Your guess is wrong. More when I have a sensible keyboard Sent from my iPhone
On Dec 15, 2017, at 10:21 AM, Gabriel Becker <gmbec...@ucdavis.edu<mailto:gmbec...@ucdavis.edu>> wrote: On Thu, Dec 14, 2017 at 12:17 PM, Gábor Csárdi <csardi.ga...@gmail.com<mailto:csardi.ga...@gmail.com>> wrote: On Thu, Dec 14, 2017 at 7:56 PM, Gabriel Becker <gmbec...@ucdavis.edu<mailto:gmbec...@ucdavis.edu>> wrote: Gabor, You can grab the connection and destroy it via getConnection and then a standard close call. Yeah, that's often a possible workaround, but since this connection was opened by readLines() internally, I don't necessarily know which one it is. E.g. I might open multiple connections to the same file, so I can't choose based on the file name. Btw. this workaround seems to work for me: read_lines <- function(con, ...) { if (is.character(con)) { con <- file(con) on.exit(close(con)) } readLines(con, ...) } This is basically the same as readLines(), but on.exit() does its job here. That's another clue that it might be an on.exit() issue. Wild guess: on.exit() does not run if an internal function errors. It seems to be the setting of a warning handler in tryCatch that does it actually; without that, it works as expected, even when errors are caught. tryCatch(readLines(tempfile(), warn=FALSE), error=function(x) NA) [1] NA *Warning message:* *In file(con, "r") :* * cannot open file '/var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T//RtmpzIZ6Qh/file1ed2e57f2ea': No such file or directory* showConnections(all=TRUE) description class mode text isopen can read can write 0 "stdin" "terminal" "r" "text" "opened" "yes" "no" 1 "stdout" "terminal" "w" "text" "opened" "no" "yes" 2 "stderr" "terminal" "w" "text" "opened" "no" "yes" tryCatch(readLines(tempfile(), warn=FALSE), warning=function(x) NA) [1] NA showConnections(all=TRUE) description 0 "stdin" 1 "stdout" 2 "stderr" 3 "/var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T//RtmpzIZ6Qh/file1ed2300ce801" class mode text isopen can read can write 0 "terminal" "r" "text" "opened" "yes" "no" 1 "terminal" "w" "text" "opened" "no" "yes" 2 "terminal" "w" "text" "opened" "no" "yes" 3 "file" "r" "text" "closed" "yes" "yes" ~G (it actually lists that it is "closed" already, but still in the set of existing connections. I can't speak to that difference). It is closed but not destroyed. G. tryCatch( + readLines(tempfile(), warn = FALSE)[1], + error = function(e) NA, + warning = function(w) NA + ) [1] NA rm(list=ls(all.names = TRUE)) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 257895 13.8 592000 31.7 416371 22.3 Vcells 536411 4.1 8388608 64.0 1795667 13.7 showConnections(all = TRUE) description 0 "stdin" 1 "stdout" 2 "stderr" 3 "/var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T// RtmpZRcxmh/file128a13bffc77" class mode text isopen can read can write 0 "terminal" "r" "text" "opened" "yes" "no" 1 "terminal" "w" "text" "opened" "no" "yes" 2 "terminal" "w" "text" "opened" "no" "yes" 3 "file" "r" "text" "closed" "yes" "yes" con = getConnection(3) con A connection with description "/var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T// RtmpZRcxmh/file128a13bffc77" class "file" mode "r" text "text" opened "closed" can read "yes" can write "yes" close(con) showConnections(all=TRUE) description class mode text isopen can read can write 0 "stdin" "terminal" "r" "text" "opened" "yes" "no" 1 "stdout" "terminal" "w" "text" "opened" "no" "yes" 2 "stderr" "terminal" "w" "text" "opened" "no" "yes" HTH, ~G On Thu, Dec 14, 2017 at 10:02 AM, Gábor Csárdi <csardi.ga...@gmail.com<mailto:csardi.ga...@gmail.com>> wrote: Consider this code. This is R 3.4.2, but based on a quick look at the NEWS, this has not been fixed. tryCatch( readLines(tempfile(), warn = FALSE)[1], error = function(e) NA, warning = function(w) NA ) rm(list=ls(all.names = TRUE)) gc() showConnections(all = TRUE) If you run it, you'll get a connection you cannot close(), i.e. the last showConnections() call prints: ❯ showConnections(all = TRUE) description 0 "stdin" 1 "stdout" 2 "stderr" 3 "/var/folders/59/0gkmw1yj2w7bf2dfc3jznv5w0000gn/T//Rtmpc7JqVS/ filecc2044b2ccec" class mode text isopen can read can write 0 "terminal" "r" "text" "opened" "yes" "no" 1 "terminal" "w" "text" "opened" "no" "yes" 2 "terminal" "w" "text" "opened" "no" "yes" 3 "file" "r" "text" "closed" "yes" "yes" AFAICT, readLines should close the connection: ❯ readLines function (con = stdin(), n = -1L, ok = TRUE, warn = TRUE, encoding = "unknown", skipNul = FALSE) { if (is.character(con)) { con <- file(con, "r") on.exit(close(con)) } .Internal(readLines(con, n, ok, warn, encoding, skipNul)) } <environment: namespace:base> so maybe this just a symptom of an on.exit() issue? Or am I missing something and it is possible to close the connection? Thanks, Gabor ______________________________________________ R-devel@r-project.org<mailto:R-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Gabriel Becker, PhD Scientist (Bioinformatics) Genentech Research -- Gabriel Becker, PhD Scientist (Bioinformatics) Genentech Research [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org<mailto:R-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
