Spec URL: http://pingou.fedorapeople.org/RPMs/R-IRanges.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-IRanges-1.0.14-1.fc10.src.rpm Description: The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions.
Package does not build for me - missing BuildRequires? ** R ** inst ** preparing package for lazy loading Error in loadNamespace(i[[1]], c(lib.loc, .libPaths())) : there is no package called 'Matrix' Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted ERROR: lazy loading failed for package 'IRanges' ** Removing '/builddir/build/BUILDROOT/R-IRanges-1.0.14-1.fc10.x86_64/usr/lib64\ /R/library/IRanges' RPM build errors: error: Bad exit status from /var/tmp/rpm-tmp.9f4Ede (%install)
Indeed R-Matrix is needed for build, I will update the spec in that way.
SPEC: http://pingou.fedorapeople.org/RPMs/R-IRanges.spec SRPM: http://pingou.fedorapeople.org/RPMs/R-IRanges-1.0.14-2.fc10.src.rpm
Created attachment 336194 [details] Review result I attach my review. In summary it looks quite good.
> ! The package license corresponds to the license as mentioned in the > DESCRIPTION file and in the website, however several source files > contain the statement: > > * This file is copyright 2002 Jim Kent, but license is hereby > * granted for all use - public, private or commercial. */ > > which is not the same as "Artistic licence 2.0". Needs some > consultation with upstream. I will ask upstream for clarification > ! Specfile is written in legible English and uses macro consitently, > however: > > The Source and URL fields uses the macro %{BioC} with is not defined > anywhere. The urls point to the right location if this macro is > assumed to be an empty string, so techncally they are correct, but > it is a source of confusion. Suggestion - remove the macros. The macro is defined (line 2 of the file), however the %define should be changed to %global according to the newly approved guidelines. > The comment that says "#i368 arch" should probaly read something > like "#architecture dependent package", because that I think is what > you really mean. That comment is generated by R2spec, it can be changed/ignored/removed (I will change R2spec to this) > ! Package compiles, but there are warnings that should be fixed: > > IntervalTree.c:48: warning: missing braces around initializer > memalloc.c:293: warning: format '%d' expects type 'int', but argument 2 has type 'size_t' > memalloc.c:293: warning: format '%d' expects type 'int', but argument 3 has type 'size_t' > > The "... may be used uninitialized" warnings might be harmless (or > not, ...) > I have no idea if these warnings are harmful or not: > > Creating a generic for "cbind" in package "IRanges" > (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (deparse.level)) > Creating a generic for "rbind" in package "IRanges" > (the supplied definition differs from and overrides the implicit generic in package "base": Signatures differ: (...), (deparse.level)) I will point these warning to upstream. > ! %check is present and check pass, but > > Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...11,12c11 > < rbind, > < sapply > --- > > rbind > > It test still says "OK", but it looks "strange". This is just the output of the test run > ! No package owns the package's main directory /usr/lib64/R/library/IRanges Oups, I will change this > Ideally both main and devel should own the main directory in order > to avoid orphaned directories after package removal, but at least > main must own it. I do not agree. Since -devel has the main package has a requirement, only the main need to own the directory. > ! Since the -devel package does not include a .pc file it should not > require pkgconfig (or is there some other reason for this?) Will be fixed
* Sun Mar 22 2009 pingou <pingou -AT- pingoured.fr> 1.0.14-3 - The main package owns the directory - Remove pkgconfig as R for the devel package - Define becomes global SPEC: http://pingou.fedorapeople.org/RPMs/R-IRanges.spec SRPM: http://pingou.fedorapeople.org/RPMs/R-IRanges-1.0.14-3.fc10.src.rpm
I got a reply to the mail I sent: ----------------------------------- > We also see some warnings while compiling it: > IntervalTree.c:48: warning: missing braces around initializer > memalloc.c:293: warning: format '%d' expects type 'int', but argument 2 > has type 'size_t' > memalloc.c:293: warning: format '%d' expects type 'int', but argument 3 > has type 'size_t' > These are probably harmless but easy to rectify. > > Creating a generic for "cbind" in package "IRanges" > (the supplied definition differs from and overrides the implicit generic > in package "base": Signatures differ: (...), (deparse.level)) > Creating a generic for "rbind" in package "IRanges" > (the supplied definition differs from and overrides the implicit generic > in package "base": Signatures differ: (...), (deparse.level)) > These are intentional and may be ignored. ------------------------------------- Nothing regarding the license yet though
Answer concerning the license: > We will add a new field to the DESCRIPTION file, like ExtraLicenses or > something that will indicate the C files that are under freely licensed for > all uses by Jim Kent, in a way that is compatible with the Artistic license.
Updated: Spec URL: http://pingou.fedorapeople.org/RPMs/R-IRanges.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-IRanges-1.1.55-1.fc10.src.rpm
Package approved.
Thanks for the review :) New Package CVS Request ======================= Package Name: R-IRanges Short Description: Low-level containers for storing set of integer ranges Owners: pingou Branches: F-9 F-10 InitialCC:
cvs done.
R-IRanges-1.1.55-1.fc10 has been submitted as an update for Fedora 10. http://admin.fedoraproject.org/updates/R-IRanges-1.1.55-1.fc10
R-IRanges-1.1.55-1.fc9 has been submitted as an update for Fedora 9. http://admin.fedoraproject.org/updates/R-IRanges-1.1.55-1.fc9
R-IRanges-1.1.55-1.fc10 has been pushed to the Fedora 10 stable repository. If problems still persist, please make note of it in this bug report.
R-IRanges-1.1.55-1.fc9 has been pushed to the Fedora 9 stable repository. If problems still persist, please make note of it in this bug report.