Spec URL: http://belegdol.fedorapeople.org/EMBOSS.spec SRPM URL: http://belegdol.fedorapeople.org/EMBOSS-6.0.1-2.fc10.src.rpm Description: EMBOSS is a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. Reference for EMBOSS: Rice,P. Longden,I. and Bleasby,A. "EMBOSS: The European Molecular Biology Open Software Suite" Trends in Genetics June 2000, vol 16, No 6. pp.276-277 This package is not yet finished, but I thought that bringing the polishing part into public cannot hurt. It builds fine on all primary architectures: https://koji.fedoraproject.org/koji/taskinfo?taskID=1302809 rpmlint is not silent yet, since I'm not sure how to handle the warnings regarding the executable permissions: 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-6.0.1/api/makeDocs.csh EMBOSS-java.x86_64: E: non-executable-script /usr/share/EMBOSS/jemboss/utils/install-jemboss-server.sh 0644 EMBOSS-java.x86_64: E: non-executable-script /usr/share/EMBOSS/jemboss/utils/makeJar.csh 0644 EMBOSS-java.x86_64: E: non-executable-script /usr/share/EMBOSS/jemboss/api/getClasses.pl 0644 EMBOSS-java.x86_64: E: non-executable-script /usr/share/EMBOSS/jemboss/utils/makeFileManagerJNLP.sh 0644 EMBOSS-java.x86_64: E: non-executable-script /usr/share/EMBOSS/jemboss/api/makeDocs.csh 0644 EMBOSS-java.x86_64: E: non-executable-script /usr/share/EMBOSS/jemboss/runJemboss.sh 0644 EMBOSS-java.x86_64: E: non-executable-script /usr/share/EMBOSS/jemboss/utils/makeJNLP.sh 0644 EMBOSS-java.x86_64: W: spurious-executable-perm /usr/share/doc/EMBOSS-java-6.0.1/api/getClasses.pl EMBOSS-java.x86_64: E: non-executable-script /usr/share/EMBOSS/jemboss/utils/keys.sh 0644 EMBOSS-java.x86_64: W: doc-file-dependency /usr/share/doc/EMBOSS-java-6.0.1/api/getClasses.pl /usr/bin/perl 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 5 packages and 0 specfiles checked; 8 errors, 9 warnings.
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. ***