Entering edit mode
Wijchers, Patrick
▴
40
@wijchers-patrick-2973
Last seen 10.2 years ago
Dear all,
I encountered a problem while working on R that I do not know how to
solve.
It started when I wanted to load the affyPLM package:
*/> library(affyPLM)
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
Loading required package: preprocessCore
Error in ls(where) : unused argument(s) (2)
Error in library(affyPLM) : .First.lib failed for 'affyPLM'/*
As packages such as 'affy', 'genefilter' and 'limma' load fine, I
thought it might be something related to the affyPLM package.
However, upon trying to re-install the package, I got a similar error:
/*> source("http://bioconductor.org/biocLite.R")
Error in ls(all.names = TRUE) : unused argument(s) (all.names =
TRUE)*/
Now, I think it may be related to the 'ls' function. Strangely enough,
when using the 'ls' command I get this:
/*> ls()
Quality control information for mouse4302:
This package has the following mappings:
Error in get(mapname) : variable "mouse4302ACCNUM" was not found*/
I can now only access my objects using 'objects()'.
Strangely, I have been using all week without problems. I have tried
restarting R, even reinstalling R, but to no avail. I hope it is
something stupid I do not see.... Does anyone have a suggestion how I
can solve this?
Any help would be greatly appreciated,
Patrick
/*> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-redhat-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_N
AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
FICATION=C
attached base packages:
[1] splines tools stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] preprocessCore_1.4.0 gcrma_2.14.1 matchprobes_1.14.1
[4] affy_1.20.0 Biobase_2.2.1 RSQLite_0.7-1
[7] DBI_0.2-4
loaded via a namespace (and not attached):
[1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2
[4] genefilter_1.22.0 mouse4302.db_2.2.5 survival_2.34-1 */
--
Patrick Wijchers, PhD
MRC Clinical Sciences Centre
Imperial College London
Hammersmith Campus
Du Cane Road
London W12 0NN
Phone: +44 (0)20 8383 8500 (office)
+44 (0)20 8383 8317 (lab)
Fax: +44 (0)20 8383 8306
Email: patrick.wijchers at csc.mrc.ac.uk