Hi All,
I would like to route the output to a file using sink(). When using the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after it was
created?
Kind regards
Georg
sink(): Cannot open file
12 messages · G.Maubach at weinwolf.de, Jim Lemon, John Sorkin +3 more
Hi Georg, I don't suppose that you have: 1) checked that the file "all.Rout" exists somewhere? 2) if so, looked at the file with Notepad, perhaps? 3) let us in on the secret by pasting the contents of "all.Rout" into your message if it is not too big? At a guess, trying: close(zz) might get you there. Jim
On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All,
I would like to route the output to a file using sink(). When using the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after it was
created?
Kind regards
Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hi Jim,
thanks for your reply.
ad 1)
"all.Rout" was created in the correct directory. It exists properly with
correct file properties on Windows, e.g. creation date and time and file
size information.
ad 2)
I can not access the file with Notepad.exe directly after it was created
by R. The error message is (translated):
"Cannot access file "all.Rout". The file is opened by another process."
ad 3)
If I close R completely the file access is released. Then I can read the
file using Notepad.exe. The contents is:
Error in log("a") : non-numeric argument to mathematical function
I tried
close(zz)
but the error persists.
To me it looks like R is still accessing the file and not releasing the
connection for other programs. close(zz) should have solved the problem
but unfortantely it doesn't.
What else could I try?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 12:50
Betreff: Re: [R] sink(): Cannot open file
Hi Georg,
I don't suppose that you have:
1) checked that the file "all.Rout" exists somewhere?
2) if so, looked at the file with Notepad, perhaps?
3) let us in on the secret by pasting the contents of "all.Rout" into
your message if it is not too big?
At a guess, trying:
close(zz)
might get you there.
Jim
On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All,
I would like to route the output to a file using sink(). When using the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after it
was
created? Kind regards Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Have you tried:
sink("all.Rout")
try(log("a"))
sink()
Jim
On Tue, May 10, 2016 at 9:05 PM, <G.Maubach at weinwolf.de> wrote:
Hi Jim,
thanks for your reply.
ad 1)
"all.Rout" was created in the correct directory. It exists properly with
correct file properties on Windows, e.g. creation date and time and file
size information.
ad 2)
I can not access the file with Notepad.exe directly after it was created
by R. The error message is (translated):
"Cannot access file "all.Rout". The file is opened by another process."
ad 3)
If I close R completely the file access is released. Then I can read the
file using Notepad.exe. The contents is:
Error in log("a") : non-numeric argument to mathematical function
I tried
close(zz)
but the error persists.
To me it looks like R is still accessing the file and not releasing the
connection for other programs. close(zz) should have solved the problem
but unfortantely it doesn't.
What else could I try?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 12:50
Betreff: Re: [R] sink(): Cannot open file
Hi Georg,
I don't suppose that you have:
1) checked that the file "all.Rout" exists somewhere?
2) if so, looked at the file with Notepad, perhaps?
3) let us in on the secret by pasting the contents of "all.Rout" into
your message if it is not too big?
At a guess, trying:
close(zz)
might get you there.
Jim
On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All,
I would like to route the output to a file using sink(). When using the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after it
was
created? Kind regards Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hi Jim,
I tried:
sink("all.Rout")
try(log("a"))
sink()
The program executes without warning or error. The file "all.Rout" is
begin created. Nothing will be written to it. The file is accessable
rights after the execution of the program by notepad.exe.
The program
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink()
close(zz)
unlink(zz)
creates the file, does not write anything to it and is not accessable
after program execution in R with notepad.exe.
