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

Thomas Lin Pedersen thomasp85 at gmail.com
Mon Feb 15 14:42:21 CET 2016

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

More information about the Bioc-devel mailing list