I can confirm that on a mingw build for windows, these computations do not succeed as intended. This is a situation where the testing and error reporting of the software are not sufficient to allow our use of R CMD check to identify nonportable code. Somewhere in the package man pages or obligatory test code the result of a computation should be checked against its known value and an error thrown if a discrepancy occurs. Some of the computations in the examples seem solvable using Biostrings. Solution for you at this moment is to use another platform. I have shown that it works on MacOSX, and just tested a linux machine, and the intended results seem to come back. But it is important for all contributors to recognize that our multiplatform build/check system cannot identify nonportability if erroneous calculations do not raise error conditions in examples or tests. On Fri, Oct 9, 2009 at 4:46 AM, avargas <avargas at="" lcg.unam.mx=""> wrote: > I apreciate the quick response, here is my code: > >> library("GeneR") >> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa" >> placeString(s) > [1] 0 >> >> getOrfs(phase = NULL,seqno=0) > NULL >> maxOrf() > [1] -1 >> >> #Problem with exact word > >> placeString("TTTTTTTTTTTT") > [1] 0 >> exactWord("TTT") > [[1]] > [1] -1 > >> sessionInfo() > R version 2.10.0 Under development (unstable) (2009-08-15 r49252) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=Spanish_Mexico.1252 ?LC_CTYPE=Spanish_Mexico.1252 > [3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C > [5] LC_TIME=Spanish_Mexico.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] GeneR_2.15.0 > > On Fri, 9 Oct 2009 04:21:58 -0400, Vincent Carey > <stvjc at="" channing.harvard.edu=""> wrote: >> Please give sessionInfo() result. ?Here are my results, installing >> GeneR from source a moment ago >> >>> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa" >>> placeString(s) >> [1] 0 >>> s >> [1] "gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa" >>> ?placeString >>> ? ?getSeq(seqno=0) >> [1] "GTCATGCATGCTAGGTGACAGTTAAAATGCGTCTAGGTGACAGTCTAACAA" >>> getOrfs(phase = NULL,seqno=0) >> ? ? ?start stop >> [1,] ? ? 4 ? 18 >> [2,] ? ? 8 ? 25 >>> maxOrf() >> [1] 18 >>> ?maxOrf >>> ?getOrfs >>> getOrfs(phase = NULL,seqno=0) >> ? ? ?start stop >> [1,] ? ? 4 ? 18 >> [2,] ? ? 8 ? 25 >>> placeString("TTTTTTTTTTTT") >> [1] 0 >>> exactWord("TTT") >> [[1]] >> ?[1] ?1 ?2 ?3 ?4 ?5 ?6 ?7 ?8 ?9 10 >> >>> sessionInfo() >> R version 2.10.0 Under development (unstable) (2009-09-09 r49642) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices datasets ?tools ? ? utils ? ? methods >> [8] base >> >> other attached packages: >> [1] GeneR_2.15.0 ? ?weaver_1.11.1 ? codetools_0.2-2 digest_0.3.1 >> >> >> >> On Fri, Oct 9, 2009 at 1:04 AM, avargas <avargas at="" lcg.unam.mx=""> wrote: >>> Dear list, i have some troubles with the GeneR package, it seems that >>> getOrfs is not working. I already try to use it with the example info of >>> the help: >>> >>> library("GeneR") >>> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa" >>> placeString(s) >>> >>> getOrfs(phase = NULL,seqno=0) >>> maxOrf() >>> >>> But returns: >>>> getOrfs(phase = NULL,seqno=0) >>> NULL >>>> maxOrf() >>> [1] -1 >>> I have the version 2.10 of R and the Package GeneR version 2.15.0 >>> I mean, the examples of >>> http://rss.acs.unt.edu/Rdoc/library/GeneR/doc/GeneR.pdf at page 5 are >> not >>> reproducible, so, which is the problem? >>> In advance, thanks. >>> >>> Amhed Missael Vargas Vel?zquez >>> avargas at lcg.unam.mx >>> LCG,UNAM >>> >>> Pd: I think that the problem is with another function named, exact word, >>> that does not work too. >>> i.e. >>> library("GeneR") >>> placeString("TTTTTTTTTTTT") >>> exactWord("TTT") >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >