Entering edit mode
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=e
n_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_ID
ENTIFICATION=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
