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Bug 240500

Summary: Review Request: R-Biobase 1.16.1 - Functions that are needed by many other packages
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, tcallawa
Target Milestone: ---Flags: alexl: fedora‑review+
kevin: fedora‑cvs+
Target Release: ---   
Hardware: All   
OS: Linux   
Whiteboard:
Fixed In Version: 1.16.1-3.fc8 Doc Type: Bug Fix
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2007-12-10 15:48:07 EST Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Bug Depends On: 241082    
Bug Blocks: 240497    

Description Pierre-Yves 2007-05-17 17:44:58 EDT
Spec URL: http://pingoured.dyndns.org/public/RPM/R-Biobase-1.14/R-Biobase.spec
SRPM URL: http://pingoured.dyndns.org/public/RPM/R-Biobase-1.14/R-Biobase-1.14.0-1.fc6.src.rpm
Description: 
Functions that are needed by many other packages or which replace R 
functions

This is my second package submited here. It is needed for my first package 
https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=240497
Comment 1 Tom "spot" Callaway 2007-05-23 16:41:15 EDT
R CMD CHECK fails here:
You forgot to run R CMD check. I added:

%check
cd ..;%{_bindir}/R CMD check %{packname}

But when I did that, R CMD check failed:

+ /usr/bin/R CMD check Biobase
* checking for working latex ... OK
* using log directory '/home/spot/rpmbuild/BUILD/Biobase.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '1.14.0'
* checking package dependencies ... ERROR
Packages required but not available:
  tkWidgets

Looks like this package really needs tkWidgets as a Requires (and a
BuildRequires, for the check).
Comment 2 Pierre-Yves 2007-05-28 16:23:16 EDT
The package tkWidgets and his dependences has been submit to bugzilla there:
R-DynDoc https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241079
R-widgetTools https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241081
R-tkWidgets https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=241082

Thanks for your help :-)
Comment 3 Pierre-Yves 2007-07-10 17:26:10 EDT
Based on the R packaging guidelines, there are the new files

SPEC:
http://pingoured.dyndns.org/public/RPM/R-Biobase-1.14/R-Biobase.spec
SRPM:
http://pingoured.dyndns.org/public/RPM/R-Biobase-1.14/R-Biobase-1.14.0-3.fc6.src.rpm

:-)
Comment 4 Alex Lancaster 2007-11-11 20:13:41 EST
(In reply to comment #3)
> Based on the R packaging guidelines, there are the new files
> 
> SPEC:
> http://pingoured.dyndns.org/public/RPM/R-Biobase-1.14/R-Biobase.spec
> SRPM:
>
http://pingoured.dyndns.org/public/RPM/R-Biobase-1.14/R-Biobase-1.14.0-3.fc6.src.rpm

The License: tag is wrong, according to
http://www.bioconductor.org/packages/2.0/bioc/html/Biobase.html it is licensed
under "Artistic 2.0" which is acceptable for Fedora but needs to made explicit:,
see: http://fedoraproject.org/wiki/Licensing

Tom, I'd like to get bioconductor into Fedora, if you don't want to review this,
I can pick it up.

Pierre-Yves: are you planning on packaging all of Bioconductor, or only parts of
it?  Is there some kind of tracker bug that would block all the relevant
packages?  Which package should I review (and build) first?
Comment 5 Tom "spot" Callaway 2007-11-11 20:48:39 EST
Go ahead and take this one. I'm more than happy to let you drive this (and the
rest of Bioconductor) forward.
Comment 6 Pierre-Yves 2007-11-12 02:47:58 EST
I will correct the license tag and update to the latest version.

I think it would be an idea to start the discussion on how to get bioconductor
on fedora on the r-devel mailing list
http://www.redhat.com/mailman/listinfo/fedora-r-devel-list

I have package until R-affy and a bit after. But with the latest release there
is a "problem" with preprocessCore that should be split on 2 packages (with one
-devel) but by doing this it means that most of the libraries that need this
package (and there are a lot) will probably need to be corrected to find the
header (meaning sed or patch).

R-tkWidget will be built soon I hope
Comment 7 Pierre-Yves 2007-11-12 14:54:36 EST
There are the new files:
SPEC
http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase.spec
SPRM
http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase-1.17.3-1.fc6.src.rpm

thanks :)
(R-tkWidget is waiting to be pushed in testing)
Comment 8 Alex Lancaster 2007-11-18 06:32:20 EST
Starting review.
Comment 9 Alex Lancaster 2007-11-18 07:21:00 EST
Full review:

