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