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)