Entering edit mode
Hello,
Since I upgraded R to version 3.4 and Bioconductor to version 3.5, I have strange warning messages saying closing unused connection after using rtracklayer directly or indirectly (through CAGEr). It seems related to the fact that functions such as import.bed leave open connections behind them. Is that needed or can it be corrected ?
The warning messages happen infrequently, but running multiple times the same import will eventually trigger them. Here is an example.
Restarting R session...
> file <- system.file("tests", "test.bed", package="rtracklayer")
> x <- rtracklayer::import.bed(file)
> showConnections()
description class mode text isopen can read
3 "/usr/local/lib/R/site-library/rtracklayer/tests/test.bed" "file" "r" "text" "opened" "yes"
can write
3 "no"
> x <- rtracklayer::import.bed(file)
Warning message:
closing unused connection 4 (/usr/local/lib/R/site-library/rtracklayer/tests/test.bed)
Dear developer,
This problem (at least for import.bed, import.bedGraph) seems still existing in v1.38.3. Connections do not get freed instantly, causing running out of connections in a loop.
Reproducible example?
Hi Michael, after reinstalling the package (same version), this problem is gone. Now it works no problem for 1000 bed or bedGraph files on Linux and MacOS. Thanks anyway.