Any ideas what happens behind the szenes?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 13:16
Betreff: Re: Re: [R] sink(): Cannot open file
Have you tried:
sink("all.Rout")
try(log("a"))
sink()
Jim
On Tue, May 10, 2016 at 9:05 PM, <G.Maubach at weinwolf.de> wrote:
Hi Jim,
thanks for your reply.
ad 1)
"all.Rout" was created in the correct directory. It exists properly with
correct file properties on Windows, e.g. creation date and time and file
size information.
ad 2)
I can not access the file with Notepad.exe directly after it was created
by R. The error message is (translated):
"Cannot access file "all.Rout". The file is opened by another process."
ad 3)
If I close R completely the file access is released. Then I can read the
file using Notepad.exe. The contents is:
Error in log("a") : non-numeric argument to mathematical function
I tried
close(zz)
but the error persists.
To me it looks like R is still accessing the file and not releasing the
connection for other programs. close(zz) should have solved the problem
but unfortantely it doesn't.
What else could I try?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 12:50
Betreff: Re: [R] sink(): Cannot open file
Hi Georg,
I don't suppose that you have:
1) checked that the file "all.Rout" exists somewhere?
2) if so, looked at the file with Notepad, perhaps?
3) let us in on the secret by pasting the contents of "all.Rout" into
your message if it is not too big?
At a guess, trying:
close(zz)
might get you there.
Jim
On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All,
I would like to route the output to a file using sink(). When using the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after it
was
created? Kind regards Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
George,
I do not know what operating system you are working with, but when I use sink() under windows, I need to specify a valid path which I don't see in your code. I might, for example specify:
sink("c:\myfile.txt")
R code goes here
sink()
with the expectation that I would create a file myfile.txt that would contain the output of my R program.
John
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
<G.Maubach at weinwolf.de> 05/10/16 11:10 AM >>>
Hi Jim,
I tried:
sink("all.Rout")
try(log("a"))
sink()
The program executes without warning or error. The file "all.Rout" is
begin created. Nothing will be written to it. The file is accessable
rights after the execution of the program by notepad.exe.
The program
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink()
close(zz)
unlink(zz)
creates the file, does not write anything to it and is not accessable
after program execution in R with notepad.exe.
Any ideas what happens behind the szenes?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 13:16
Betreff: Re: Re: [R] sink(): Cannot open file
Have you tried:
sink("all.Rout")
try(log("a"))
sink()
Jim
On Tue, May 10, 2016 at 9:05 PM, <G.Maubach at weinwolf.de> wrote:
Hi Jim,
thanks for your reply.
ad 1)
"all.Rout" was created in the correct directory. It exists properly with
correct file properties on Windows, e.g. creation date and time and file
size information.
ad 2)
I can not access the file with Notepad.exe directly after it was created
by R. The error message is (translated):
"Cannot access file "all.Rout". The file is opened by another process."
ad 3)
If I close R completely the file access is released. Then I can read the
file using Notepad.exe. The contents is:
Error in log("a") : non-numeric argument to mathematical function
I tried
close(zz)
but the error persists.
To me it looks like R is still accessing the file and not releasing the
connection for other programs. close(zz) should have solved the problem
but unfortantely it doesn't.
What else could I try?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 12:50
Betreff: Re: [R] sink(): Cannot open file
Hi Georg,
I don't suppose that you have:
1) checked that the file "all.Rout" exists somewhere?
2) if so, looked at the file with Notepad, perhaps?
3) let us in on the secret by pasting the contents of "all.Rout" into
your message if it is not too big?
At a guess, trying:
close(zz)
might get you there.
Jim
On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All,
I would like to route the output to a file using sink(). When using the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after it
was
created? Kind regards Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Confidentiality Statement: This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Try closing the type of sink you're actually opening:
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink(type = "message")
close(zz)
unlink(zz)
If you look carefully at the example in?sink, there are two close
statements, one for each stream being sent to that file.
Sarah
On Tue, May 10, 2016 at 11:05 AM, <G.Maubach at weinwolf.de> wrote:
Hi Jim,
I tried:
sink("all.Rout")
try(log("a"))
sink()
The program executes without warning or error. The file "all.Rout" is
begin created. Nothing will be written to it. The file is accessable
rights after the execution of the program by notepad.exe.
