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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