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. (it actually lists that it is "closed" already, but
still in the set of existing connections. I can't speak to that difference).

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

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