Bugzilla Bug 120446

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 an attachment (id=94077) [edit]
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 an attachment (id=94083) [edit]
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).