[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-09-18 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Jussi Lehtola jussi.leht...@iki.fi changed:

   What|Removed |Added

 Blocks|505154(FE-SCITECH)  |

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-07-14 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #22 from Fedora Update System upda...@fedoraproject.org 
2011-07-14 20:02:50 EDT ---
bowtie-0.12.7-2.el6 has been pushed to the Fedora EPEL 6 stable repository.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-07-14 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #21 from Fedora Update System upda...@fedoraproject.org 
2011-07-14 20:01:35 EDT ---
bowtie-0.12.7-2.el5 has been pushed to the Fedora EPEL 5 stable repository.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-07-14 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Fedora Update System upda...@fedoraproject.org changed:

   What|Removed |Added

   Fixed In Version|bowtie-0.12.7-2.el5 |bowtie-0.12.7-2.el6

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-07-14 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Fedora Update System upda...@fedoraproject.org changed:

   What|Removed |Added

   Fixed In Version|bowtie-0.12.7-2.fc14|bowtie-0.12.7-2.el5

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-07-11 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Fedora Update System upda...@fedoraproject.org changed:

   What|Removed |Added

 Status|ON_QA   |CLOSED
   Fixed In Version||bowtie-0.12.7-2.fc15
 Resolution||ERRATA
Last Closed||2011-07-12 00:48:46

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-07-11 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #19 from Fedora Update System upda...@fedoraproject.org 
2011-07-12 00:48:37 EDT ---
bowtie-0.12.7-2.fc15 has been pushed to the Fedora 15 stable repository.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-07-11 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Fedora Update System upda...@fedoraproject.org changed:

   What|Removed |Added

   Fixed In Version|bowtie-0.12.7-2.fc15|bowtie-0.12.7-2.fc14

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-07-11 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #20 from Fedora Update System upda...@fedoraproject.org 
2011-07-12 01:18:58 EDT ---
bowtie-0.12.7-2.fc14 has been pushed to the Fedora 14 stable repository.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Adam Huffman bl...@verdurin.com changed:

   What|Removed |Added

   Flag||fedora-cvs?

--- Comment #12 from Adam Huffman bl...@verdurin.com 2011-06-28 03:03:49 EDT 
---
New Package SCM Request
===
Package Name: bowtie
Short Description: An ultrafast, memory-efficient short read aligner
Owners: verdurin
Branches: f14 f15 el5 el6
InitialCC:

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #13 from Jon Ciesla l...@jcomserv.net 2011-06-28 08:00:01 EDT ---
Git done (by process-git-requests).

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #14 from Fedora Update System upda...@fedoraproject.org 
2011-06-28 09:11:59 EDT ---
bowtie-0.12.7-2.el6 has been submitted as an update for Fedora EPEL 6.
https://admin.fedoraproject.org/updates/bowtie-0.12.7-2.el6

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Fedora Update System upda...@fedoraproject.org changed:

   What|Removed |Added

 Status|ASSIGNED|MODIFIED

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #15 from Fedora Update System upda...@fedoraproject.org 
2011-06-28 09:19:19 EDT ---
bowtie-0.12.7-2.el5 has been submitted as an update for Fedora EPEL 5.
https://admin.fedoraproject.org/updates/bowtie-0.12.7-2.el5

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #16 from Fedora Update System upda...@fedoraproject.org 
2011-06-28 10:12:30 EDT ---
bowtie-0.12.7-2.fc15 has been submitted as an update for Fedora 15.
https://admin.fedoraproject.org/updates/bowtie-0.12.7-2.fc15

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #17 from Fedora Update System upda...@fedoraproject.org 
2011-06-28 10:19:15 EDT ---
bowtie-0.12.7-2.fc14 has been submitted as an update for Fedora 14.
https://admin.fedoraproject.org/updates/bowtie-0.12.7-2.fc14

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Fedora Update System upda...@fedoraproject.org changed:

   What|Removed |Added

 Status|MODIFIED|ON_QA

--- Comment #18 from Fedora Update System upda...@fedoraproject.org 
2011-06-28 11:47:12 EDT ---
bowtie-0.12.7-2.el5 has been pushed to the Fedora EPEL 5 testing repository.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-27 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Jon Ciesla l...@jcomserv.net changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
 CC||l...@jcomserv.net
 AssignedTo|nob...@fedoraproject.org|l...@jcomserv.net
   Flag||fedora-review?

