Spec URL: http://pingou.fedorapeople.org/RPMs/R-Biostrings.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-Biostrings-2.10.21-1.fc10.src.rpm Description: Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences.
Fedora review R-Biostrings-2.10.21-1.fc10.src.rpm (2009-03-25) * OK ! Needs attention * rpmlint output R-Biostrings.x86_64: W: one-line-command-in-%post /usr/lib/rpm/R-make-search-index.sh R-Biostrings.x86_64: W: one-line-command-in-%postun /usr/lib/rpm/R-make-search-index.sh R-Biostrings-devel.x86_64: W: only-non-binary-in-usr-lib R-Biostrings-devel.x86_64: W: no-documentation 4 packages and 1 specfiles checked; 0 errors, 4 warnings. The one-line-command warnings are standard for R packages The no-documentation warning for devel is OK (documentation is in main) The only-non-binary-in-usr-lib devel for devel can be ignored (the previous rpmlint version listed this one as an error) * Package is named according to R packaging guidlines * Package follows R packaging guidelines * The package is licensed under a Fedora approved license (Artistic 2.0) * The package license corresponds to the license mentioned in the DESCRIPTION file, no conflicting license statements are present in the package's source files. (There is a different license [LGPL] mentioned in the Biostrings1 subdirectory, but no files from this subdirectory are packaged or used during the build.) * License text not included in the package (OK since the stated licence does not require it). ! Specfile is written in legible English and uses macros consitently, however: The URL field uses the macro %{BioC} with is not defined anywhere. The url 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. [Sorry for putting this comment in the R-IRanges review, where it didn't belong (as you rightly pointed out) - the intention was to put it in this review.] The comment that says "#i368 arch" should probaly read something like "#architecture dependent package", because that I think is what you really mean. The NEWS file might belong in %doc * Sources match upstream and are the latest version: 59e67acb017722ace830721d2edcb3de Biostrings_2.10.21.tar.gz 59e67acb017722ace830721d2edcb3de SRPM/Biostrings_2.10.21.tar.gz ! Package compiles, but there are some warnings The warnings from the C code are all of types that usually can be ignored. There are some warnings from R that I can not judge: Warning in matchSignature(signature, fdef, where) : in the method signature for function "XString" no definition for class: "AsIs" Warning in matchSignature(signature, fdef, where) : in the method signature for function "XStringSet" no definition for class: "AsIs" Warning in matchSignature(signature, fdef, where) : in the method signature for function "BStringViews" no definition for class: "file" Warning in matchSignature(signature, fdef, where) : in the method signature for function "PDict" no definition for class: "AsIs" Warning in matchSignature(signature, fdef, where) : in the method signature for function "eq" no definition for class: "BioString" Are these benign or an indication of missing BuildRequires? * BuildRequires look sane (but see comment on the previous point) * %check is present, but disabled with the comment: # Ask for R-BSgenome which cannot build without R-Biostring Disabling the test in this case is OK, since you otherwise would have a chicken and egg problem. Changing "Ask" to "Asks" in the comment would be better grammar, and saying "Requires" instead might be even better, but that is just details that are not really significant. * The package owns the directories it creates * No duplicate files * %files has %defattrs, and permissions are sane. * %clean clears %buildroot * Package contains code * Headers are in -devel ! Since the -devel package does not include a .pc file it should not require pkgconfig * -devel requires main with fully qualified version * Package doesn't own other's directories * %install clears %buildroot * Installed filenames are valid UTF8 (even valid ASCII) * Package builds in mock (Fedora 10) * Scriptlets are sane
Updated: Spec URL: http://pingou.fedorapeople.org/RPMs/R-Biostrings.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-Biostrings-2.10.21-2.fc10.src.rpm
This looks quite good, but if I try to use this package to build the R-BSgenome package I get this error: Loading required package: Biostrings Warning: Multiple methods tables found for 'score' Warning: Multiple methods tables found for 'substr' Warning: Multiple methods tables found for 'substring' Warning: Multiple methods tables found for 'chartr' Error in insertMethod(m1, as.character(sigi), args, el(methods, i), FALSE) : inserting method with invalid signature matching argument '...' to class "ANY\ " Error: package 'Biostrings' could not be loaded Execution halted Is this error caused by the R-Biostrings package not working, or is it used in the wrong way by the R-BSgenome package?
Hm indeed I run in the same problem while just trying to load Biostrings in R. Thanks for pointing this out I will investigate the source of the problem.
After asking the Bioconductor-devel mailing list the answer is that the bug comes from the IRanges. I used the developmental version of IRanges to get the corrected DESCRIPTION file, this seems to not be compatible with the current Biostrings. I normally only package the stable version of Bioconductor but since the new release is coming before the end of the month I took the risk and there is the bug. I will update Biostrings to the development version aswell so that we can finish the review.
Any progress with this package?
Yes, I have updated all the bioconductor packages to the latest stable version and update Biostrings as well: SPEC: http://pingou.fedorapeople.org/RPMs/R-Biostrings.spec SRPM: http://pingou.fedorapeople.org/RPMs/R-Biostrings-2.12.1-1.fc10.src.rpm
Package fails to build: Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : there is no package called 'Biobase' ERROR: lazy loading failed for package 'Biostrings' Missing Requires and BuildRequires on R-Biobase?
Depends : R , methods , IRanges Imports : methods , utils , IRanges , Biobase -_- I love Bioconductor's dependencies... SPEC: http://pingou.fedorapeople.org/RPMs/R-Biostrings.spec SRPM: http://pingou.fedorapeople.org/RPMs/R-Biostrings-2.12.1-2.fc10.src.rpm Does not build on koji since R-IRanges does not have the right version available yet.
Package approved.
New Package CVS Request ======================= Package Name: R-Biostrings Short Description: String objects representing biological sequences Owners: pingou Branches: F-10 F-11 InitialCC:
cvs done.
R-Biostrings-2.12.1-2.fc10 has been pushed to the Fedora 10 stable repository. If problems still persist, please make note of it in this bug report.
R-Biostrings-2.12.1-2.fc11 has been pushed to the Fedora 11 stable repository. If problems still persist, please make note of it in this bug report.