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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