Bug 240497

Summary: Review Request: R-multtest 1.18.0 - Resampling-based multiple hypothesis testing library
Product: [Fedora] Fedora Reporter: Pierre-Yves <pingoufc4>
Component: Package ReviewAssignee: Alex Lancaster <alexl>
Status: CLOSED ERRATA QA Contact: Fedora Package Reviews List <fedora-package-review>
Severity: medium Docs Contact:
Priority: medium    
Version: rawhideCC: alexl, chitlesh, splinux
Target Milestone: ---Flags: alexl: fedora‑review+
kevin: fedora‑cvs+
Target Release: ---   
Hardware: All   
OS: Linux   
Whiteboard:
Fixed In Version: 1.18.0-3.fc8 Doc Type: Bug Fix
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2008-01-15 17:54:01 EST Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: ---
Bug Depends On: 240500    
Bug Blocks:    

Description Pierre-Yves 2007-05-17 17:34:13 EDT
Spec URL: http://pingoured.dyndns.org/public/RPM/R-multtest/R-multtest.spec
SRPM URL: http://pingoured.dyndns.org/public/RPM/R-multtest/R-multtest-1.14.0-1.fc6.src.rpm
Description: 
Non-parametric bootstrap and permutation resampling-based multiple testing
procedures for controlling the family-wise error rate (FWER), generalized 
family-wise error rate (gFWER), tail probability of the proportion of 
false positives (TPPFP), and false discovery rate (FDR).

It is my first package 
I am seeking for a sponsor
Comment 1 Pierre-Yves 2007-05-23 17:58:54 EDT
The spec file has been changed to include the section %check
Then the news src.prm is
http://pingoured.dyndns.org/public/RPM/R-multtest/R-multtest-1.14.0-2.fc6.src.rpm
Comment 2 Pierre-Yves 2007-07-10 17:28:40 EDT
Based on the R packaging guidelines, there are the new files:

SPEC:
http://pingoured.dyndns.org/public/RPM/R-multtest/R-multtest.spec
SRPM:
http://pingoured.dyndns.org/public/RPM/R-multtest/R-multtest-1.14.0-4.fc6.src.rpm

:-)
Comment 5 Alex Lancaster 2007-12-04 18:38:52 EST
For a start the URLs are wrong for stable:

http://www.bioconductor.org/packages/2.2/bioc/html/multtest.html

should be:

http://www.bioconductor.org/packages/2.1/bioc/html/multtest.html
Comment 7 Alex Lancaster 2008-01-07 02:50:05 EST
Full review:

 - Package meets naming and packaging guidelines
 - Spec file matches base package name.
 - Spec has consistant macro usage.
 - Meets Packaging Guidelines.
 x License
 - License field in spec matches
 x License file  is not included in package
 - Spec in American English
 - Spec is legible.
 - Sources match upstream md5sum:
2a09d139ef362f0675c99e2e6d5ebe30  multtest_1.18.0.tar.gz
 - Package does not need ExcludeArch
 x BuildRequires:
Should have R-devel, not just R for arch-specific R packages
 - Spec handles locales/find_lang (N/A)
 - Package is not relocatable 
 - Package has %defattr and permissions on files is good.
 - Package has a correct %clean section.
 - Package has correct buildroot
      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 - Package is code or permissible content.
 - Doc subpackage needed/used.
 - Packages %doc files don't affect runtime.

 - Headers/static libs in -devel subpackage.
 - Spec has needed ldconfig in post and postun
 - .pc files in -devel subpackage/requires pkgconfig
 - .so files in -devel subpackage.
 - -devel package Requires: %{name} = %{version}-%{release}
 - .la files are removed.
 - Package compiles and builds on at least one arch.
 - Package has no duplicate files in %files.
 - Package doesn't own any directories other packages own.
 - Package owns all the directories it creates.
 - rpmlint output (can be ignored according to
http://fedoraproject.org/wiki/Packaging/R):
R-multtest.i386: W: one-line-command-in-%post /usr/lib/rpm/R-make-search-index.sh
R-multtest.i386: W: one-line-command-in-%postun /usr/lib/rpm/R-make-search-index.sh
 - final provides and requires are sane:
 - Has dist tag

Issues:

1. Does not build OK on koji:
http://koji.fedoraproject.org/koji/taskinfo?taskID=330245

2. Does this package actually need R-Biobase at build-time?  i.e. does the
install script actually check for it, or does it just need it at install time

3. BR: R-devel

4. Might be good to include something about this being part of Bioconductor in
%summary

These two can be dealt with after import:

3. It isn't clear what version of LGPL is meant from
http://www.bioconductor.org/packages/2.1/bioc/html/multtest.html please ask
upstream to clarify
4. Ask upstream to include LGPL license in package and/or in source code itself.
Comment 8 Pierre-Yves 2008-01-07 03:14:50 EST
1- has to found out indeed
2- Yes since it runs the %{_bindir}/R CMD check %{packname} command, this check
whether Biobase is present or not
3- corrected
4- corrected
5- They should since R-2.6.0 but they did not... and on BioC 2.2 it is not
clearer (it is one of the biggest problem with bioconductor)

New files 

SPEC
http://pingoured.dyndns.org/public/RPM/R-multtest/R-multtest.spec
SRPM
http://pingoured.dyndns.org/public/RPM/R-multtest/R-multtest-1.18.0-3.fc8.src.rpm

Comment 9 Alex Lancaster 2008-01-07 03:29:01 EST
Thanks, on the assumption that we can fix in rawhide and that you pester
upstream again on license issues, this package is:

APPROVED.
Comment 10 Alex Lancaster 2008-01-07 10:37:54 EST
SRPM from comment #10 works fine in koji now:

http://koji.fedoraproject.org/koji/taskinfo?taskID=330931

The problem was that "R CMD INSTALL" was moved to R-devel in rawhide, so the BR:
R-devel fixed it (which should always be present as per review guidelines in any
case).
Comment 11 Alex Lancaster 2008-01-07 19:43:58 EST
New Package CVS Request
=======================
Package Name: R-multtest
Short Description: Multiple hypothesis testing library from Bioconductor
Owners: pingou, alexlan
Branches: F-7 F-8
InitialCC: alexlan
Cvsextras Commits: yes
Comment 12 Kevin Fenzi 2008-01-07 22:34:15 EST
cvs done.
Comment 13 Fedora Update System 2008-01-11 17:08:45 EST
R-multtest-1.18.0-3.fc7 has been pushed to the Fedora 7 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update R-multtest'
Comment 14 Fedora Update System 2008-01-11 17:21:55 EST
R-multtest-1.18.0-3.fc8 has been pushed to the Fedora 8 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update R-multtest'
Comment 15 Fedora Update System 2008-01-15 17:53:59 EST
R-multtest-1.18.0-3.fc8 has been pushed to the Fedora 8 stable repository.  If problems still persist, please make note of it in this bug report.
Comment 16 Fedora Update System 2008-01-15 18:10:06 EST
R-multtest-1.18.0-3.fc7 has been pushed to the Fedora 7 stable repository.  If problems still persist, please make note of it in this bug report.