--- Comment #8 from Jon Ciesla l...@jcomserv.net 2011-06-27 10:53:17 EDT ---
Other than trivial spelling errors, rpmlint gives:

bowtie.x86_64: E: script-without-shebang
/usr/share/bowtie/scripts/gen_dnamasks2colormask.pl
This text file has executable bits set or is located in a path dedicated for
executables, but lacks a shebang and cannot thus be executed.  If the file is
meant to be an executable script, add the shebang, otherwise remove the
executable bits or move the file elsewhere.

Patch for this, and drop the patch when upstream fixes it.

bowtie.x86_64: W: no-manual-page-for-binary bowtie
Each executable in standard binary directories should have a man page.

bowtie.x86_64: W: no-manual-page-for-binary bowtie-inspect
Each executable in standard binary directories should have a man page.

bowtie.x86_64: W: no-manual-page-for-binary bowtie-build
Each executable in standard binary directories should have a man page.

No man pages exist, unfortunately, but you might suggest that upstream create
some.

Otherwise:

Good:

- rpmlint checks return:

- package meets naming guidelines
- package meets packaging guidelines
- license ( ) OK, text in %doc, matches source
- spec file legible, in am. english
- source matches upstream
- package compiles on devel (x86)
- no missing BR
- no unnecessary BR
- no locales
- not relocatable
- owns all directories that it creates
- no duplicate files
- permissions ok
- %clean ok
- macro use consistent
- code, not content
- no need for -docs
- nothing in %doc affects runtime
- no need for .desktop file 

To fix:
Patch for shebang.
Include the doc/ dir in %doc.

Mock build in progress for BR check.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-27 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #9 from Jon Ciesla l...@jcomserv.net 2011-06-27 11:11:37 EDT ---
Mock build was good, so it's just the two issues above.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-27 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #10 from Adam Huffman bl...@verdurin.com 2011-06-27 18:16:11 EDT 
---
Many thanks for taking a look - I was beginning to give up hope...

New version that should address those problems is up at:

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

http://verdurin.fedorapeople.org/reviews/bowtie/bowtie-0.12.7-2.fc14.src.rpm

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-06-27 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Jon Ciesla l...@jcomserv.net changed:

   What|Removed |Added

   Flag|fedora-review?  |fedora-review+

--- Comment #11 from Jon Ciesla l...@jcomserv.net 2011-06-27 21:44:13 EDT ---
Anytime.  Much better, APPROVED.


If you're feeling particularly grateful:

https://bugzilla.redhat.com/buglist.cgi?emailreporter1=1classification=Fedoraemailtype1=exactquery_format=advancedbug_status=NEWbug_status=ASSIGNEDbug_status=MODIFIEDbug_status=ON_DEVbug_status=ON_QAbug_status=VERIFIEDbug_status=RELEASE_PENDINGbug_status=POSTemail1=limb%40jcomserv.netcomponent=Package%20Reviewproduct=Fedora

Or:  http://fedoraproject.org/PackageReviewStatus/NEW.html

:)

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-04-07 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Adam Huffman bl...@verdurin.com changed:

   What|Removed |Added

 Blocks||505154(FE-SCITECH)

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-03-12 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #7 from Adam Huffman bl...@verdurin.com 2011-03-12 19:44:20 EST 
---
Brennan, thanks for catching that.  There hasn't been an upstream release since
0.12.7, so the issue with /usr/share/bowtie/scripts/gen_dnamasks2colormask.pl
remains.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2011-03-05 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Brennan Ashton bash...@brennanashton.com changed:

   What|Removed |Added

 CC||bash...@brennanashton.com
  Component|0x  |Package Review

--- Comment #6 from Brennan Ashton bash...@brennanashton.com 2011-03-05 
16:56:41 EST ---
Please make sure that the component is set correctly so that that reviewer will
see this bug.  I have fixed it.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2010-11-14 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Adam Huffman bl...@verdurin.com changed:

   What|Removed |Added

 CC||dw...@infradead.org
  Component|Package Review  |0x

--- Comment #5 from Adam Huffman bl...@verdurin.com 2010-11-14 14:01:51 EST 
---
Upstream says that the shebang will be included in the next release.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2010-09-13 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #4 from Adam Huffman bl...@verdurin.com 2010-09-13 18:21:44 EDT 
---
New version with latest upstream release:

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

http://verdurin.fedorapeople.org/reviews/bowtie/bowtie-0.12.7-1.fc13.src.rpm

There's a new rpmlint error:


bowtie.x86_64: E: script-without-shebang
/usr/share/bowtie/scripts/gen_dnamasks2colormask.pl
This text file has executable bits set or is located in a path dedicated for
executables, but lacks a shebang and cannot thus be executed.  If the file is
meant to be an executable script, add the shebang, otherwise remove the
executable bits or move the file elsewhere.

