[Bioc-devel] Close connections continuously in fasta.index in Biostrings

Hervé Pagès hpages at fredhutch.org
Thu Mar 3 19:44:03 CET 2016

Hi Thomas,

Sorry for not getting back to you earlier on this. Opening/closing
each file inside the loop (i.e. at the beginning/end of each iteration)
instead of opening all files before entering the loop would indeed
address the problem. I'll look into this and will let you know.


On 02/15/2016 05:42 AM, Thomas Lin Pedersen wrote:
> Hi (mostly Hervé)
> I’m running into problems trying to run fasta.index() from Biostrings on a list of 4700 files, as the limit on open files are reached. Is it possible to continuously open and close the connections in the C code to circumvent this? I expect this problem also arises with readXStringSet..? I know dealing with such a high number of files in one chunk is probably an edge case, so I can understand if this is not something you wish to change the code for...
> with best wishes
> Thomas Lin Pedersen
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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