Version 1.6.0 released 10/10/2005. Significant improvements to speed and total number of reads that can be loaded.
Hi Jonathan, I was aware that Staden 1.6.0 was released, but decided not to make an ebuild for it. The reason is that the build system for the package (that was already extremely confusing and broken) seems to be getting worse. If you succeed in installing version 1.6.0 on a Gentoo system, please tell me how you did it; I will then be glad to update the package in Portage with your fixes. Otherwise, I think my time is better invested working on packages that are more developer friendly. Sorry,
cc -L/var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src/lib/linux-binaries -shared -o /var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src/lib/linux-binaries/libgap.so -L/var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src/lib/linux-binaries linux-binaries/gap-local.o linux-binaries/gap-remote.o linux-binaries/gap-if.o linux-binaries/gap-init.o linux-binaries/gap-dbstruct.o linux-binaries/gap-create.o linux-binaries/gap-error.o linux-binaries/stack_dump.o linux-binaries/gap-io.o linux-binaries/IO.o linux-binaries/io-reg.o linux-binaries/actf.o linux-binaries/IO2.o linux-binaries/seqInfo.o linux-binaries/parse_ft.o linux-binaries/IO3.o linux-binaries/io_utils.o linux-binaries/io_handle.o linux-binaries/gap-tcl.o linux-binaries/tk-io-reg.o linux-binaries/gap_cli_arg.o linux-binaries/gap_globals.o linux-binaries/newgap_cmds.o linux-binaries/init.o linux-binaries/consen.o linux-binaries/gap_hash.o linux-binaries/qual.o linux-binaries/qualIO.o linux-binaries/bubbl3.o linux-binaries/tagdb.o linux-binaries/notedb.o linux-binaries/active_tags.o linux-binaries/dbcheck.o linux-binaries/clones.o linux-binaries/extract.o linux-binaries/preass.o linux-binaries/list.o linux-binaries/reactions.o linux-binaries/probe.o linux-binaries/template.o linux-binaries/template_display.o linux-binaries/ruler_display.o linux-binaries/gap_canvas_box.o linux-binaries/hash.o linux-binaries/gap_array.o linux-binaries/show_relationships.o linux-binaries/fij.o linux-binaries/hash_lib.o linux-binaries/do_fij.o linux-binaries/auto_assemble.o linux-binaries/dis_readings.o linux-binaries/find_repeats.o linux-binaries/break_contig.o linux-binaries/quality_plot.o linux-binaries/readpair.o linux-binaries/contig_selector.o linux-binaries/complement.o linux-binaries/cs-object.o linux-binaries/list_proc.o linux-binaries/dstrand.o linux-binaries/oligo_sel.o linux-binaries/primlib.o linux-binaries/alter_rel.o linux-binaries/restriction_enzymes.o linux-binaries/stop_codon.o linux-binaries/assemble_direct.o linux-binaries/check_assembly.o linux-binaries/tagU2.o linux-binaries/mess.o linux-binaries/find_oligo.o linux-binaries/copy_db.o linux-binaries/contig_order.o linux-binaries/clip.o linux-binaries/notes.o linux-binaries/consistency_display.o linux-binaries/consistency_canvas_box.o linux-binaries/confidence_graph.o linux-binaries/reading_coverage.o linux-binaries/readpair_coverage.o linux-binaries/strand_coverage.o linux-binaries/find_fragments.o linux-binaries/vseqs.o linux-binaries/legacy.o linux-binaries/f2c.o linux-binaries/allelic_discreps.o linux-binaries/tkEditor.o linux-binaries/tkEdNames.o linux-binaries/tkEdUtils.o linux-binaries/edInterface.o linux-binaries/edUtils2.o linux-binaries/tagU1.o linux-binaries/undo.o linux-binaries/edExtend.o linux-binaries/edCommands.o linux-binaries/edMutations.o linux-binaries/tagEditor.o linux-binaries/searchUtils.o linux-binaries/tman_interface.o linux-binaries/tman_display.o linux-binaries/tman_cons.o linux-binaries/tman_diff.o linux-binaries/contigEditor.o linux-binaries/join.o linux-binaries/oligo.o -lread -lseq_utils -ltk_utils -L/var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src/lib/linux-binaries -ltk8.4 -L/var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src/lib/linux-binaries -ltcl8.4 -lm -L/usr/X11R6/lib -lX11 -lg -lmutlib -lmisc -lprimer3 -lg2c /usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../../../i686-pc-linux-gnu/bin/ld: cannot find -lg2c collect2: ld returned 1 exit status make[2]: *** [/var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src/lib/linux-binaries/libgap.so] Error 1 make[2]: Leaving directory `/var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src/gap4' make[1]: *** [gap4] Error 2 make[1]: Leaving directory `/var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src' make: *** [all] Error 2 !!! ERROR: sci-biology/staden-1.5.3-r1 failed. Call stack: ebuild.sh, line 1543: Called dyn_compile ebuild.sh, line 938: Called src_compile staden-1.5.3-r1.ebuild, line 130: Called die Any idea where that library should come from?
