Marcel Baumgartner
2021-Jan-29 08:57 UTC
[R] Error when calling (R 4.0.x on Windows) from Python
Dear Bill, Duncan and Martin, thanks for your investigation. Can you clarify on next steps? Is this now an official bug, or have you found a workaround? For your information: the issue showed up the first time when I called R 4.0.2 from within a software called "IDEA" (from Caseware Analytics), using their scripting language (similar to Visual Basic). With my colleague we then simply reproduce the error calling R from Python, so that we could share it more easily. When we run this command directly on the CMD in Windows, all works fine. The issue only happens when R is called within another software. Best regards Marcel Le 2021-01-27T23:14:36.000+01:00, Bill Dunlap <williamwdunlap at gmail.com> a ?crit :>?I?tried?the?following?change,?that?adds?quotes?if?the?argument?does >? >?not?include?">". >? >?Index:?front-ends/rcmdfn.c >? >?==================================================================>? >?---?front-ends/rcmdfn.c?(revision?79883) >? >?+++?front-ends/rcmdfn.c?(working?copy) >? >?@@?-173,9?+173,13?@@ >? >?????????????????fprintf(stderr,?"command?line?too?long\n"); >? >?????????????????return(27); >? >?????????????} >? >?-???????????strcat(cmd,?"\""); >? >?+???????????if?(!strchr(argv[i],?'>'))?{ >? >?+????????????????strcat(cmd,?"\""); >? >?+????????????} >? >?????????????strcat(cmd,?argv[i]); >? >?-???????????strcat(cmd,?"\""); >? >?+???????????if?(!strchr(argv[i],?'>'))?{ >? >?+???????????????strcat(cmd,?"\""); >? >?+????????????} >? >?????????} >? >?????????/*?the?outermost?double?quotes?are?needed?for?cmd.exe?*/ >? >?????????strcat(cmd,?"\""); >? >?It?lets?the?python?example?work.??I?am?not?sure?that?quoting?all?the >? >?arguments?buys?you?much,?as?shQuote()?is?still?needed?for?arguments >? >?that?include?spaces.??E.g.,??with?3.6.3,?4.0.3,?and?my?development >? >?build?with?the?above?patch?we?get >? >>??stopifnot(dir.create(dirname?<-?file.path(tempfile(),?"A?SPACE"), >>??recursive=TRUE)) >>?? >>???logname?<-?file.path(dirname,?"log.txt") >>?? >>???unlink(logname) >>?? >>???system(paste(?"C:\\R\\R-3.6.3\\bin\\R.exe?--quiet?--vanilla?-e >>??\"commandArgs()\"?1>",?logname)) >? >??ARGUMENT?'SPACE/log.txt'?__ignored__ >? >?[1]?0 >? >>??tryCatch(readLines(logname),?error=function(e)conditionMessage(e)) >? >??[1]?"cannot?open?the?connection" >? >?Warning?message: >? >?In?file(con,?"r")?: >? >??cannot?open?file >? >?'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A >? >?SPACE/log.txt':?No?such?file?or?directory >? >>??system(paste(?"C:\\R\\R-4.0.3\\bin\\R.exe?--quiet?--vanilla?-e >>??\"commandArgs()\"?1>",?logname)) >>?? >>???commandArgs() >? >??[1]?"C:\\R\\R-40~1.3/bin/x64/Rterm.exe" >? >?[2]?"--quiet" >? >?[3]?"--vanilla" >? >?[4]?"-e" >? >?[5]?"commandArgs()" >? >?[6]?"1>" >? >?[7] >?"C:\\Users\\willi\\AppData\\Local\\Temp\\RtmpM5tsC7\\file1a1068734a49/A" >? >?[8]?"SPACE/log.txt" >? >>?? >? >??[1]?0 >? >>??tryCatch(readLines(logname),?error=function(e)conditionMessage(e)) >? >??[1]?"cannot?open?the?connection" >? >?Warning?message: >? >?In?file(con,?"r")?: >? >??cannot?open?file >? >?'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A >? >?SPACE/log.txt':?No?such?file?or?directory >? >>??unlink(logname) >>?? >>???system(paste( >>??"C:\\msys64\\home\\willi\\ucrt3\\r\\trunk\\bin\\R.exe?--quiet >>??--vanilla?-e?\"commandArgs()\"?1>",?logname)) >? >??[1]?0 >? >>??tryCatch(readLines(logname),?error=function(e)conditionMessage(e)) >? >??[1]?"cannot?open?the?connection" >? >?Warning?message: >? >?In?file(con,?"r")?: >? >??cannot?open?file >? >?'