cannot destroy connection (?) created by readLines in a tryCatch

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, G?bor Cs?rdi <csardi.gabor at 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

cannot destroy connection (?) created by readLines in a tryCatch

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