Bug 496133

For those not following the devel list, it turned out that the symlinks from -devel package are required by jemboss at runtime. One more thing that needs fixing.

Was any progress made on getting this package into shape?

Unfortunately not, my thesis work is taking up too much time currently. If somebody wants to contribute, feel free to do so.

Please clear the Whiteboard when this package is ready to show back up in the review queue.

New release:
Spec URL: http://belegdol.fedorapeople.org/EMBOSS.spec
SRPM URL: http://belegdol.fedorapeople.org/EMBOSS-6.1.0-1.fc11.src.rpm

Changes:
- Updated to 6.1.0
- Dropped pcre-devel from BuildRequires for the time being
- Ditto --with-java and --with-javaos
- Patched jemboss/Makefile.am not to include DESTDIR in runJemboss.sh
- Install the header files in EMBOSS subdir
- Added the missing executable bits

All the rpmlint errors have been eliminated, the following warnings remain:
EMBOSS.src: W: patch-not-applied Patch1: %{name}-system-pcre.patch
EMBOSS.x86_64: W: conffile-without-noreplace-flag /etc/profile.d/emboss.sh
EMBOSS.x86_64: W: conffile-without-noreplace-flag /etc/profile.d/emboss.csh
EMBOSS-devel.x86_64: W: no-documentation
EMBOSS-java.x86_64: W: spurious-executable-perm /usr/share/doc/EMBOSS-java-6.1.0/api/getClasses.pl
EMBOSS-java.x86_64: W: spurious-executable-perm /usr/share/doc/EMBOSS-java-6.1.0/api/makeDocs.csh
EMBOSS-java.x86_64: W: class-path-in-manifest /usr/share/EMBOSS/jemboss/lib/client.jar
EMBOSS-java.x86_64: W: class-path-in-manifest /usr/share/EMBOSS/jemboss/lib/axis/commons-logging.jar
EMBOSS-libs.x86_64: W: shared-lib-calls-exit /usr/lib64/libeplplot.so.3.2.7 exit.5
EMBOSS-libs.x86_64: W: no-documentation
6 packages and 0 specfiles checked; 0 errors, 10 warnings.

New release:
Spec URL: http://belegdol.fedorapeople.org/EMBOSS.spec
SRPM URL: http://belegdol.fedorapeople.org/EMBOSS-6.1.0-2.fc11.src.rpm

Changes:
- Added the upstream 1-2 patch

Created attachment 362799 [details]
patch to make EMBOSS use system pcre

Fixed and working (it compiles) patch to use system pcre attached. Please test if the software is working correctly.

(In reply to comment #5)
> All the rpmlint errors have been eliminated, the following warnings remain:
> EMBOSS-java.x86_64: W: class-path-in-manifest
> /usr/share/EMBOSS/jemboss/lib/client.jar

https://fedoraproject.org/wiki/Packaging:Java#class-path-in-manifest

> EMBOSS-java.x86_64: W: class-path-in-manifest
> /usr/share/EMBOSS/jemboss/lib/axis/commons-logging.jar

Isn't this the same as ant-commons-logging or jakarta-commons-logging, which are in Fedora already? If yes, then this needs to be fixed to use the system-provided package. If not, see above.

> EMBOSS-libs.x86_64: W: shared-lib-calls-exit /usr/lib64/libeplplot.so.3.2.7
> exit.5

It shouldn't do that. Please explain that to upstream.

The patch you posted seems to work correctly. When it comes to other comments, I'm not sure how to get rid of the class path from manifest files. That's because afaik the .jar files are already shipped as compressed.

I have a crazy idea of dropping the jemboss part altogether, given that I feel it's beyond me to fix all issues with it. What do you think?

(In reply to comment #9)
> I'm not sure how to get rid of the class path from manifest files. That's
> because afaik the .jar files are already shipped as compressed.  

Wait. You mean they are not built from source? You can't ship them like that. See https://fedoraproject.org/wiki/Packaging:Guidelines#No_inclusion_of_pre-built_binaries_or_libraries

(In reply to comment #10)
> I have a crazy idea of dropping the jemboss part altogether, given that I feel
> it's beyond me to fix all issues with it. What do you think?  

