.4.2 sys-apps/sandbox: 1.2.13 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.15.92.0.2-r1, 2.16.1 sys-devel/libtool: 1.5.20 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="amd64 ~amd64" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=athlon64 -O2 -pipe -nopie -fno-stack-protector -fno-stack-protector-all" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-march=athlon64 -O2 -pipe -nopie -fno-stack-protector -fno-stack-protector-all" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks sfperms strict" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="amd64 X alsa apache2 arts avi bash-completion berkdb bitmap-fonts bonobo bzlib cdr crypt cups curl dba dv dvdr dvdread eds emboss encode esd faad fam fame ffmpeg flac foomaticdb fortran gd gd-external gdbm ggi gif gimpprint gnome gpm gstreamer gtk gtk2 gtkhtml imagemagick imap imlib ipv6 jabber java jikes joystick jpeg junit kde kerberos ldap libwww lzw lzw-tiff mad mjpeg motif mozilla mp3 mpeg mysql ncurses nls nptl offensive ogg opengl pam pcre pdflib perl pic png pop ppds python qt quicktime readline ruby samba scanner sdk sdl session slang spell ssl svg tcltk tcpd tetex theora tiff truetype truetype-fonts type1-fonts unicode usb userlocales vorbis xine xinerama xml xml2 xmms xosd xpm xv zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS
and I would like to add that 1.5.1 is available now as well: http://news.open-bio.org/archives/2005_10.html#000084
Olivier or sci herd, before we can keyword this ~amd64, please fix the following: *) REQUIRED: bioperl-run requires at least an RDEPEND on bioperl. Most of the perl modules installed by -run have the line "use Bio::Root::Root", which is provided by the base bioperl package Greg: you already filed a bug on that. bug #79459 <-- please
amd64: Dependencies are now fixed. Do you want to keyword this?
Can you provide test cases outside of the perl-driven make test? make test passed, but mostly for a lack of tools to test with, but when I try running the samples and examples (with a threaded perl, which may or may not be the issue) I get this every time: STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib64/perl5/vendor_perl/5.8.8/Bio/Root/Root.pm:328 STACK: try{} block /usr/lib64/perl5/vendor_perl/5.8.8/Bio/Tools/Run/Analysis/soap.pm:107 STACK: SOAP::Lite::call /usr/lib64/perl5/vendor_perl/5.8.8/SOAP/Lite.pm:3387 STACK: try{} block /usr/lib64/perl5/vendor_perl/5.8.8/SOAP/Lite.pm:3352 STACK: Bio::Tools::Run::Analysis::soap::input_spec /usr/lib64/perl5/vendor_perl/5.8.8/Bio/Tools/Run/Analysis/soap.pm:305 STACK: ./papplmaker.PLS:137 Also, shouldn't bioperl-run-1.5.1 depend on bioperl-1.5.1 instead of the generic bioperl? (I thought the versions were linked)
Quoting from http://www.bioperl.org/wiki/Main_Page : # Core package provides the main parsers, this is the basic package and it's required by all the other packages (bioperl-live CVS directory) # Run package provides wrappers for executing some 60 common bioinformatics applications (bioperl-run in CVS) # Ext package is for C-language extensions including some alignment algorithms and an interface to the Staden IO library (bioperl-ext in CVS). # GUI package includes some basic widgets in Perl-Tk (bioperl-gui in CVS). # BioPerl db is a subproject to store sequence and annotation data in a BioSQL relational database (bioperl-db in CVS). # Pedigree package is for manipulating genotype, marker, and individual data for linkage studies (bioperl-pedigree in CVS) # Microarray package has preliminary objects for manipulating some microarray data formats (bioperl-microarray in CVS) # Network package parses and analyzes protein-protein interaction data (bioperl-network in CVS). # Pipeline package is a project for creating analysis pipelines out of bioperl-run modules (bioperl-pipeline in CVS).
File collision during emerge: * checking 366 files for package collisions existing file /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux/auto/Bio/.packlist is not owned by this package Searching all installed packages for file collisions... Press Ctrl-C to Stop * sci-biology/bioperl-1.5.1-r1: '/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux/auto/Bio/.packlist' Without collision-protect this emerges fine, passes the tests (though most of them are skipped due to missing tools). sci-biology: Can you please provide some test cases so we can make sure this actually works before keywording it? Or are the few tests during emerge enough?
The burden is still on sci-biology here, no matter who you reassign it to. We're just looking for some verification of the install working beyond it emerging and passing the tests (that don't seem to be too viable anyway).
(In reply to comment #7) > The burden is still on sci-biology here, no matter who you reassign it to. > We're just looking for some verification of the install working beyond it > emerging and passing the tests (that don't seem to be too viable anyway). So how's it going? ;)
Sorry, but I have no time for that right now and I am pretty much the only more or less active dev in sci-biology. If amd64 wants to go ahead, that is fine by me, but I cannot provide help at this time. Marking as LATER, feel free to reopen.
I'm working on it too Olivier...it just takes me a long time to test things thoroughly...
I also watch sci-biology and will help out; however, since I am the only dev in sci-mathematics right now time is pretty scarce at the moment ;) Markus
