[BioC] Error in assign while calling the vmatchPattern function

[Henrik Bengtsson]

FYI, from the R devel list:

On Mon, Jun 15, 2009 at 7:38 AM, Peter Dalgaard<P.Dalgaard at biostat.ku.dk> 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 <hpages at fhcrc.org>:
> 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$Sequence[i])
>>>   matchRes = matchPattern(seq, Hsapiens[[chr]])
>>>   SurroundingSequence[i] = as.character(subseq(Hsapiens[[chr]],
>>>        start=start(matchRes)-250, end=end(matchRes)+250))
>>>
>>> within the loop. In run i=187 I get the error message:
>>> Error in assign(".target", method at target, envir = envir) :
>>>  formal argument "envir" matched by multiple actual arguments
>>> Calls: as.character ... RawPtr.read -> dec_lkup -> loadMethod ->
>>> loadMethod -> assign
>>>
>>> However, it works when I match the 187th sequence manually (without
>>> matching the 186 other sequences before). That makes it hard to debug.
>>>
>>> Best wishes,
>>> Hans-Ulrich
>>>
>>> PS: my session info:
>>>  > sessionInfo()
>>> R version 2.8.1 (2008-12-22)
>>> x86_64-pc-linux-gnu
>>>
>>> locale:
>>> C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>> other attached packages:
>>> [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 BSgenome_1.10.3
>>>  [3] Biostrings_2.10.16                 IRanges_1.0.12
>>>  loaded via a namespace (and not attached):
>>> [1] Matrix_0.999375-21 grid_2.8.1         lattice_0.17-20    tools_2.8.1
>>>
>>>
>>> mattia pelizzola wrote:
>>>>
>>>> Hi,
>>>>
>>>> I have a recurrent but not reproducible error.. If I run the same
>>>> piece of code twice the error will disappear, but it will likely shop
>>>> up the day after.
>>>> This is the error message:
>>>>
>>>> Error in assign(".defined", method at defined, envir = envir) :
>>>>  formal argument "envir" matched by multiple actual arguments
>>>> Calls: vmatchPattern ... lapply -> FUN -> loadMethod -> loadMethod ->
>>>> assign
>>>>
>>>> this is the code where the error show up calling the vmatchPattern
>>>> function for one chromosome. The code is actually repeated several
>>>> times for all the chromosomes during the same R session:
>>>>
>>>> chrseq=Hsapiens$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
> 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
>
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