Hi Michael,
Because of a recent change to IRanges, some information about the
"as.list" method table is now out-of-sync in your installed
AnnotationDbi (granted it was installed before the new IRanges
propagated to you). Re-installing AnnotationDbi should clear this.
I bumped AnnotationDbi version yesterday night (even though
AnnotationDbi has not changed) to help clear this up for other
users. The new version won't become available before tomorrow though.
But, again, this new version (1.25.18) is similar to the current
version (1.25.17), so you can re-install now with
biocLite("AnnotationDbi"). No need to wait until tomorrow.
HTH,
H.
On 04/09/2014 12:23 AM, Michael Stadler wrote:
Dear Bioc gurus,
Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some
unit tests, which turns out to be reproducible independent of QuasR and
might be related to R getting the wrong method for "[[<-".
The following works fine...
library(GenomicRanges)
grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)),
r2=GRanges("chr2",IRanges(3,4)))
grl[[1]] <- GRanges("chr1",IRanges(10,11))
...but this produces an error:
library(GenomicRanges)
library(GenomicFeatures)
grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)),
r2=GRanges("chr2",IRanges(3,4)))
grl[[1]] <- GRanges("chr1",IRanges(10,11))
#Error in as.list(x, use.names = FALSE) :
# could not find function ".as.list.CompressedList"
My guess is that loading the GenomicFeatures library in addition to
GenomicRanges influences the methods dispatch, but with my limited
understanding of R and S4 classes I was not able to narrow it further down.
I noticed that I am using a slightly older version of R (r65206)
compared to the build system (r65358), however I also see the error with
the most recent release candidate (r65385).
Michael
My session info:
R version 3.1.0 alpha (2014-03-17 r65206)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17 Biobase_2.23.6
[4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30 IRanges_1.21.43
[7] BiocGenerics_0.9.3 RColorBrewer_1.0-5
loaded via a namespace (and not attached):
[1] BBmisc_1.5 BSgenome_1.31.13
[3] BatchJobs_1.2 BiocParallel_0.5.19
[5] Biostrings_2.31.21 DBI_0.2-7
[7] GenomicAlignments_0.99.37 RCurl_1.95-4.1
[9] RSQLite_0.11.4 Rcpp_0.11.1
[11] Rsamtools_1.15.41 XML_3.98-1.1
[13] XVector_0.3.7 biomaRt_2.19.3
[15] bitops_1.0-6 brew_1.0-6
[17] codetools_0.2-8 digest_0.6.4
[19] fail_1.2 foreach_1.4.1
[21] iterators_1.0.6 plyr_1.8.1
[23] rtracklayer_1.23.22 sendmailR_1.1-2
[25] stats4_3.1.0 stringr_0.6.2
[27] tools_3.1.0 zlibbioc_1.9.0
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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