[Bug 496133] New: Review Request: EMBOSS - The European Molecular Biology Open Software Suite

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Summary: Review Request: EMBOSS - The European Molecular Biology Open Software Suite

https://bugzilla.redhat.com/show_bug.cgi?id=496133

           Summary: Review Request: EMBOSS - The European Molecular
                    Biology Open Software Suite
           Product: Fedora
           Version: rawhide
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: medium
          Priority: medium
         Component: Package Review
        AssignedTo: nobody at fedoraproject.org
        ReportedBy: belegdol at gmail.com
         QAContact: extras-qa at fedoraproject.org
                CC: notting at redhat.com, fedora-package-review at redhat.com
   Estimated Hours: 0.0
    Classification: Fedora


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 at GLIBC_2.2.5
EMBOSS-libs.x86_64: W: no-documentation
5 packages and 0 specfiles checked; 8 errors, 9 warnings.

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