On 29 January 2013 at 19:58, Andreas Tille wrote: | Hi, | | because I'm lacking the relevant R knowledge (and I also fail in finding | some relevant R/CRAN packaging team inside Debian) I'm writing to Debian | Mentors and main R packages maintainer. I guess with some basic R knowledge | the problem below is easy to solve. I checked the source of r-cran-genabel | package and found the problematic function only in one single file: | | ../r-cran-genabel-1.7-0$ grep -Rl "stringSplit" | R/checkPackageVersionOnCRAN.R | | When reading its only quite short function | | checkPackageVersionOnCRAN <- function(packageName,baseUrlCRAN="http://cran.r-project.org/web/packages/";, timeout = 10) | { | # change default timout | svtmo <- options("timeout") | options("timeout"=timeout) | # page to check is | pageAddress <- paste(baseUrlCRAN,packageName,sep="/") | ... | # parse the page and get string starting with "Package source:" | targetLine <- pageContent[grep("Package source:",pageContent)] | # split the string at "Package_" and ".tar.gz"; the element before the last will contain the version | splitPattern <- paste(packageName,"_|.tar.gz",sep="") | stringSplit <- strsplit(targetLine,splitPattern) | cranVersion <- stringSplit[[1]][length(stringSplit[[1]])-1] | # return version | return(cranVersion) | }
That is so wrong on so many levels. There are much better ways to get version information from CRAN. That said, your diagnosis may be faulty. All we see is > Error : .onLoad failed in loadNamespace() for 'GenABEL', details: > call: stringSplit[[1]] > error: subscript out of bounds and loadNamespace() is an internal function. Very generally speaking, not all package functions are being triggered on build/install -- in fact, very few are. I suspect something else such as one of the package GenABEL depends upon. [ Goes checking ] Well those are standard. Odd. Dunno. Not my package, I don't use it, and there are 4200 other ones on CRAN. If it refuses to build ... throw it out. Dirk | | this heavily smells like the attempt to verify a web page while beeing | offline. IMHO the proper fix for this would be to return for instance | the version of the Debian package or some other reasonable thing - but | in any case it should be avoided trying to split a non-existing string | or so. | | Any hint for a reasonable patch? | | Thanks for any help | | Andreas. | | | On Tue, Jan 29, 2013 at 04:16:45PM +0100, Lucas Nussbaum wrote: | > Source: r-cran-genabel | > Version: 1.7-0-1 | > Severity: serious | > Tags: wheezy sid | > User: debian...@lists.debian.org | > Usertags: qa-ftbfs-20130129 qa-ftbfs | > Justification: FTBFS in wheezy on amd64 | > | > Hi, | > | > During a rebuild of all packages in *wheezy*, your package failed to | > build on amd64. | > | > Relevant part: | > > make[1]: Entering directory `/«PKGBUILDDIR»/src' | > > make[1]: Leaving directory `/«PKGBUILDDIR»/src' | > > installing to /«PKGBUILDDIR»/debian/r-cran-genabel/usr/lib/R/site-library/GenABEL/libs | > > ** R | > > ** data | > > ** demo | > > ** inst | > > ** preparing package for lazy loading | > > ** help | > > *** installing help indices | > > ** building package indices | > > ** installing vignettes | > > ** testing if installed package can be loaded | > > Error : .onLoad failed in loadNamespace() for 'GenABEL', details: | > > call: stringSplit[[1]] | > > error: subscript out of bounds | > > Error: loading failed | > > Execution halted | > > ERROR: loading failed | > > * removing '/«PKGBUILDDIR»/debian/r-cran-genabel/usr/lib/R/site-library/GenABEL' | > > make: *** [R_any_arch] Error 1 | > | > The full build log is available from: | > http://people.debian.org/~lucas/logs/2013/01/29/r-cran-genabel_1.7-0-1_wheezy.log | > | > A list of current common problems and possible solutions is available at | > http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! | > | > About the archive rebuild: The rebuild was done on EC2 VM instances from | > Amazon Web Services, using a clean, minimal and up-to-date chroot. Every | > failed build was retried once to eliminate random failures. | > | > _______________________________________________ | > Debian-med-packaging mailing list | > debian-med-packag...@lists.alioth.debian.org | > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging | > | | -- | http://fam-tille.de -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