The program
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink()
close(zz)
unlink(zz)
creates the file, does not write anything to it and is not accessable
after program execution in R with notepad.exe.
Any ideas what happens behind the szenes?
Kind regards
Georg
Hi Sarah, John, Jim,
Hi All,
I have set my envrionment variable
path <- file.path("H:", "2016", "Analysis")
setwd(dir = path)
This works well cause the file is created in that directory.
I have tried
close(zz)
unlink(zz)
and neither worked nor did it work out using them together.
I had this before when working with IBM SPSS Statistics. There was a
workaround for the problem in SPSS.
Is there one for R?
Kind regards
Georg
Von: Sarah Goslee <sarah.goslee at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 17:17
Betreff: Re: [R] Antwort: Re: Re: sink(): Cannot open file
Try closing the type of sink you're actually opening:
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink(type = "message")
close(zz)
unlink(zz)
If you look carefully at the example in?sink, there are two close
statements, one for each stream being sent to that file.
Sarah
----- Weitergeleitet von Georg Maubach/WWBO/WW/HAW am 10.05.2016 18:29
-----
Von: "John Sorkin" <jsorkin at grecc.umaryland.edu>
An: <drjimlemon at gmail.com>, <G.Maubach at weinwolf.de>,
Kopie: <r-help at r-project.org>
Datum: 10.05.2016 17:20
Betreff: Re: [R] Antwort: Re: Re: sink(): Cannot open file
George,
I do not know what operating system you are working with, but when I use
sink() under windows, I need to specify a valid path which I don't see in
your code. I might, for example specify:
sink("c:\myfile.txt")
R code goes here
sink()
with the expectation that I would create a file myfile.txt that would
contain the output of my R program.
John
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and
Geriatric Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
On Tue, May 10, 2016 at 11:05 AM, <G.Maubach at weinwolf.de> wrote:
Hi Jim,
I tried:
sink("all.Rout")
try(log("a"))
sink()
The program executes without warning or error. The file "all.Rout" is
begin created. Nothing will be written to it. The file is accessable
rights after the execution of the program by notepad.exe.
The program
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink()
close(zz)
unlink(zz)
creates the file, does not write anything to it and is not accessable
after program execution in R with notepad.exe.
Any ideas what happens behind the szenes?
Kind regards
Georg
On 10/05/2016 11:15 AM, John Sorkin wrote:
George,
I do not know what operating system you are working with, but when I use sink() under windows, I need to specify a valid path which I don't see in your code. I might, for example specify:
sink("c:\myfile.txt")
Note that the backslash should be doubled (so it isn't interpreted as an escape for the "m" that follows it), or replaced with a forward slash. Duncan Murdoch
R code goes here sink() with the expectation that I would create a file myfile.txt that would contain the output of my R program. John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing)
<G.Maubach at weinwolf.de> 05/10/16 11:10 AM >>>
Hi Jim,
I tried:
sink("all.Rout")
try(log("a"))
sink()
The program executes without warning or error. The file "all.Rout" is
begin created. Nothing will be written to it. The file is accessable
rights after the execution of the program by notepad.exe.
The program
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink()
close(zz)
unlink(zz)
creates the file, does not write anything to it and is not accessable
after program execution in R with notepad.exe.
Any ideas what happens behind the szenes?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 13:16
Betreff: Re: Re: [R] sink(): Cannot open file
Have you tried:
sink("all.Rout")
try(log("a"))
sink()
Jim
On Tue, May 10, 2016 at 9:05 PM, <G.Maubach at weinwolf.de> wrote:
Hi Jim,
thanks for your reply.
ad 1)
"all.Rout" was created in the correct directory. It exists properly with
correct file properties on Windows, e.g. creation date and time and file
size information.
ad 2)
I can not access the file with Notepad.exe directly after it was created
by R. The error message is (translated):
"Cannot access file "all.Rout". The file is opened by another process."
ad 3)
If I close R completely the file access is released. Then I can read the
file using Notepad.exe. The contents is:
Error in log("a") : non-numeric argument to mathematical function
I tried
close(zz)
but the error persists.
