[Bug 717473] New: Review Request: SeqAn - Biological sequence analysis library - package-review

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[Bug 717473] New: Review Request: SeqAn - Biological sequence analysis library

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[Bug 505154] Tracker: Review...

Red Hat Bugzilla

28 Jun 2011 28 Jun '11

4:39 p.m.

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Summary: Review Request: SeqAn - Biological sequence analysis library

https://bugzilla.redhat.com/show_bug.cgi?id=717473

Summary: Review Request: SeqAn - Biological sequence analysis library Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: medium Component: Package Review AssignedTo: nobody@fedoraproject.org ReportedBy: bloch@verdurin.com QAContact: extras-qa@fedoraproject.org CC: notting@redhat.com, package-review@lists.fedoraproject.org Classification: Fedora Story Points: ---

Spec URL: http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn.spec SRPM URL: http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn-1.3-4.fc15.src.rpm Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

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Red Hat Bugzilla

28 Jun 28 Jun

4:40 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=717473

Adam Huffman bloch@verdurin.com changed:

What |Removed |Added ---------------------------------------------------------------------------- Blocks| |708402

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Red Hat Bugzilla

5:25 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

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https://bugzilla.redhat.com/show_bug.cgi?id=717473

Volker Fröhlich volker27@gmx.at changed:

What |Removed |Added ---------------------------------------------------------------------------- CC| |volker27@gmx.at

--- Comment #1 from Volker Fröhlich volker27@gmx.at 2011-06-28 18:25:32 EDT --- Rabema and Stellar are licensed as GPLv3+, other components are LGPLv3+.

Did you manage to use the system wide samtools?

The package doesn't build in Mock or with rpmbuild: rm: cannot remove `SeqAn-1.3/apps/stellar/examples/reads.fasta': Permission denied ...

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Red Hat Bugzilla

29 Jun 29 Jun

1:58 a.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #2 from Adam Huffman bloch@verdurin.com 2011-06-29 02:58:17 EDT --- Thanks for looking - it definitely needs more work, I just wanted to start the process.

Puzzled by the error as it builds fine in Mock for me (for F15 - for some reason it complains about not being able to find samtools-devel on F14).

There's also a question of naming. Upstream they oscillate between SeqAn, Seqan and seqan...

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Red Hat Bugzilla

5:41 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #3 from Volker Fröhlich volker27@gmx.at 2011-06-29 18:41:02 EDT --- The tests aren't executed.

I found out, what causes my build troubles:

+ rm -rf SeqAn-1.3 rm: cannot remove `SeqAn-1.3/apps/stellar/examples/reads.fasta': Permission denied rm: cannot remove `SeqAn-1.3/apps/stellar/examples/NC_001477.fasta': Permission denied rm: cannot remove `SeqAn-1.3/apps/stellar/examples/NC_001474.fasta': Permission denied

The examples directory ends up with 644, although it isn't like that in the tarball. I happens while installing:

+ chmod 0644 /builddir/build/BUILD/SeqAn-1.3/apps/stellar/README /builddir/build/BUILD/SeqAn-1.3/apps/stellar/examples [...]

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Red Hat Bugzilla

5:46 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

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https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #4 from Adam Huffman bloch@verdurin.com 2011-06-29 18:46:39 EDT --- Yes, I added that to fix the rpmlint complaint about executable files. Will take a closer look.

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Red Hat Bugzilla

30 Nov 30 Nov

1:08 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

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https://bugzilla.redhat.com/show_bug.cgi?id=717473

Alex Lancaster alexl@users.sourceforge.net changed:

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Red Hat Bugzilla

8 Jan 8 Jan

6:19 a.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

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https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #5 from Adam Huffman bloch@verdurin.com 2012-01-08 07:19:41 EST --- Taking another look at this now.

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Red Hat Bugzilla

30 Jan 30 Jan

4:46 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #6 from Adam Huffman bloch@verdurin.com 2012-01-30 17:46:06 EST --- Updated to include BR for Boost:

http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn.spec

http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn-1.3-5.fc16.src.rpm

Still needs more work.