       - OK: rpmlint output (can probably ignore these warnings):
R-Biobase.i386: W: one-line-command-in-%post /usr/lib/rpm/R-make-search-index.sh
R-Biobase.i386: W: one-line-command-in-%postun /usr/lib/rpm/R-make-search-index.sh
       - NEEDS-WORK: install line should be similar to
%{_bindir}/R CMD INSTALL -l $RPM_BUILD_ROOT%{_libdir}/R/library %{packname}
      - NEEDS-WORK: "Requires: R" may not be necessary because this is compiled
against libR.so and therefore gets the R dependency automatically
      - OK: License text is not in package, ask upstream to include it, if possible
      - OK: License is OK (Artistic 2.0)
      - OK: Meets Package Naming Guidelines.
      - NEEDS-WORK: Summary is vague and doesn't indicate that this is part of
Bioconductor
"Functions that are needed by many other packages" doesn't mention Bioconductor,
I would use something similar description from here
http://www.bioconductor.org/packages/2.2/bioc/html/Biobase.html "Base functions
for Bioconductor".
      - NEEDS-WORK: Description is also vague and almost identical to Summary,
this would be a good place to mention this part of the Bioconductor project etc.
 This is also true of the other dependent packages from Bioconductor that you
maintain: R-tkWidgets, the descriptions and summary should indicate that they
are part of Bioconductor
      - NEEDS-WORK Group is inappropriate  should be Applications/Engineering
rather than Applications/Productivity (this also applies to R-tkWidgets etc.)
      - OK: The spec file name
      - OK: Meets the Packaging Guidelines
      - OK: Spec file in American English
      - OK: The spec file legible
      - NEEDS-WORK: %changelog is badly formatted, there needs to be spaces
between each dated entry and spaces between "*" and "-"
      - NEEDS-WORK:  not using most recent upstream which is 1.17.5 here are the
MD5sums:
ed57a9494bd88ff6d81eb92f1363bbaa  Biobase_1.17.3.tar.gz
63d808d3ea0b662d58a339ddbf71639a  Biobase_1.17.5.tar.gz
      - OK: Builds OK on F-7 in koji
      - OK: no %find_lang, no locales as yet
      - OK: ldconfig: not required (noarch)
      - OK: not relocatable
      - OK: Own all directories that it creates
      - OK: No duplicate files
      - OK: %defattr(...):
      - OK: %clean section
      - OK: Consistently use macros
      - OK: Contains code
      - OK: No large doc
      - OK: %doc not critical for run-time
      - OK: no devel package
      - OK: no static libraries
      - OK: No pkgconfig(.pc) files
      - OK: no library files with suffix

SHOULD:
       - OK: builds in moch/koji
       - OK: module loads properly in R
       - NEEDS-WORK: query upstream to include license
       - OK: have translations of summary and description in fr
Comment 10 Pierre-Yves 2007-11-18 07:47:15 EST
       - OK: rpmlint output (can probably ignore these warnings):
R-Biobase.i386: W: one-line-command-in-%post /usr/lib/rpm/R-make-search-index.sh
R-Biobase.i386: W: one-line-command-in-%postun /usr/lib/rpm/R-make-search-index.sh

As written in the packaging guidelines, yes they can be ignored, they are
present in every R packages.

- NEEDS-WORK:  not using most recent upstream which is 1.17.5
- NEEDS-WORK: query upstream to include license
These are two points that I would have like to discuss with you on the R-devel
mailing list.

Else the new spec is available there
http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase.spec
And the SRPM
http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase-1.17.3-2.fc8.src.rpm
Comment 11 Alex Lancaster 2007-11-18 08:01:26 EST
(In reply to comment #10)
>        - OK: rpmlint output (can probably ignore these warnings):
> R-Biobase.i386: W: one-line-command-in-%post /usr/lib/rpm/R-make-search-index.sh
> R-Biobase.i386: W: one-line-command-in-%postun /usr/lib/rpm/R-make-search-index.sh

> As written in the packaging guidelines, yes they can be ignored, they are
> present in every R packages.

Yep.

> - NEEDS-WORK:  not using most recent upstream which is 1.17.5
> - NEEDS-WORK: query upstream to include license
> These are two points that I would have like to discuss with you on the R-devel
> mailing list.

I'm not currently subscribed to fedora-r-devel-list, can we discuss this on IRC
if you are around?  Or we can use bugzilla for the moment.

> Else the new spec is available there
> http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase.spec
> And the SRPM
> http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase-1.17.3-2.fc8.src.rpm

Hmm, it doesn't look like you updated the spec file, it's still 1.17.3-1.

Also, you might have noticed on bug #241082 that there appears to be problems
with the various noarch R packages, do the libraries load for you?
Comment 12 Pierre-Yves 2007-11-18 08:54:00 EST
Based on our discussion on #fedora-devel, we have decided to use the stable
version of Bioconductor.

There are then the new spec file and the new srpm
http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase.spec
http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase-1.16.1-2.fc8.src.rpm
Comment 14 Alex Lancaster 2007-12-03 04:23:38 EST
(In reply to comment #13)

> http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase-1.16.1-3.fc8.src.rpm

Getting a 404 on this file.  Doesn't seem to be present in:

http://pingoured.dyndns.org/public/RPM/R-Biobase/
Comment 15 Pierre-Yves 2007-12-03 13:05:46 EST
Sorry for that I do not know what happened, there they are again :)

SPEC
http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase.spec
SRPM
http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase-1.16.1-3.fc8.src.rpm


Thanks for wake me up, I have been quite busy the last days...

Regards
Comment 16 Alex Lancaster 2007-12-04 06:50:23 EST
Builds, installs and runs successfully in F-7.  Koji build here:

http://koji.fedoraproject.org/koji/taskinfo?taskID=273113

All MUST items in comment #9 are addressed, so package is:

--------
APPROVED
--------
Comment 17 Pierre-Yves 2007-12-04 07:04:23 EST
New Package CVS Request
=======================
Package Name: R-Biobase 
Short Description: Base functions for Bioconductor
Owners: pingou
Branches: F-7, F-8
Cvsextras Commits: yes
Comment 18 Kevin Fenzi 2007-12-04 14:50:02 EST
cvs done.
Comment 19 Fedora Update System 2007-12-06 15:51:55 EST
R-Biobase-1.16.1-3.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-Biobase'
Comment 20 Fedora Update System 2007-12-06 15:53:35 EST
R-Biobase-1.16.1-3.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-Biobase'
Comment 21 Fedora Update System 2007-12-10 15:48:06 EST
R-Biobase-1.16.1-3.fc8 has been pushed to the Fedora 8 stable repository.  If problems still persist, please make note of it in this bug report.
Comment 22 Fedora Update System 2007-12-10 15:48:15 EST
R-Biobase-1.16.1-3.fc7 has been pushed to the Fedora 7 stable repository.  If problems still persist, please make note of it in this bug report.