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Gábor Csárdi

2017-Dec-14 18:02 UTC

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

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

Gabriel Becker

2017-Dec-14 19:56 UTC

head link

[Rd] 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



-- 
Gabriel Becker, PhD
Scientist (Bioinformatics)
Genentech Research

	[[alternative HTML version deleted]]

Gábor Csárdi

2017-Dec-14 20:17 UTC

head link

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

On Thu, Dec 14, 2017 at 7:56 PM, Gabriel Becker <gmbecker at 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, 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
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
>
> --
> Gabriel Becker, PhD
> Scientist (Bioinformatics)
> Genentech Research

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