On 26/06/2013 10:56, Kamal wrote:
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.
Nothing here is reproducible, so we need to guess. In particular, you
give so details of clRes but sapply is called on 'result', an object not
otherwise mentioned.
My guess is that you are using different functions rbind() in the two
cases, and that your package forgot to import an S4 generic for rbind.
Remember that in a package's namespace 'base' is implicitly imported, so
it takes priority over everything not in the namespace or explicitly
imported.
But it is equally possible you used different objects.
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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