[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Susi Lehtola  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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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Björn besser82 Esser bjoern.es...@gmail.com changed:

   What|Removed |Added

 CC|package-review@lists.fedora |
   |project.org |
 Blocks|177841 (FE-NEEDSPONSOR) |




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=177841
[Bug 177841] Tracker: Review requests from new Fedora packagers who need a
sponsor
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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Ray Pete raymondp...@fedoraproject.org changed:

   What|Removed |Added

 Status|NEW |CLOSED
 Resolution|--- |WONTFIX
Last Closed||2013-09-01 15:01:25



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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #20 from Ray Pete raymondp...@fedoraproject.org ---
Tx Jason.
So based on your last comments. You will see the exact src.zip file now used
with patch files applied to fix various errors, which were picked up with the
newer GCC.
rpmlint is clean. Appreciate the guidance while I work through the SOP. Koji
make was clean.

http://raymondpete.fedorapeople.org/plink-1.07-5.fc19.src.rpm
http://raymondpete.fedorapeople.org/plink.spec

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #19 from Jason Tibbitts ti...@math.uh.edu ---
There are only very limited situations where it is permissible to modify the
upstream source archive.  Basically when we cannot distribute some part of it
due to legal reasons.

Please either detail the legal reasons why we cannot redistribute the upstream
source archive as is, or fix this package to use the archive unmodified.  You
can of course remove the unneeded jar file in %prep, and I suppose you could
add the autoconf stuff there as well though generally we frown on such things. 
Could you detail the specific reasons why the upstream makefile is not useful,
and cannot be minimally fixed with basic patching?

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Jason Tibbitts ti...@math.uh.edu changed:

   What|Removed |Added

  Flags||needinfo?(raymondpete@fedor
   ||aproject.org)

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Ray Pete raymondp...@fedoraproject.org changed:

   What|Removed |Added

  Flags|needinfo?(raymondpete@fedor |
   |aproject.org)   |

--- Comment #17 from Ray Pete raymondp...@fedoraproject.org ---
Thanks for the poke.
indeed I failed to run rpmlint. reviewing now
With respect to the src mismatch. The zip original contains a jar file with no
source, which is merely a gui. I removed that due to source missing, and also
created the autoconf stuff since it only had a static Makefile

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #18 from Ray Pete raymondp...@fedoraproject.org ---
http://raymondpete.fedorapeople.org/plink.spec
http://raymondpete.fedorapeople.org/plink-1.07-4.fc19.src.rpm

rpmlint comes back clean with the exception of the aforementioned upstream size
mismatch due to the jar file.

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #16 from Jason Tibbitts ti...@math.uh.edu ---
So I downloaded and built this; anyone who is still interested after nearly a
year certainly deserves a review.  However, I immediately noticed a few issues:

The package doesn't build with the mandatory compiler flags.  If that's a
regular autoconf-generated script (and it sure looks like it is), why not use
the usual %configure macro to call it, so that everything gets set and passed
correctly?

Did you look at the rpmlint output at all?  I see a bunch of stuff which is
trivially fixable and some other stuff I don't understand at all.

  plink-debuginfo.x86_64: E: debuginfo-without-sources
This comes from not building with the mandatory compiler flags.  (-g isn't
there, so no debug info was compiled in.)

  plink.x86_64: W: manual-page-warning /usr/share/man/man1/plink.1.gz 28: 
   warning: numeric expression expected (got a tab character)
A whole bunch of these which I don't understand.  Generally you should not
compress manpages; rpm will do it automatically, and will use the proper
compression system if we decide to switch from gzip in the future.

  plink.src: W: summary-not-capitalized C whole genome association analysis 
   toolset
Should capitalize the summary.

  plink.src:28: W: configure-without-libdir-spec
The configure script should be called via %configure if it is
autoconf-generated.

  plink.src:10: W: mixed-use-of-spaces-and-tabs (spaces: line 10, tab: line 1)
Please be consistent with indentation.

  plink.src: W: file-size-mismatch plink-1.07-src.zip = 692437, 
   http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip = 2257297
So, what happened here?  The file in the src.rpm is pretty much completely
different than what's at the upstream web site.

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #15 from Ray Pete raymondp...@fedoraproject.org ---
Spec fix per Volker's info.

http://raymondpete.fedorapeople.org/plink.spec
http://raymondpete.fedorapeople.org/plink-1.07-3.fc19.src.rpm

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Jason Tibbitts ti...@math.uh.edu changed:

   What|Removed |Added

 CC||raymondpete@fedoraproject.o
   ||rg
  Flags||needinfo?(raymondpete@fedor
   ||aproject.org)

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Ray Pete raymondp...@fedoraproject.org changed:

   What|Removed |Added

  Flags|needinfo?(raymondpete@fedor |
   |aproject.org)   |

--- Comment #14 from Ray Pete raymondp...@fedoraproject.org ---
Sorry Volker missed your emails.
updates to follow with the corrected spec.