I've contacted the authors to clarify the status of this file.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2010-08-31 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #3 from Adam Huffman bl...@verdurin.com 2010-08-31 06:13:28 EDT 
---
Yes, you're right - I meant to say 'compilation flags'.

Have applied your suggested fix:

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

http://verdurin.fedorapeople.org/reviews/bowtie/bowtie-0.12.5-3.fc13.src.rpm

I do want to build for EL5 - would you suggest conditionals?  Personally I
would prefer to keep it as is, to improve readability.

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2010-08-28 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

Thomas Spura toms...@fedoraproject.org changed:

   What|Removed |Added

 CC||toms...@fedoraproject.org

--- Comment #2 from Thomas Spura toms...@fedoraproject.org 2010-08-28 
06:56:36 EDT ---
- Hmm, there are no CFLAGS defintions in the Makefile...
  How about: make %{?_smp_mflags} -p EXTRA_FLAGS=%{optflags}
  Then the debuginfo-without-sources error is gone and the rest should be
ignorable.


- When you don't want to build this for EL5, you can delete quite a lot of
stuff:
  See: bug #603233 comment 11

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[Bug 627936] Review Request: bowtie - An ultrafast, memory-efficient short read aligner

2010-08-27 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=627936

--- Comment #1 from Adam Huffman bl...@verdurin.com 2010-08-27 08:54:39 EDT 
---
There are some problems that still need to be fixed, such as the fact that the
CFLAGS are hard-coded in the Makefile.  I've mentioned this to upstream and
asked that they amend the Makefile so as to allow command-line overriding of
the CFLAGS.  There's been no response yet.

Here's the rpmlint output:


bowtie.src: W: spelling-error Summary(en_US) ultrafast - ultra fast,
ultra-fast, ultrafilter
bowtie.src: W: spelling-error %description -l en_US ultrafast - ultra fast,
ultra-fast, ultrafilter
bowtie.src: W: spelling-error %description -l en_US Langmead - Lang mead,
Lang-mead, Langmuir
bowtie.src: W: spelling-error %description -l en_US Ultrafast - Ultra fast,
Ultra-fast, Ultrafilter
bowtie.x86_64: W: spelling-error Summary(en_US) ultrafast - ultra fast,
ultra-fast, ultrafilter
bowtie.x86_64: W: spelling-error %description -l en_US ultrafast - ultra fast,
ultra-fast, ultrafilter
bowtie.x86_64: W: spelling-error %description -l en_US Langmead - Lang mead,
Lang-mead, Langmuir
bowtie.x86_64: W: spelling-error %description -l en_US Ultrafast - Ultra fast,
Ultra-fast, Ultrafilter
bowtie.x86_64: W: no-manual-page-for-binary bowtie
bowtie.x86_64: W: no-manual-page-for-binary bowtie-inspect
bowtie.x86_64: W: no-manual-page-for-binary bowtie-build
bowtie.x86_64: W: spelling-error Summary(en_US) ultrafast - ultra fast,
ultra-fast, ultrafilter
bowtie.x86_64: W: spelling-error %description -l en_US ultrafast - ultra fast,
ultra-fast, ultrafilter
bowtie.x86_64: W: spelling-error %description -l en_US Langmead - Lang mead,
Lang-mead, Langmuir
bowtie.x86_64: W: spelling-error %description -l en_US Ultrafast - Ultra fast,
Ultra-fast, Ultrafilter
bowtie.x86_64: W: no-manual-page-for-binary bowtie
bowtie.x86_64: W: no-manual-page-for-binary bowtie-inspect
bowtie.x86_64: W: no-manual-page-for-binary bowtie-build
bowtie-debuginfo.x86_64: E: debuginfo-without-sources
bowtie-debuginfo.x86_64: E: debuginfo-without-sources

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