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Red Hat Bugzilla

21 Feb 21 Feb

4:35 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #7 from Volker Fröhlich volker27@gmx.at 2012-02-21 17:35:15 EST --- You can remove defattr. By stating Python >= 2.5, you excluded EPEL 5 and can therefore remove clean section, rm in install section and buildroot definition too.

I fail to see where the library is. If there is no library, the devel package doesn't make any sense, as far as I know.

The license file should be in the main package.

Repeating for completeness' sake: Parts of this package are GPL and LGPL. The overall license can not be BSD therefore.

The trouble from comment #3 is still there, by the way.

The tests don't seem to run:

+ cd /builddir/build/BUILD + cd SeqAn-1.3 + unset DISPLAY + ctest ********************************* No test configuration file found! *********************************

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Red Hat Bugzilla

20 May 20 May

4:33 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #8 from Volker Fröhlich volker27@gmx.at --- Adam, are you still working on this package?

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Red Hat Bugzilla

21 May 21 May

3:32 a.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #9 from Adam Huffman verdurin@fedoraproject.org --- (In reply to comment #8)

...

Adam, are you still working on this package?

Haven't looked at it in a while. I've changed jobs now and am no longer in the biology field, so this is less of a personal priority. However, if people do want it, I'm happy to try and complete the initial packaging.

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Red Hat Bugzilla

2 Nov 2 Nov

11:12 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

https://bugzilla.redhat.com/show_bug.cgi?id=717473

Sébastien Boisvert seb@boisvert.info changed:

What |Removed |Added ---------------------------------------------------------------------------- CC| |seb@boisvert.info

--- Comment #10 from Sébastien Boisvert seb@boisvert.info --- So as I understand, there is a confusion regarding the licensing (comment #7). Is that right ?

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Red Hat Bugzilla

18 Nov 18 Nov

4:13 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #11 from Volker Fröhlich volker27@gmx.at --- Not really confusion; the overall license just can't be BSD, because parts of the code are GPL and LGPL of some version.

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Red Hat Bugzilla

28 Apr 28 Apr

2:27 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=717473

Jason Tibbitts tibbs@math.uh.edu changed:

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Red Hat Bugzilla

4 May 4 May

4:43 a.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=717473

--- Comment #12 from Volker Fröhlich volker27@gmx.at --- Adam, what are your plans about SeqAn? If you don't plan to proceed, we can close this ticket.

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Red Hat Bugzilla

9:56 a.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=717473

Adam Huffman bloch@verdurin.com changed:

--- Comment #13 from Adam Huffman bloch@verdurin.com --- No, I'll close this so someone else can take over.

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Red Hat Bugzilla

6 Jun 6 Jun

4:29 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

https://bugzilla.redhat.com/show_bug.cgi?id=717473

Dave Love d.love@liv.ac.uk changed:

What |Removed |Added ---------------------------------------------------------------------------- CC| |d.love@liv.ac.uk

--- Comment #14 from Dave Love d.love@liv.ac.uk --- I've worked on this. Presumably it will need a new review request, and I'll have to check the build of tophat against it, which may take me a while, but I thought it was worth recording that it's in progress.

http://arc.liv.ac.uk/downloads/misc/SPECS/seqan.spec

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Red Hat Bugzilla

9:15 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

https://bugzilla.redhat.com/show_bug.cgi?id=717473

Christopher Meng i@cicku.me changed:

What |Removed |Added ---------------------------------------------------------------------------- Resolution|WONTFIX |DUPLICATE

--- Comment #15 from Christopher Meng i@cicku.me ---

*** This bug has been marked as a duplicate of bug 1105730 ***

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Red Hat Bugzilla

24 Jun 24 Jun

4:41 p.m.

New subject: [Bug 717473] Review Request: SeqAn - Biological sequence analysis library

https://bugzilla.redhat.com/show_bug.cgi?id=717473

Dominik 'Rathann' Mierzejewski dominik@greysector.net changed:

What |Removed |Added ---------------------------------------------------------------------------- Blocks|505154 (FE-SCITECH) |

Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=505154 [Bug 505154] Tracker: Review Requests for Science and Technology related packages

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