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
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).
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 :-)
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 :-)
(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?
Go ahead and take this one. I'm more than happy to let you drive this (and the rest of Bioconductor) forward.
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
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)
Starting review.
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
- 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
(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?
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
the corrected version http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase.spec http://pingoured.dyndns.org/public/RPM/R-Biobase/R-Biobase-1.16.1-3.fc8.src.rpm
(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/
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
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 --------
New Package CVS Request ======================= Package Name: R-Biobase Short Description: Base functions for Bioconductor Owners: pingou Branches: F-7, F-8 Cvsextras Commits: yes
cvs done.
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'
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'
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.
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.