To me it looks like R is still accessing the file and not releasing the
connection for other programs. close(zz) should have solved the problem
but unfortantely it doesn't.
What else could I try?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 12:50
Betreff: Re: [R] sink(): Cannot open file
Hi Georg,
I don't suppose that you have:
1) checked that the file "all.Rout" exists somewhere?
2) if so, looked at the file with Notepad, perhaps?
3) let us in on the secret by pasting the contents of "all.Rout" into
your message if it is not too big?
At a guess, trying:
close(zz)
might get you there.
Jim
On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All,
I would like to route the output to a file using sink(). When using the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after it
was
created? Kind regards Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Confidentiality Statement: This email message, including any attachments, is for ...{{dropped:7}}
Duncan,
thanks for the hint.
I have done it correctly in R fashion
## capture all the output to a file.
zz <- file("C:/Temp/all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
unlink("C:/Temp/all.Rout")
But the error persits.
Kind regards
Georg
Von: Duncan Murdoch <murdoch.duncan at gmail.com>
An: John Sorkin <jsorkin at grecc.umaryland.edu>, drjimlemon at gmail.com,
G.Maubach at weinwolf.de,
Kopie: r-help at r-project.org
Datum: 10.05.2016 19:03
Betreff: Re: [R] Antwort: Re: Re: sink(): Cannot open file
On 10/05/2016 11:15 AM, John Sorkin wrote:
George, I do not know what operating system you are working with, but when I use
sink() under windows, I need to specify a valid path which I don't see in your code. I might, for example specify:
sink("c:\myfile.txt")
Note that the backslash should be doubled (so it isn't interpreted as an escape for the "m" that follows it), or replaced with a forward slash. Duncan Murdoch
R code goes here sink() with the expectation that I would create a file myfile.txt that would
contain the output of my R program.
John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and
Geriatric Medicine
Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing)
<G.Maubach at weinwolf.de> 05/10/16 11:10 AM >>>
Hi Jim,
I tried:
sink("all.Rout")
try(log("a"))
sink()
The program executes without warning or error. The file "all.Rout" is
begin created. Nothing will be written to it. The file is accessable
rights after the execution of the program by notepad.exe.
The program
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink()
close(zz)
unlink(zz)
creates the file, does not write anything to it and is not accessable
after program execution in R with notepad.exe.
Any ideas what happens behind the szenes?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 13:16
Betreff: Re: Re: [R] sink(): Cannot open file
Have you tried:
sink("all.Rout")
try(log("a"))
sink()
Jim
On Tue, May 10, 2016 at 9:05 PM, <G.Maubach at weinwolf.de> wrote:
Hi Jim, thanks for your reply. ad 1) "all.Rout" was created in the correct directory. It exists properly
with
correct file properties on Windows, e.g. creation date and time and
file
size information. ad 2) I can not access the file with Notepad.exe directly after it was
created
by R. The error message is (translated): "Cannot access file "all.Rout". The file is opened by another
process."
ad 3) If I close R completely the file access is released. Then I can read
the
file using Notepad.exe. The contents is:
Error in log("a") : non-numeric argument to mathematical function
I tried
close(zz)
but the error persists.
