Question: rtracklayer::import.bed does not close connections.
gravatar for Charles Plessy
10 months ago by
Charles Plessy30 wrote:


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)
ADD COMMENTlink modified 10 months ago by Michael Lawrence9.9k • written 10 months ago by Charles Plessy30
gravatar for Michael Lawrence
10 months ago by
United States
Michael Lawrence9.9k wrote:

My bad, it should be fixed in 1.36.1 (release). Also devel.

ADD COMMENTlink written 10 months ago by Michael Lawrence9.9k
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