FYI, from the R devel list: On Mon, Jun 15, 2009 at 7:38 AM, Peter Dalgaard<[email protected]> wrote: > This is to announce that we plan to release R version 2.9.1 on Friday, > June 26, 2009.
/Henrik 2009/6/16 Hervé Pagès <[email protected]>: > Hi Biostrings/BSgenome users, > > So the good news is that the infamous/spooky "formal argument envir matched > by multiple actual arguments" error was a bug in R and it has been fixed > in svn in recent revisions of R release and devel. This means that you > need to get and compile R yourself directly from subversion or just wait > the bug-fix release R-2.9.1 which should be out in a month or so. > > A big thanks to all those who helped on this issue! > > H. > > Hervé Pagès wrote: >> >> Hi Mattia, Hans-Ulrich, >> >> Thanks for reporting this. I'm aware of the problem. It shows up sometimes >> on the build/check report e.g. today: >> >> http://bioconductor.org/checkResults/2.3/bioc-LATEST/BSgenome/wilson2-buildsrc.html >> Some days it's here, some days no, sometimes on one platform, sometimes on >> the other. It's a weird issue that is indeed very hard to reproduce as you >> noticed. >> I'll keep you posted when I find something. >> >> Cheers, >> H. >> >> >> Hans-Ulrich Klein wrote: >>> >>> Hi all, >>> >>> I encountered a similar (probably related) error today. I wanted to match >>> a few hundred sequences against the UCSC genome from the package >>> "BSgenome.Hsapiens.UCSC.hg18". I implemented a simple "for" loop and called >>> >>> seq = DNAString(sequences$Sequence[i]) >>> matchRes = matchPattern(seq, Hsapiens[[chr]]) >>> SurroundingSequence[i] = as.character(subseq(Hsapiens[[chr]], >>> start=start(matchRes)-250, end=end(matchRes)+250)) >>> >>> within the loop. In run i=187 I get the error message: >>> Error in assign(".target", met...@target, envir = envir) : >>> formal argument "envir" matched by multiple actual arguments >>> Calls: as.character ... RawPtr.read -> dec_lkup -> loadMethod -> >>> loadMethod -> assign >>> >>> However, it works when I match the 187th sequence manually (without >>> matching the 186 other sequences before). That makes it hard to debug. >>> >>> Best wishes, >>> Hans-Ulrich >>> >>> PS: my session info: >>> > sessionInfo() >>> R version 2.8.1 (2008-12-22) >>> x86_64-pc-linux-gnu >>> >>> locale: >>> C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> other attached packages: >>> [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 BSgenome_1.10.3 >>> [3] Biostrings_2.10.16 IRanges_1.0.12 >>> loaded via a namespace (and not attached): >>> [1] Matrix_0.999375-21 grid_2.8.1 lattice_0.17-20 tools_2.8.1 >>> >>> >>> mattia pelizzola wrote: >>>> >>>> Hi, >>>> >>>> I have a recurrent but not reproducible error.. If I run the same >>>> piece of code twice the error will disappear, but it will likely shop >>>> up the day after. >>>> This is the error message: >>>> >>>> Error in assign(".defined", met...@defined, envir = envir) : >>>> formal argument "envir" matched by multiple actual arguments >>>> Calls: vmatchPattern ... lapply -> FUN -> loadMethod -> loadMethod -> >>>> assign >>>> >>>> this is the code where the error show up calling the vmatchPattern >>>> function for one chromosome. The code is actually repeated several >>>> times for all the chromosomes during the same R session: >>>> >>>> chrseq=Hsapiens$chr1 >>>> Gviews = Views(chrseq, starts, ends) # where length(starts)> 20000 >>>> Gset = DNAStringSet(Gviews) >>>> querySeq=DNAString('ATTH') >>>> a = startIndex(vmatchPattern(querySeq, Gset, fixed=F)) >>>> >>>> >>>> >>>> and finally this is my sessionInfo: >>>> >>>> R version 2.8.1 (2008-12-22) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 BSgenome_1.10.3 >>>> [3] Biostrings_2.10.15 IRanges_1.0.11 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] grid_2.8.1 lattice_0.17-17 Matrix_0.999375-20 >>>> >>>> >>>> >>>> thanks, >>>> >>>> mattia >>>> >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: [email protected] > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioconductor mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