That's acceptable as well. Just make sure all the issues are fixed when you decide to enable it later.

FYI, /usr/bin/chaos conflicts with the 'chaos aligment tool' from the lagan package.

New release:
Spec URL: http://belegdol.fedorapeople.org/EMBOSS.spec
SRPM URL: http://belegdol.fedorapeople.org/EMBOSS-6.1.0-4.fc11.src.rpm

Changes:
* Mon Oct 05 2009 Julian Sikorski <belegdol> - 6.1.0-4
- Renamed conflicting binaries
- Disabled jemboss

* Tue Sep 29 2009 Julian Sikorski <belegdol> - 6.1.0-3
- Re-enabled system pcre usage
- Initial attempt at using system-wide .jar files

I have decided to yank jemboss for the time being. The shared-lib-calls-exit issue has been reported upstream.

Builds fine in mock/F-10/x86_64

$ rpmlint /var/lib/mock/fedora-10-x86_64/result
EMBOSS-devel.x86_64: W: no-documentation
EMBOSS.x86_64: W: conffile-without-noreplace-flag /etc/profile.d/emboss.sh
EMBOSS.x86_64: W: conffile-without-noreplace-flag /etc/profile.d/emboss.csh
EMBOSS-libs.x86_64: W: shared-lib-calls-exit /usr/lib64/libeplplot.so.3.2.7 exit.5
EMBOSS-libs.x86_64: W: no-documentation
5 packages and 0 specfiles checked; 0 errors, 5 warnings.

According to licensecheck from rpmdevtools, files in
scripts/
plplot/
ajax/
and some files in jemboss/ are missing licensing information. Please upstream to add appropriate license headers to these files.

MD5 checksum OK:
6c5163c571bc0be94d64420ce0d71824  EMBOSS-6.1.0.tar.gz

Please add comments explaining the purpose of each patch and if it has been sent upstream.

Other than that, this package looks fine and is APPROVED. Thanks for your hard work.

New release:
Spec URL: http://belegdol.fedorapeople.org/EMBOSS.spec
SRPM URL: http://belegdol.fedorapeople.org/EMBOSS-6.1.0-5.fc11.src.rpm

Changes:
* Sat Oct 17 2009 Julian Sikorski <belegdol> - 6.1.0-5
- Added comments explaining the purpose of each patch

New Package CVS Request
=======================
Package Name: EMBOSS
Short Description: The European Molecular Biology Open Software Suite
Owners: belegdol
Branches: devel F-12 F-11
InitialCC:

Thanks for packaging this!
Is it possible to add it to F-10 as well?

Cheers.

On the second thought, F-10 will still be around for a while, so why not.

New Package CVS Request
=======================
Package Name: EMBOSS
Short Description: The European Molecular Biology Open Software Suite
Owners: belegdol
Branches: F-12 F-11 F-10
InitialCC:

Thanks!

cvs done.

It turned out that the package triggers an error in gcc.

EMBOSS-6.1.0-5.fc10 has been submitted as an update for Fedora 10.
http://admin.fedoraproject.org/updates/EMBOSS-6.1.0-5.fc10

EMBOSS-6.1.0-5.fc11 has been submitted as an update for Fedora 11.
http://admin.fedoraproject.org/updates/EMBOSS-6.1.0-5.fc11

EMBOSS-6.1.0-5.fc12 has been submitted as an update for Fedora 12.
http://admin.fedoraproject.org/updates/EMBOSS-6.1.0-5.fc12

EMBOSS-6.1.0-5.fc10 has been pushed to the Fedora 10 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update EMBOSS'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F10/FEDORA-2009-10641

EMBOSS-6.1.0-5.fc11 has been pushed to the Fedora 11 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update EMBOSS'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F11/FEDORA-2009-10649

EMBOSS-6.1.0-5.fc10 has been pushed to the Fedora 10 stable repository.  If problems still persist, please make note of it in this bug report.

EMBOSS-6.1.0-5.fc11 has been pushed to the Fedora 11 stable repository.  If problems still persist, please make note of it in this bug report.

*** Bug 555100 has been marked as a duplicate of this bug. ***