Gábor Csárdi
2017-Dec-14 20:17 UTC
[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
Gabriel Becker
2017-Dec-14 21:21 UTC
[Rd] cannot destroy connection (?) created by readLines in a tryCatch
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 [[alternative HTML version deleted]]
Tierney, Luke
2017-Dec-14 22:05 UTC
[Rd] cannot destroy connection (?) created by readLines in a tryCatch
Your guess is wrong. More when I have a sensible keyboard
Sent from my iPhone
On Dec 15, 2017, at 10:21 AM, Gabriel Becker <gmbecker at
ucdavis.edu<mailto:gmbecker at ucdavis.edu>> wrote:
On Thu, Dec 14, 2017 at 12:17 PM, G?bor Cs?rdi <csardi.gabor at
gmail.com<mailto:csardi.gabor at gmail.com>>
wrote:
On Thu, Dec 14, 2017 at 7:56 PM, Gabriel Becker <gmbecker at
ucdavis.edu<mailto: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<mailto: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<mailto: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
[[alternative HTML version deleted]]
______________________________________________
R-devel at r-project.org<mailto:R-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[[alternative HTML version deleted]]
luke-tierney at uiowa.edu
2017-Dec-14 23:46 UTC
[Rd] cannot destroy connection (?) created by readLines in a tryCatch
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
Gábor Csárdi
2017-Dec-15 06:48 UTC
[Rd] cannot destroy connection (?) created by readLines in a tryCatch
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
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