| Summary: | sci-biology/staden-2.0.0: version bump | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Martin Mokrejš <mmokrejs> |
| Component: | New packages | Assignee: | Default Assignee for New Packages <maintainer-wanted> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | sci-biology, tcltk |
| Priority: | High | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | 311845, 311857 | ||
| Bug Blocks: | |||
| Attachments: |
staden-2.0.0.ebuild
staden-2.0.0.ebuild staden-2.0.0b7.ebuild staden-2.0.0.ebuild Makefile.in.patch ax_lib_samtools.m4.patch staden-2.0.0.ebuild staden-2.0.0.ebuild |
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Description
Martin Mokrejš
2010-03-28 23:07:00 UTC
Created attachment 225607 [details]
staden-2.0.0.ebuild
Created attachment 225615 [details] staden-2.0.0.ebuild Depend on app-arch/xz-utils and not app-arch/lzma. Depends on sci-biology/samtools also (bug #311857). Created attachment 241029 [details]
staden-2.0.0b7.ebuild
Version bump and added missing tklib dependency. The ebuild filename does not comply ebuild numbering scheme. Just stave it as staden-2.0.0.ebuild. ;)
tcltk@: please help with the tklib issue. Do we really have to specify hardcoded --with-tklib=/usr/lib/tklib0.5 in ebuild? I suspect the tklib-0.5.ebuild did not properly "register" itself into tkConfig.sh file? Or should there be tklibConfig.sh file instead? Created attachment 241065 [details] staden-2.0.0.ebuild Except sanbox violations this is a working ebuild. If you use distcc use just one CPU, sometimes some threads progress too quickly while some other does not (https://sourceforge.net/tracker/index.php?func=detail&aid=3038189&group_id=100316&atid=627058). It requires few patches, made by upstream for us during my attempts to get the package done. I think the Makefiles have to be tweaked to put something like ${IMAGEDIR} in front of the actual path. Please help. Created attachment 241067 [details]
Makefile.in.patch
Created attachment 241069 [details]
ax_lib_samtools.m4.patch
I need help with this:
>>> Install staden-2.0.0 into /var/tmp/portage/sci-biology/staden-2.0.0/image/ category sci-biology
mkdir -p /usr/lib/staden
mkdir -p /usr/bin
mkdir -p /usr/share/staden/etc
mkdir -p /usr/share/staden
mkdir -p /usr/share/staden/scripts
mkdir -p /usr/share/staden/tcl
mkdir -p /usr/share/doc
mkdir -p /usr/share/man
cp shlib.conf /usr/share/staden/etc
ACCESS DENIED open_wr: /usr/share/staden/etc/shlib.conf
cp: cannot create regular file `/usr/share/staden/etc/shlib.conf': Permission denied
make: *** [install] Error 1
* ERROR: sci-biology/staden-2.0.0 failed:
* make install failed
*
* Call stack:
* ebuild.sh, line 54: Called src_install
* environment, line 3293: Called die
* The specific snippet of code:
* make install || die "make install failed"
*
* If you need support, post the output of 'emerge --info =sci-biology/staden-2.0.0',
* the complete build log and the output of 'emerge -pqv =sci-biology/staden-2.0.0'.
* This ebuild is from an overlay: '/usr/local/portage/'
* The complete build log is located at '/var/tmp/portage/sci-biology/staden-2.0.0/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sci-biology/staden-2.0.0/temp/environment'.
* S: '/var/tmp/portage/sci-biology/staden-2.0.0/work/staden-2.0.0'
--------------------------- ACCESS VIOLATION SUMMARY ---------------------------
LOG FILE "/var/log/sandbox/sandbox-31424.log"
VERSION 1.0
FORMAT: F - Function called
FORMAT: S - Access Status
FORMAT: P - Path as passed to function
FORMAT: A - Absolute Path (not canonical)
FORMAT: R - Canonical Path
FORMAT: C - Command Line
F: open_wr
S: deny
P: /usr/share/staden/etc/shlib.conf
A: /usr/share/staden/etc/shlib.conf
R: /usr/share/staden/etc/shlib.conf
C: cp shlib.conf /usr/share/staden/etc
--------------------------------------------------------------------------------
(In reply to comment #8) > I need help with this: > DESTDIR or similar is not respecteded. Check the makefile for that. (In reply to comment #4) > tcltk@: please help with the tklib issue. Do we really have to specify > hardcoded --with-tklib=/usr/lib/tklib0.5 in ebuild? I suspect the > tklib-0.5.ebuild did not properly "register" itself into tkConfig.sh file? Or > should there be tklibConfig.sh file instead? > I removed the versioning in 0.5-r1 which should be actaully better. Created attachment 249855 [details]
staden-2.0.0.ebuild
This ebuild explicitly passes DESTDIR to "emake install".
Current svn contains some necessary fixes for DESTDIR support. The fixes will be in 2.0.0b8 once it is out (which will happen after some restructuring of the code and better 64bit support).
I am obsoleting the two patches which were here because for the DESTDIR support several extra were necessary and I do not have them I think handy anymore. Finally, there was a change to system.mk.in.
I propose we place into gentoo an svn snapshot or wait for some more time.
Created attachment 249912 [details]
staden-2.0.0.ebuild
Properly append ' --enable-64bit' to ${myconf}.
Comment on attachment 249912 [details]
staden-2.0.0.ebuild
Little bit tuned ebuild is in science overlay as of now. It looks for 2.0.0b8 which is tagged in svn sources of upstream but not yet available as tar.gz file on sourceforge. However, I made staden-9999.ebuild which works fine for me and is in the tree as well.
Closing myself because the ebuild are now in the tree. This was file when 2.0.0b8 was current and needed some extra patches. |