To me it looks like R is still accessing the file and not releasing
the
connection for other programs. close(zz) should have solved the
problem
but unfortantely it doesn't. What else could I try? Kind regards Georg Von: Jim Lemon <drjimlemon at gmail.com> An: G.Maubach at weinwolf.de, Kopie: r-help mailing list <r-help at r-project.org> Datum: 10.05.2016 12:50 Betreff: Re: [R] sink(): Cannot open file Hi Georg, I don't suppose that you have: 1) checked that the file "all.Rout" exists somewhere? 2) if so, looked at the file with Notepad, perhaps? 3) let us in on the secret by pasting the contents of "all.Rout" into your message if it is not too big? At a guess, trying: close(zz) might get you there. Jim On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All, I would like to route the output to a file using sink(). When using
the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after
it
was
created? Kind regards Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Confidentiality Statement:
This email message, including any attachments, is for ...{{dropped:14}}
Sounds like it would be helpful to find out exactly which process is holding on to the file in order to figure out what's going on. From a quick look, it seems that http://superuser.com/questions/117902/find-out-which-process-is-locking-a-file-or-folder-in-windows gives some useful info on how to track down the process that looks the file. /Henrik
On Wed, May 11, 2016 at 9:47 AM, <G.Maubach at weinwolf.de> wrote:
Duncan,
thanks for the hint.
I have done it correctly in R fashion
## capture all the output to a file.
zz <- file("C:/Temp/all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
unlink("C:/Temp/all.Rout")
But the error persits.
Kind regards
Georg
Von: Duncan Murdoch <murdoch.duncan at gmail.com>
An: John Sorkin <jsorkin at grecc.umaryland.edu>, drjimlemon at gmail.com,
G.Maubach at weinwolf.de,
Kopie: r-help at r-project.org
Datum: 10.05.2016 19:03
Betreff: Re: [R] Antwort: Re: Re: sink(): Cannot open file
On 10/05/2016 11:15 AM, John Sorkin wrote:
George, I do not know what operating system you are working with, but when I use
sink() under windows, I need to specify a valid path which I don't see in your code. I might, for example specify:
sink("c:\myfile.txt")
Note that the backslash should be doubled (so it isn't interpreted as an escape for the "m" that follows it), or replaced with a forward slash. Duncan Murdoch
R code goes here sink() with the expectation that I would create a file myfile.txt that would
contain the output of my R program.
John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and
Geriatric Medicine
Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing)
<G.Maubach at weinwolf.de> 05/10/16 11:10 AM >>>
Hi Jim,
I tried:
sink("all.Rout")
try(log("a"))
sink()
The program executes without warning or error. The file "all.Rout" is
begin created. Nothing will be written to it. The file is accessable
rights after the execution of the program by notepad.exe.
The program
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink()
close(zz)
unlink(zz)
creates the file, does not write anything to it and is not accessable
after program execution in R with notepad.exe.
Any ideas what happens behind the szenes?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 13:16
Betreff: Re: Re: [R] sink(): Cannot open file
Have you tried:
sink("all.Rout")
try(log("a"))
sink()
Jim
On Tue, May 10, 2016 at 9:05 PM, <G.Maubach at weinwolf.de> wrote:
Hi Jim, thanks for your reply. ad 1) "all.Rout" was created in the correct directory. It exists properly
with
correct file properties on Windows, e.g. creation date and time and
file
size information. ad 2) I can not access the file with Notepad.exe directly after it was
created
by R. The error message is (translated): "Cannot access file "all.Rout". The file is opened by another
process."
ad 3) If I close R completely the file access is released. Then I can read
the
file using Notepad.exe. The contents is:
Error in log("a") : non-numeric argument to mathematical function
I tried
close(zz)
but the error persists.
To me it looks like R is still accessing the file and not releasing
the
connection for other programs. close(zz) should have solved the
problem
but unfortantely it doesn't. What else could I try? Kind regards Georg Von: Jim Lemon <drjimlemon at gmail.com> An: G.Maubach at weinwolf.de, Kopie: r-help mailing list <r-help at r-project.org> Datum: 10.05.2016 12:50 Betreff: Re: [R] sink(): Cannot open file Hi Georg, I don't suppose that you have: 1) checked that the file "all.Rout" exists somewhere? 2) if so, looked at the file with Notepad, perhaps? 3) let us in on the secret by pasting the contents of "all.Rout" into your message if it is not too big? At a guess, trying: close(zz) might get you there. Jim On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All, I would like to route the output to a file using sink(). When using
the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after
it
was
created? Kind regards Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Confidentiality Statement: This email message, including any attachments, is for ...{{dropped:14}} ______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hi Henrik, Jim, Sarah, Duncan,
Hi All,
I have tried the built-in solution using PowerShell:
$lockedFile="C:\Windows\System32\wshtcpip.dll"
Get-Process | foreach{$processVar = $_;$_.Modules | foreach{if($_.FileName
-eq $lockedFile){$processVar.Name + " PID:" + $processVar.id}}}
It did not show any processes.
