[BioC] Error in assign while calling the vmatchPattern function

[Hervé Pagès]

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;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
>>
>>
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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