I did not manage to compile staden-1-6-0 using the make -f makefile.thirdparty approach. I haven't actually investitaged how the ebuild does that. :( The bug is filed at However, why do not you make a binary ebuild? I think it is easier way to provide the package. There are linux binaries at sourceforge. Further, it seems some features in bioperl need staden (file format conversion uses staden, some bioperl-ext cvs branch which is not in portage yet either).
Sorry, the URL is http://sourceforge.net/tracker/index.php?func=detail&aid=1536497&group_id=100316&atid=627058
bioperl-ext/README contains the following (therefore I thing io_lib and staden should be bumped up to get of those problems): o Notes for Bio::SeqIO::staden::read This extension needs the rest of the main bioperl distribution to function properly. It is only useful as a helper module for the SeqIO system to read sequence trace files handled by the Staden package's io_lib "read" library. You should have this library installed prior to installing Bio::SeqIO::staden::read, it's currently available at: ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/ Many users have noted that the io_lib install process often forgets to install the "os.h" file along with the rest of the include files; you may have to do this manually. If so, you may also have to install the "config.h" file for "os.h" to find all the information it needs. Finally, you may also need to edit "os.h" to #include <config.h> instead of #include "config.h" if you continue to get undefined symbol errors during compilation. On some OSes you may in fact have to do the OPPOSITE, meaning change <config.h> to "config.h". The bioperl-ext make process will prompt you for the LIB and INCLUDE locations (usually /usr/local/lib and usr/local/include/io_lib, respectively) of the io_lib "libread" library and Read.h header files, after trying to automatically find them. You may also specify these via the environment variables "IOLIB_LIB" and "IOLIB_INC", or via identically named options to perl Makefile.PL: perl Makefile.PL IOLIB_LIB=/opt/lib IOLIB_INC=/opt/include/io_lib Ignore any warnings about these options being unknown to MakeMaker. A failed compilation is most likely due to an incomplete io_lib installation; make sure that all the required io_lib ".h" files are in place (see above regarding "os.h" and "config.h").
Created attachment 94077 [details] sci-libs/io_lib/io_lib-1.9.0.ebuild There are some significant performance changes to the io_lib and io_lib should be upgraded with staden. io_lib now uses configure for build process. tested on ~x86.
Created attachment 94083 [details] sci-libs/io_lib/io_lib-1.9.0.ebuild Sorry, the libdir was wrong. I have managed to get compiled bioperl-ext against this io_lib installation: $ perl Makefile.PL Writing Makefile for Bio::Ext::Align Please tell us where your Staden io_lib "read" library is installed: [/usr/local/lib] /usr/lib Please tell us where your Staden io_lib "Read.h" header is installed: [/usr/include/io_lib] Writing Makefile for Bio::SeqIO::staden::read Writing Makefile for Bio One or more DATA sections were not processed by Inline. $ make [...] $ make install
Hi Martin, Thanks for your ebuild, which I just added to Portage. In light of the fact that our current Staden ebuild no longer compiles with GCC4, I will have a look at providing a replacement binary package (for 1.6). If you (or anyone else) happen to have such an ebuild, do not hesitate to post it here.
Maybe someone from the graphics are could have a look at the makefile and disable the bundled libpng tree and force usage of system-wide libpng? Sorry, I don't have the time myself now.
Olivier, pelase note bioperl only supports 1.8.12b and below. The 1.9 version has incompatible API. Probably provide also ebuild for 1.8.12b and keep 1.9 version masked until bioperl supports it. This was found by Chris Fields from bioperl email list.
Sorry, my previous answer was about io_lib, while this bugreport is named 'staden'. ;)
BioPerl (1.5.1-r1) now depends on io_lib 1.8* and blocks newer versions of the library.
Hmm, I keep bioperl installed manully from cvs sources. So, in my case, protage offers me to upgrade to io_lib-1.9-r1. :( I will have to block it manually ... But adding "<=sci-libs/io_lib-1.9.0" to /etc/portage/package.mask does not help and it still appears in "emerge -up world". :( Clues?
Hi Martin, You should use ">=sci-libs/io_lib-1.9" in package.mask. The line you suggest actually masks everything *before* 1.9.0 (and also 1.9.0). The BioPerl and io_lib (1.9.0 and later) ebuilds in Portage block each other to avoid this problem. I know I have not been very active lately, but I do plan to add a new staden-bin package in the tree soon. Cheers,
At last, Staden 1.7 (and io_lib 1.10.1) are in Portage as a new binary package (since upstream does not support building from sources, and the build system is unworkable).
(In reply to comment #2) -L/var/tmp/portage/staden-1.5.3-r1/work/staden-src-1-5-3/src/lib/linux-binaries > -ltcl8.4 -lm -L/usr/X11R6/lib -lX11 -lg -lmutlib -lmisc > -lprimer3 -lg2c > /usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../../../i686-pc-linux-gnu/bin/ld: > cannot find -lg2c > collect2: ld returned 1 exit status > make[2]: *** [cut] > Any idea where that library should come from? That was the fortran library belonging to g77, defined in staden-src-*/src/mk/linux.mk