Then I tried the solution using "RessourceMonitor". There I found two
processes:
rstudio.exe
rsession.exe
Right-clicking on rstudio.exe and selecting "Warteschlange analysieren" (=
analyse queue?) showed nothing. Right-clicking on rsession.exe and
selecting "Warteschlage" said:
"Mindestens ein Thread von rsession.exe wartet auf die Fertigstellung von
Netzwerk E/A". (= "At least one thread of "rsession.exe" is waiting for
finishing a network i/o operation").
Putting rsession.exe into the search field of the handles tap of
RessourceMonitor gave no results. No handles were identified.
I can not follow the suggestions where installation of software is
required due to security rules of the company I work for.
I had a look at different R versions on my machine:
1) R i386 3.2.2
2) R i386 3.2.4 (revised)
3) R i386 3.2.5
4) R x54 3.2.2
5) R x64 3.2.4 (revised)
6) R x64 3.2.5
I did
## capture all the output to a file.
zz <- file("C:/Temp/all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
unlink("C:/Temp/all.Rout")
on R i386 3.2.2 and R x64 3.2.2 directly without RStudio. In both cases
the file was locked.
Adding
close(zz)
solved the problem in both versions.
Encouraged by this I tired (successivly refered to as "complete code")
## capture all the output to a file.
zz <- file("C:/Temp/all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
unlink("C:/Temp/all.Rout")
close(zz)
on R i386 3.2.4 (revised) and R x64 3.2.4 (revised) without RStudio. Works
in both cases. The same with R i386 3.2.5 and R x64 3.2.5 each without
RStudio.
It did the same with RStudio altering the R version in the RStudio session
using "complete code". The results are:
R i386 3.2.2: OK
R. x64 3.2.2: OK
R i386 3.2.4 (revised): OK
R x64 3.2.4 (revised): OK
R i386 3.2.5: OK
R x64 3.2.5: OK
This got me lost. I had tried the complete code the last days a hundred
times. It never worked.
Then I restarted my machine powering up RStudio x64 3.2.5 using the
"complete code" and ... it worked.
I have no idea what was wrong the last days.
As far as I can say today the documentation of ?sink in R is currently
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
and should be - in my opinion - supplemented with
close(zz).
Any thoughts?
Kind regards
Georg
Von: Henrik Bengtsson <henrik.bengtsson at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: Duncan Murdoch <murdoch.duncan at gmail.com>, "r-help at r-project.org"
<r-help at r-project.org>
Datum: 11.05.2016 21:48
Betreff: Re: [R] Antwort: Re: Antwort: Re: Re: sink(): Cannot open
file
Sounds like it would be helpful to find out exactly which process is
holding on to the file in order to figure out what's going on. From a
quick look, it seems that
http://superuser.com/questions/117902/find-out-which-process-is-locking-a-file-or-folder-in-windows
gives some useful info on how to track down the process that looks the
file.
/Henrik
On Wed, May 11, 2016 at 9:47 AM, <G.Maubach at weinwolf.de> wrote:
Duncan,
thanks for the hint.
I have done it correctly in R fashion
## capture all the output to a file.
zz <- file("C:/Temp/all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
unlink("C:/Temp/all.Rout")
But the error persits.