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #13 from Volker Fröhlich volke...@gmx.at ---
You seem to have ignored a few of my previous commments. I'm repeating some of
them here.

Use the %{_mandir} macro.

Why is the binary in /usr/sbin?
http://www.pathname.com/fhs/pub/fhs-2.3.html#USRSBINNONESSENTIALSTANDARDSYSTEMBI

mkdir -p %{buildroot}%{_mandir}/man1 is enough. You don't need 4 mkdir
invocations.

Why are you not using make %{?_smp_mflags}?

Use the version macro in Source0.

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #12 from Ray Pete raymondp...@fedoraproject.org ---
made configure script, added plink man page, took out gplink.jar file

http://raymondpete.fedorapeople.org/plink-1.07-2.fc17.src.rpm
http://raymondpete.fedorapeople.org/plink.spec

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #10 from Volker Fröhlich volke...@gmx.at ---
Whenever you publish a new version of your files in the future, please bump the
release number. That makes work easier for reviewers.

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #11 from Ray Pete raymondp...@fedoraproject.org ---
Spec URL: http://www.iski.tv/plink.spec
SRPM URL: http://www.iski.tv/plink-1.07-1.fc17.src.rpm

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #8 from Ray Pete raymondp...@fedoraproject.org ---
Hi Volker,

So updated spec and srpm linked

Spec URL: www.iski.tv/plink.spec
SRPM URL: www.iski.tv/plink-1.07-1.fc17.src.rpm

I believe things are in better shape now.
Please let me know if you notice something missed? And tx for your help
reviewing

FYI, the R plugin is merely an option in the plink binary to output R code

http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml


Cheers,

Ray

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #9 from Ray Pete raymondp...@fedoraproject.org ---
umm.. typo..

s/output R code/input R plugin code/

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=841266

Volker Fröhlich volke...@gmx.at changed:

   What|Removed |Added

  Flags||needinfo?(raymondpete@fedor
   ||aproject.org)

--- Comment #6 from Volker Fröhlich volke...@gmx.at ---
Are you still interested in this package?

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

Product: Fedora
https://bugzilla.redhat.com/show_bug.cgi?id=841266

Ray Pete raymondp...@fedoraproject.org changed:

   What|Removed |Added

  Flags|needinfo?(raymondpete@fedor |
   |aproject.org)   |

--- Comment #7 from Ray Pete raymondp...@fedoraproject.org ---
Hi Volker,

Indeed I have updated the spec per your requests above. 
I'll submit the new srpm to koji and update the ticket when all is completed.

Regarding the .jar file. This is a gui application, which does not seem to
include src.
I also dealt with a few of the warnings mentioned above, but this is not
included on the website source yet.

Cheers,

Ray

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #5 from Volker Fröhlich volke...@gmx.at ---
The license must be stated as GPLv2.
https://fedoraproject.org/wiki/Licensing:Main?rd=Licensing

The build does not respect Fedora's optflags.
http://fedoraproject.org/wiki/Packaging:Guidelines#Compiler_flags

What is it about the R plug-in?

There are a couple of compiler warnings that could be dealt with.

Please use the name and version macro in the Source0 line.

Drop the two Requires.
http://fedoraproject.org/wiki/Packaging:Guidelines#Requires

install -m 0755 plink %{buildroot}%{_sbindir}/plink should be fine.

Why is that installed to sbindir?

Add COPYING.txt and README via the doc macro.

I noticed a jar file in the tarball. What is it?

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Volker Fröhlich volke...@gmx.at changed:

   What|Removed |Added

 CC||volke...@gmx.at
 Blocks|505154 (FE-SCITECH) |177841 (FE-NEEDSPONSOR)

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Volker Fröhlich volke...@gmx.at changed:

   What|Removed |Added

 Blocks||505154 (FE-SCITECH)

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Dmitrij S. Kryzhevich kr...@land.ru changed:

   What|Removed |Added

 CC||kr...@land.ru

--- Comment #4 from Dmitrij S. Kryzhevich kr...@land.ru ---
If you need to be sponsored, please, mark this in Blocks.

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Ray Pete raymondp...@fedoraproject.org changed:

   What|Removed |Added

 Blocks||505154 (FE-SCITECH)

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

Rasmus Ory Nielsen r...@ron.dk changed:

   What|Removed |Added

 CC||r...@ron.dk

--- Comment #2 from Rasmus Ory Nielsen r...@ron.dk ---
URL tag has an extra http

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #3 from Ray Pete raymondp...@fedoraproject.org ---
Thanks Rasmus fixed the duplicate http:// tag

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[Bug 841266] Review Request: plink - whole genome association analysis toolset

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=841266

--- Comment #1 from Ray Pete rayandkate...@gmail.com ---
Created attachment 598901
  -- https://bugzilla.redhat.com/attachment.cgi?id=598901action=edit
koji build log

built on i686 and x86_64 fine
source needed to be modified to build with gcc-4.7
Variable duplication errors
Also needed to add auto detection on 32 versus 64 during make

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