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$Sequence[i]) > matchRes = matchPattern(seq, Hsapiens[[chr]]) > SurroundingSequence[i] = as.character(subseq(Hsapiens[[chr]], > start=start(matchRes)-250, end=end(matchRes)+250)) > > within the loop. In run i=187 I get the error message: > Error in assign(".target", method at target, envir = envir) : > formal argument "envir" matched by multiple actual arguments > Calls: as.character ... RawPtr.read -> dec_lkup -> loadMethod -> > loadMethod -> assign > > However, it works when I match the 187th sequence manually (without > matching the 186 other sequences before). That makes it hard to debug. > > Best wishes, > Hans-Ulrich > > PS: my session info: > > sessionInfo() > R version 2.8.1 (2008-12-22) > x86_64-pc-linux-gnu > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 BSgenome_1.10.3 > [3] Biostrings_2.10.16 IRanges_1.0.12 > loaded via a namespace (and not attached): > [1] Matrix_0.999375-21 grid_2.8.1 lattice_0.17-20 tools_2.8.1 > > > mattia pelizzola wrote: >> Hi, >> >> I have a recurrent but not reproducible error.. If I run the same >> piece of code twice the error will disappear, but it will likely shop >> up the day after. >> This is the error message: >> >> Error in assign(".defined", method at defined, envir = envir) : >> formal argument "envir" matched by multiple actual arguments >> Calls: vmatchPattern ... lapply -> FUN -> loadMethod -> loadMethod -> >> assign >> >> this is the code where the error show up calling the vmatchPattern >> function for one chromosome. The code is actually repeated several >> times for all the chromosomes during the same R session: >> >> chrseq=Hsapiens$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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=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 > 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 -- 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: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319