Kind regards
Georg
Von: Duncan Murdoch <murdoch.duncan at gmail.com>
An: John Sorkin <jsorkin at grecc.umaryland.edu>, drjimlemon at gmail.com,
G.Maubach at weinwolf.de,
Kopie: r-help at r-project.org
Datum: 10.05.2016 19:03
Betreff: Re: [R] Antwort: Re: Re: sink(): Cannot open file
On 10/05/2016 11:15 AM, John Sorkin wrote:
George, I do not know what operating system you are working with, but when I
use
sink() under windows, I need to specify a valid path which I don't see
in
your code. I might, for example specify:
sink("c:\myfile.txt")
Note that the backslash should be doubled (so it isn't interpreted as an escape for the "m" that follows it), or replaced with a forward slash. Duncan Murdoch
R code goes here sink() with the expectation that I would create a file myfile.txt that would
contain the output of my R program.
John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and
Geriatric Medicine
Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing)
<G.Maubach at weinwolf.de> 05/10/16 11:10 AM >>>
Hi Jim,
I tried:
sink("all.Rout")
try(log("a"))
sink()
The program executes without warning or error. The file "all.Rout" is
begin created. Nothing will be written to it. The file is accessable
rights after the execution of the program by notepad.exe.
The program
zz <- file("all.Rout", open = "wt")
sink(zz, type = "message")
try(log("a"))
sink()
close(zz)
unlink(zz)
creates the file, does not write anything to it and is not accessable
after program execution in R with notepad.exe.
Any ideas what happens behind the szenes?
Kind regards
Georg
Von: Jim Lemon <drjimlemon at gmail.com>
An: G.Maubach at weinwolf.de,
Kopie: r-help mailing list <r-help at r-project.org>
Datum: 10.05.2016 13:16
Betreff: Re: Re: [R] sink(): Cannot open file
Have you tried:
sink("all.Rout")
try(log("a"))
sink()
Jim
On Tue, May 10, 2016 at 9:05 PM, <G.Maubach at weinwolf.de> wrote:
Hi Jim, thanks for your reply. ad 1) "all.Rout" was created in the correct directory. It exists properly
with
correct file properties on Windows, e.g. creation date and time and
file
size information. ad 2) I can not access the file with Notepad.exe directly after it was
created
by R. The error message is (translated): "Cannot access file "all.Rout". The file is opened by another
process."
ad 3) If I close R completely the file access is released. Then I can read
the
file using Notepad.exe. The contents is:
Error in log("a") : non-numeric argument to mathematical function
I tried
close(zz)
but the error persists.
To me it looks like R is still accessing the file and not releasing
the
connection for other programs. close(zz) should have solved the
problem
but unfortantely it doesn't. What else could I try? Kind regards Georg Von: Jim Lemon <drjimlemon at gmail.com> An: G.Maubach at weinwolf.de, Kopie: r-help mailing list <r-help at r-project.org> Datum: 10.05.2016 12:50 Betreff: Re: [R] sink(): Cannot open file Hi Georg, I don't suppose that you have: 1) checked that the file "all.Rout" exists somewhere? 2) if so, looked at the file with Notepad, perhaps? 3) let us in on the secret by pasting the contents of "all.Rout" into your message if it is not too big? At a guess, trying: close(zz) might get you there. Jim On Tue, May 10, 2016 at 5:25 PM, <G.Maubach at weinwolf.de> wrote:
Hi All, I would like to route the output to a file using sink(). When using
the
example from the ?sink documentation:
sink("sink-examp.txt")
i <- 1:10
outer(i, i, "*")
sink()
unlink("sink-examp.txt")
## capture all the output to a file.
zz <- file("all.Rout", open = "wt")
sink(zz)
sink(zz, type = "message")
try(log("a"))
## back to the console
sink(type = "message")
sink()
file.show("all.Rout")
I can not open the file in Windows Explorer. The error message is:
"Cannot open file. File is in use be another proces."
How can I close the file in a manner that I can open it right after
it
was
created? Kind regards Georg
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Confidentiality Statement: This email message, including any attachments, is for ...{{dropped:14}} ______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.