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Spec URL: http://pingou.fedorapeople.org/RPMs/R-affy.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-affy-1.22.0-1.fc11.src.rpm Description: The package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
This one doesn't build for me: gcc -m64 -std=gnu99 -I/usr/include/R -DHAVE_ZLIB=1 -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rma2.c -o rma2.o rma2.c:109:29: error: rma_background4.h: No such file or directory rma2.c:120:45: error: preprocessCore_background_stubs.c: No such file or directory rma2.c:121:48: error: preprocessCore_normalization_stubs.c: No such file or directory rma2.c:122:48: error: preprocessCore_summarization_stubs.c: No such file or directory rma2.c:124:31: error: R_subColSummarize.h: No such file or directory rma2.c:125:37: error: R_subColSummarize_stubs.c: No such file or directory rma2.c: In function 'do_RMA2': rma2.c:134: warning: implicit declaration of function 'R_subColSummarize_medianpolish_log' rma2.c:134: warning: assignment makes pointer from integer without a cast rma2.c: In function 'rma_c_call': rma2.c:186: warning: implicit declaration of function 'qnorm_c' rma2.c: In function 'rma_c_complete': rma2.c:247: warning: implicit declaration of function 'rma_bg_correct' make: *** [rma2.o] Error 1 ERROR: compilation failed for package 'affy' A scratch build is at http://koji.fedoraproject.org/koji/taskinfo?taskID=1572805
I'm also concerned that this has the same licensing issue as preprocessCore. Only src/rma2.c carries any license information, and it says GPLv2+.
This one need R-preprocessCore to build (and I am seing that both R-affyio and R-preprocessCore are not listed while they should...) There are the updated version: Spec URL: http://pingou.fedorapeople.org/RPMs/R-affy.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-affy-1.22.0-2.fc11.src.rpm I will also contact upstream for this library then. Thanks
There is the answer from upstream to my email: > Pierre, > > It should all be LGPL. Do you need me to go in and change it or is this > email enough? > > Good luck! > -r
cvs has been updated: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy/src/rma2.c
Setting the blocker since this won't build until R-preprocessCore is in rawhide.
License tag has been corrected in the cvs: http://fgc.lsi.umich.edu/cgi-bin/blosxom3.cgi/affy R-preprocessCore is in stable now :-)
Did you want to somehow update this package to include the proper licensing information? Either the updated source with proper licensing information or the email from the author clarifying the license needs to make it into the package. If I download the srpm from comment #3, and just look at what's in the package, the licensing situation is still unclear.
There is a new upstream release that correct the license issue There are the updated version: Spec URL: http://pingou.fedorapeople.org/RPMs/R-affy.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-affy-1.22.1-1.fc11.src.rpm
That fails to compile for me. gcc -m64 -std=gnu99 -I/usr/include/R -DHAVE_ZLIB=1 -I/usr/local/include -I"/usr/lib64/R/library/preprocessCore/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rma2.c -o rma2.o rma2.c:109:29: error: rma_background4.h: No such file or directory rma2.c:120:45: error: preprocessCore_background_stubs.c: No such file or directory rma2.c:121:48: error: preprocessCore_normalization_stubs.c: No such file or directory rma2.c:122:48: error: preprocessCore_summarization_stubs.c: No such file or directory rma2.c:124:31: error: R_subColSummarize.h: No such file or directory rma2.c:125:37: error: R_subColSummarize_stubs.c: No such file or directory rma2.c: In function 'do_RMA2': rma2.c:134: warning: implicit declaration of function 'R_subColSummarize_medianpolish_log' rma2.c:134: warning: assignment makes pointer from integer without a cast rma2.c: In function 'rma_c_call': rma2.c:186: warning: implicit declaration of function 'qnorm_c' rma2.c: In function 'rma_c_complete': rma2.c:247: warning: implicit declaration of function 'rma_bg_correct' make: *** [rma2.o] Error 1 ERROR: compilation failed for package 'affy' Scratch build: http://koji.fedoraproject.org/koji/taskinfo?taskID=1615456
Damn stupid mistake... I forgot to use R-preprocessCore-devel in the BR. Corrected in : Spec URL: http://pingou.fedorapeople.org/RPMs/R-affy.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-affy-1.22.1-2.fc11.src.rpm
scratch build F11 : http://koji.fedoraproject.org/koji/taskinfo?taskID=1616636
hm, do we still miss something ?
Hmm, I had typed up a whole review and thought I was waiting on you, but now that I look at the ticket I don't see any of it. Sorry about that; I'll do it again.
OK, it indeed builds fine and rpmlint has only the expected two complaints. You probably want "dependency" instead of "dependance" in %description. Note also that the templates in the R guidelines changed from using "tetex-latex" to "tex(latex)" to use what modern tex packages use and to prepare for the next texlive upheaval. I'm sure the texlive packages will provide the old symbols for compatibility so the existing packages won't break, but at some point I guess they'll need to be fixed up. * source files match upstream. sha256sum: b04fb91a451f75504c939e4d2b5eff6bd65ab1bf3f7417e293c8267e16fb60c8 affy_1.22.1.tar.gz * package meets naming and versioning guidelines. * specfile is properly named, is cleanly written and uses macros consistently. * summary is OK. * dist tag is present. * build root is OK. * license field matches the actual license. * license is open source-compatible. * license text not included upstream. * latest version is being packaged. * BuildRequires are proper. * compiler flags are appropriate. * %clean is present. * package builds in mock (rawhide, x86_64). * package installs properly. * debuginfo package looks complete. * rpmlint has acceptable complaints. * final provides and requires are sane: affy.so()(64bit) R-affy = 1.22.1-2.fc12 R-affy(x86-64) = 1.22.1-2.fc12 = /bin/sh R R >= 2.8.0 R-Biobase R-affyio R-preprocessCore R-tkWidgets libR.so()(64bit) libz.so.1()(64bit) * %check is necessarily disabled. * owns the directories it creates. * doesn't own any directories it shouldn't. * no duplicates in %files. * file permissions are appropriate. * no generically named files. * scriptlets are OK (R package registration). * code, not content. * documentation is small, so no -doc subpackage is necessary. * %docs are not necessary for the proper functioning of the package. APPROVED
Thanks a lot for the review :) I'll do the two correction before importing in the CVS. New Package CVS Request ======================= Package Name: R-affy Short Description: Methods for Affymetrix Oligonucleotide Arrays Owners: pingou Branches: F-10, F-11 InitialCC:
Don't forget to set the fedora-cvs flag; otherwise most CVS admins won't see your request. CVS done.
Thanks about that :) (and sorry for the tag, I forgot)
R-affy-1.22.1-3.fc10 has been submitted as an update for Fedora 10. http://admin.fedoraproject.org/updates/R-affy-1.22.1-3.fc10
R-affy-1.22.1-3.fc11 has been submitted as an update for Fedora 11. http://admin.fedoraproject.org/updates/R-affy-1.22.1-3.fc11
R-affy-1.22.1-3.fc11 has been pushed to the Fedora 11 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-affy'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F11/FEDORA-2009-9146
R-affy-1.22.1-3.fc10 has been pushed to the Fedora 10 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-affy'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F10/FEDORA-2009-9181
R-affy-1.22.1-3.fc10 has been pushed to the Fedora 10 stable repository. If problems still persist, please make note of it in this bug report.
R-affy-1.22.1-3.fc11 has been pushed to the Fedora 11 stable repository. If problems still persist, please make note of it in this bug report.