Dear Henrik,
Until now I have used aroma.affymetrix_1.1.0 with R-2.8.1 and could
run my analysis on our sge-cluster w/o any problems.
Now I have upgraded to R-2.11.1 and to aroma.affymetrix_1.6.2 and are
curently testing with 8 chips whether my package based on
aroma.affymetrix still works on the cluster. The normalization step on
a server did run fine, howeever, distributing the 8 samples on the
cluster to run GladModel() resulted in the problem that 3 of 8 cluster
nodes did stop with the following error message:
Loading required package: GLAD
...
Loading required package: RColorBrewer
Loading required package: Cairo
Error in list(`computeCN(aroma, model = model, arrays = arrays[i],
chromosomes = 1:23, ref` = <environment>, :
[2010-06-29 15:08:49] Exception: Cannot save to file. Temporary file
already exists: ~/.Rcache/aroma.affymetrix/idChecks/
a1c33926939ee43fbed83ae69301d215.tmp
at throw(Exception(...))
at throw.default("Cannot save to file. Temporary file already
exists: ", pathn
at throw("Cannot save to file. Temporary file already exists: ",
pathnameT)
at saveObject.default(list(key = key, keyIds = lapply(key, digest2),
id = id),
at saveObject(list(key = key, keyIds = lapply(key, digest2), id =
id), idPathn
at getAverageFile.AffymetrixCelSet(ces, force = force, verbose =
less(verbose)
at NextMethod(generic = "getAverageFile", object = this, indices =
indices, ..
at getAverageFile.ChipEffectSet(ces, force = force, verbose =
less(verbose))
at NextMethod(generic = "getAverageFile", object = this, ...)
at getAverageFile.SnpChipEffectSet(ces, force = force, verbose =
less(verbose)
at NextMethod(generic = "getAverageFile", object = this, ...)
at getAverageFile.CnChipEffectS
Calls: computeCN ... saveObject.default -> throw -> throw.default ->
throw -> throw.Exception
Execution halted
Interestingly, on the other 5 nodes GladModel() seems to run fine.
Do you have any idea what the reason for this problem might be?
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] Cairo_1.4-5 RColorBrewer_1.0-2
GLAD_2.10.0
[4] biasnp_0.2.54 RODBC_1.3-1
aroma.affymetrix_1.6.2
[7] aroma.apd_0.1.7 affxparser_1.20.0
R.huge_0.2.0
[10] aroma.core_1.6.2 aroma.light_1.16.0
matrixStats_0.2.1
[13] R.rsp_0.3.6 R.cache_0.3.0
R.filesets_0.8.2
[16] digest_0.4.2 R.utils_1.4.2
R.oo_1.7.3
[19] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
Warning message:
'DESCRIPTION' file has 'Encoding' field and re-encoding is not
possible
Best regards
Christian
P.S.:
Is Google groups still the place to post questions?
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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