Hi all,
I am interested in using the tool BICseq for a CNV detection analysis. Unfortunately, I am writing you because I cannot solve a problem related to BICseq R package.
The R package is correctly installed and I am testing it on chr22 extracted from a in home BAM file. Running the function getBICseg with default parameters and a correctly generated bicseq object using the BICseq function, the following error is reported:
Error in .C("sort_rms_binning", as.integer(sample), length(sample), as.integer(reference), : "sort_rms_binning" not resolved from current namespace (BICseq)"
Please, could you help me fixing the problem?
I am using the R version 3.0.1.
I found other posts related to this problem here but no answers.
Many thanks in advance!
Nicola
•
written
by
Nicola Casiraghi
Hi Kiz,
thank you for the suggestion, however I need tool for WGS data analysis.
•
written
by
Nicola Casiraghi
Log in to answer this question.
There's been an update to the way C libraries are handled with R 3.0.x. You'll need to untar the R package and edit the NAMESPACE file to include the following line:
Save the file and run R CMD check BICseq then R CMD INSTALL BICseq (note the use of the unpacked directory name instead of the tar.gz file). Hope this helps!
Please add this as a solution rather than a comment. We've been looking for an answer to this issue for literally months, but have instead been hanging on to a 2.15.x copy of R.
We've stopped using it completely because of this issue.