[BioC] Error in assign while calling the vmatchPattern function

[Hervé Pagès]

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
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