[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2012-01-05 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #10 from Alex Lancaster  2012-01-05 
16:09:27 EST ---
koji scratch build worked fine: 

http://koji.fedoraproject.org/koji/taskinfo?taskID=3623169

I'll try to have a look at this in more detail soon.

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2012-01-05 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #9 from Adam Huffman  2012-01-05 07:40:40 EST 
---
Updated to 0.1.7:

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

http://verdurin.fedorapeople.org/reviews/vcftools/vcftools-0.1.7-1.fc17.src.rpm

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-11-30 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

Alex Lancaster  changed:

   What|Removed |Added

 CC||al...@users.sourceforge.net
  Alias||vcftools

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-07-31 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #8 from Adam Huffman  2011-07-31 18:33:15 EDT 
---
Updated to 0.1.6:

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

http://verdurin.fedorapeople.org/reviews/vcftools/vcftools-0.1.6-1.fc17.src.rpm

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-05-03 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #7 from Adam Huffman  2011-05-03 09:21:49 EDT 
---
I've applied your patches with some changes and other fixes.  Results are at:

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

http://verdurin.fedorapeople.org/reviews/vcftools/vcftools-0.1.5-2.fc16.src.rpm

Thanks for the assistance.

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-05-01 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #6 from Jack Tanner  2011-05-01 21:06:25 EDT ---
vcftools 0.1.15 builds and installs with the enclosed patches.

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-05-01 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #4 from Jack Tanner  2011-05-01 21:05:18 EDT ---
Created attachment 496148
  --> https://bugzilla.redhat.com/attachment.cgi?id=496148
Patch to vcftools.spec

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-05-01 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #5 from Jack Tanner  2011-05-01 21:05:55 EDT ---
Created attachment 496149
  --> https://bugzilla.redhat.com/attachment.cgi?id=496149
Patch to perl/Makefile

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-05-01 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #3 from Jack Tanner  2011-05-01 15:36:29 EDT ---
Actually, no, it doesn't work.

Error: Package: vcftools-0.1.5-1.el6.x86_64 (/vcftools-0.1.5-1.el6.x86_64)
   Requires: perl(VcfStats)

The spec file probably needs to be patched to include VcfStats.pm under the
perl mv step and under %files. Also, it looks like vcftools_0.1.5/perl/Makefile
needs to be patched to include to VcfStats.pm in the MOD target. [I haven't
tried this, just taking notes.]

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-05-01 Thread bugzilla 
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comments should be made in the comments box of this bug.


https://bugzilla.redhat.com/show_bug.cgi?id=689488

Jack Tanner  changed:

   What|Removed |Added

 CC||i...@hotmail.com

--- Comment #2 from Jack Tanner  2011-05-01 15:17:33 EDT ---
FYI, the spec works for the new vcftools 0.1.5 with the following changes.

First, the tarball is not _v0.1.5.tar.gz, just _0.1.5.tar.gz.

Second, compare-vcf, query-vcf and and merge-vcf have been renamed to
vcf-compare, vcf-query, and vcf-merge.

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-04-07 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

Adam Huffman  changed:

   What|Removed |Added

 Blocks||505154(FE-SCITECH)

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[Bug 689488] Review Request: vcftools - VCF file manipulation tools

2011-03-21 Thread bugzilla 
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https://bugzilla.redhat.com/show_bug.cgi?id=689488

--- Comment #1 from Adam Huffman  2011-03-21 12:30:53 EDT 
---
There are two errors found by rpmlint:


vcftools.src:35: E: hardcoded-library-path in %{buildroot}/usr/lib/FaSlice.pm
A library path is hardcoded to one of the following paths: /lib, /usr/lib. It
should be replaced by something like /%{_lib} or %{_libdir}.

vcftools.src:36: E: hardcoded-library-path in %{buildroot}/usr/lib/Vcf.pm
A library path is hardcoded to one of the following paths: /lib, /usr/lib. It
should be replaced by something like /%{_lib} or %{_libdir}.

This is because some of the installation paths are hardcoded in the Makefiles,
so I had to move files in the .spec.  If it's preferable to patch the Makefile,
let me know.

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