This has nothing to do with on.exit. It is an iteraction between where
the warning is signaled in 'file' and your _exiting_ warning handler.
This combination has the same issue,
tryCatch(file(tempfile(), "r"), warning = identity)
showConnections(all = TRUE)
as does
options(warn=2)
file(tempfile(), "r")
showConnections(all = TRUE)
I haven't looked at the internals of 'file' but it looks like
what it does is
add an entry to connections table
warn about non-existent file
realize it has to fail
remove the connections table entry
signal an error
This misses the possibility that the warning can result in a jump
if it is turned into a error or handled by an exiting handler.
It's worth filing a bug report on 'file'.
It's not clear what you are really trying to do, but establishing
an _exiting_ handler for warnings is usually not what you
want. If you are trying to suppress warnings you need to use a
calling handler, e.g. via suppressWarnings. If you want to do
something more sophisticated that does not terminate the
computation on a warniing you can build on what suppressWarnigns
does.
Best,
luke
On Thu, 14 Dec 2017, Gábor Csárdi wrote:
On Thu, Dec 14, 2017 at 7:56 PM, Gabriel Becker <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 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>
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
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--
Gabriel Becker, PhD
Scientist (Bioinformatics)
Genentech Research
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--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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