Hi Kamal,
I suspect this to be because you did not load the package on each core so the
S4 definitions are not available there. The solution would be to specifically
load the library at each core prior to calling clusterApplyLB. (I vaguely
remember once having a similar problem where something worked only in
interactive mode and this was the solution)
The help page of clusterApply gives an example. If your package is called
"foo", it would be something like the following before the problematic call to
clusterApplyLB:
clusterEvalQ(cl, library(foo))
Hope this helps,
Henrik
Am 26/06/2013 11:56, schrieb Kamal:
Hi,
I am currently building an R package and I am facing a peculiar problem
where some of the functions does not work within the package. However, if I
source the script the function works.
For example, in a method for parallelization of analysis on each chromosome
simultaneously I am receiving error at the following position of the code:
# this profile the information chromosome wise and results in "clRes"
clRes = clusterApplyLB(cl, Chrs, profilingChr, GenoRanges = GenoRanges,
Sample = Sample)
class(clRes)
[1] "list"
clRes
[[1]]
S4 Object of class GElist; 14 features
start : 14350 69251 84185 116264 153924
end : 18349 73250 88184 120263 157923
chr : chr20 chr20 chr20 chr20 chr20
strand : * * * * *
binscore : NA
chrcomb <- sapply(result, function(x) rbind(x))
Error in rbind(x) : no method for coercing this S4 class to a vector
The above code is part of a function. If I run this code interactively or
by sourcing the script it runs fine. However, when I execute the function
from the installed package it gives me the above error. I could not find
any solution to this. Any insight into the above problem would be highly
appreciated.
sessionInfo()
R version 3.0.0 (2013-04-03)
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] BSgenome.Hsapiens.UCSC.hg18_1.3.19 BSgenome_1.28.0
[3] methylPipe_0.99.0 Rsamtools_1.12.3
[5] Biostrings_2.28.0 GenomicRanges_1.12.4
[7] IRanges_1.18.1 GOstats_2.26.0
[9] RSQLite_0.11.4 DBI_0.2-7
[11] graph_1.38.2 Category_2.26.0
[13] AnnotationDbi_1.22.6 Biobase_2.20.0
[15] BiocGenerics_0.6.0 snow_0.3-12
loaded via a namespace (and not attached):
[1] AnnotationForge_1.2.1 GO.db_2.9.0 GSEABase_1.22.0
[4] RBGL_1.36.2 RCurl_1.95-4.1 XML_3.96-1.1
[7] annotate_1.38.0 bitops_1.0-5 gdata_2.12.0.2
[10] genefilter_1.42.0 gplots_2.11.0.1 gtools_2.7.1
[13] limma_3.16.5 marray_1.38.0 rtracklayer_1.20.2
[16] splines_3.0.0 stats4_3.0.0 survival_2.37-4
[19] tools_3.0.0 xtable_1.7-1 zlibbioc_1.6.0
Thanks,
Kamal
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--
Dipl. Psych. Henrik Singmann
PhD Student
Albert-Ludwigs-Universität Freiburg, Germany
http://www.psychologie.uni-freiburg.de/Members/singmann
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