From gmbecker at ucdavis.edu  Thu Dec 14 22:21:15 2017
From: gmbecker at ucdavis.edu (Gabriel Becker)
Date: Thu, 14 Dec 2017 13:21:15 -0800
Subject: [Rd] cannot destroy connection (?) created by readLines in a
	tryCatch
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Message-ID: <CADwqtCOm8R4E827krkM5Vg+_AwB190tOXeh3w+mxSxu=aBWcCA@mail.gmail.com>

On Thu, Dec 14, 2017 at 12:17 PM, G?bor Cs?rdi <csardi.gabor at gmail.com>
wrote:

> 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 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, 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
>



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

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