From csardi.gabor at gmail.com  Fri Dec 15 07:48:54 2017
From: csardi.gabor at gmail.com (=?UTF-8?B?R8OhYm9yIENzw6FyZGk=?=)
Date: Fri, 15 Dec 2017 06:48:54 +0000
Subject: [Rd] cannot destroy connection (?) created by readLines in a
	tryCatch
In-Reply-To: <alpine.OSX.2.20.1712141746070.1706@lukes-macbook-air.local>
References: <CABtg=KnWVVSvq6dogNG9fnYWhTJNNadJcyaMDif0_EV7Gd_VaA@mail.gmail.com>
 <CADwqtCPwpURQqLs0NrX7Hg9CtEX4huLj+Z=DTKvzTb9bHX=vbA@mail.gmail.com>
 <CABtg=KnTE+5n-4wQgty0yMVr1_vuUhvYgJ2fJGux143Pz-T0bQ@mail.gmail.com>
 <alpine.OSX.2.20.1712141746070.1706@lukes-macbook-air.local>
Message-ID: <CABtg=KkADSVkwsEN=nm_8Xs5eONABqfy9fZwVW__wcmzP_jS5Q@mail.gmail.com>

Thanks for tracking this down. Yeah, I should use suppressWarnings(),
you are right.
Although, readLines() might throw another warning, e.g. for incomplete
last lines,
and you don't necessarily want to suppress that.

TBH I am not sure why that warning is given:

? con <- file(tempfile())
? open(con)
Error in open.connection(con) : cannot open the connection
In addition: Warning message:
In open.connection(con) :
  cannot open file
'/var/folders/59/0gkmw1yj2w7bf2dfc3jznv5w0000gn/T//RtmpilJLXL/filed0ab5adb9a18':
No such file or directory

It seems that open() also throws an error, so why give the warning?
Because it is more specific?
Would it make sense to turn that warning into an error?

Gabor

On Thu, Dec 14, 2017 at 11:46 PM,  <luke-tierney at uiowa.edu> wrote:
> 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, G?bor Cs?rdi 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 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
>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
> --
> 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-tierney at uiowa.edu
> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu



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