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A >? >?SPACE/log.txt':?No?such?file?or?directory >? >>??tryCatch(readLines(sub("?.*$",?"",?logname)), >>??error=function(e)conditionMessage(e)) >? >??[1]?">?commandArgs()" >? >??"[1] >? >?\"C:\\\\msys64\\\\home\\\\willi\\\\ucrt3\\\\r\\\\trunk/bin/x64/Rterm.exe\"" >? >?[3]?"[2]?\"--quiet\" >? >?"?"[3]?\"--vanilla\" >? >??" >? >?[5]?"[4]?\"-e\" >? >?"?"[5]?\"commandArgs()\" >? >??" >? >?[7]?"[6]?\"SPACE/log.txt\" >? >?"?">?" >? >?[9]?">?" >? >>??unlink(logname) >>?? >>???system(paste( >>??"C:\\msys64\\home\\willi\\ucrt3\\r\\trunk\\bin\\R.exe?--quiet >>??--vanilla?-e?\"commandArgs()\"?1>",?shQuote(logname))) >? >??[1]?0 >? >>??tryCatch(readLines(logname),?error=function(e)conditionMessage(e)) >? >??[1]?">?commandArgs()" >? >??"[1] >? >?\"C:\\\\msys64\\\\home\\\\willi\\\\ucrt3\\\\r\\\\trunk/bin/x64/Rterm.exe\"" >? >?[3]?"[2]?\"--quiet\" >? >?"?"[3]?\"--vanilla\" >? >??" >? >?[5]?"[4]?\"-e\" >? >?"?"[5]?\"commandArgs()\" >? >??" >? >?[7]?">?" >? >??">?" >? >?-Bill >? >?On?Wed,?Jan?27,?2021?at?1:25?PM?Duncan?Murdoch >?<murdoch.duncan at gmail.com>?wrote: >? >>??On?27/01/2021?3:40?p.m.,?Bill?Dunlap?wrote: >>?? >>>???I?believe?the?problem?is?from?svn?77925?in >>>???gnuwin/front-ends/rcmdfn.c, >>>??? >>>????which?was?committed?a?few?days?after?3.6.3?was?released.?Rterm >>>???used >>>??? >>>????to?put?double?quotes?around?a?command?line?argument?only?if?it >>>??? >>>????contained?a?space,?now?it?double?quotes?all?arguments.?It?sees >>>???shell >>>??? >>>????constructs?like?"1>"?and?the?following?file?name?as?arguments >>>???and >>>??? >>>????double?quoting?them?hides?them?from?the?shell,?leading?to?this >>>??? >>>????problem.?I?think?we?may?have?to?rely?on?the?user?supplying >>>???quotes?as >>>??? >>>????needed?instead?of?blindly?adding?them. >>?? >>???Okay,?now?I?see?what?you?mean. >>?? >>???If?you?invoke?R?using?R.exe,?it?asks?cmd.exe?to?run?Rterm.exe,?so >>??it?is >>?? >>???possible?that?redirection?would?be?handled. >>?? >>???If?you?invoke?R?directly?using?Rterm.exe,?then?my?description >>??down?below >>?? >>???would?be?correct. >>?? >>???Duncan?Murdoch >>?? >>>???-Bill >>>??? >>>????On?Wed,?Jan?27,?2021?at?12:28?PM?Duncan?Murdoch >>>??? >>>????<murdoch.duncan at gmail.com>?wrote: >>>??? >>>>????On?27/01/2021?3:17?p.m.,?Duncan?Murdoch?wrote: >>>>???? >>>>>?????On?27/01/2021?3:38?a.m.,?Martin?Maechler?wrote: >>>>>????? >>>>>>>>>>>???????????Martin?Maechler >>>>>>>>>>>??????????? >>>>>>>>>>>????????????on?Tue,?26?Jan?2021?12:37:58?+0100?writes: >>>>>>?????? >>>>>>>>>>>???????????Marcel?Baumgartner >>>>>>>>>>>??????????? >>>>>>>>>>>????????????on?Tue,?26?Jan?2021?08:55:48?+0100?writes: >>>>>>?????? >>>>>>???????Dear?all,?my?colleague?posted?our?issue?on?stackoverflow: >>>>>>?????? >>>>>>???????Calling?R?script?from?Python?does?not?save?log?file?in >>>>>>?????? >>>>>>???????version?4?-?Stack?Overflow >>>>>>?????? >>>>>>???????[stackoverflow.com/questions... >>>>>>??????[https://stackoverflow.com/questions/65887485/calling-r-script-from-python-does-not-save-log-file-in-version-4]] >>>>>>?????? >>>>>>???????It?is?about?this?kind?of?call?to?R: >>>>>>?????? >>>>>>???????R.exe?-f?code.R?--args?"~/file.txt"?1>?"~/log.txt"?2>&1". >>>>>>?????? >>>>>>???????The?issue?is?that?the?log.txt?file?is?not?created?when >>>>>>?????? >>>>>>???????running?R?4.x.x.?The?same?code?works?perfectly?fine?with >>>>>>?????? >>>>>>???????R?3.6.x. >>>>>>?????? >>>>>>???????Any?idea?what's?going?wrong?as?of?version?4??Regards >>>>>>?????? >>>>>>???????Marcel >>>>>>?????? >>>>>>???????Dear?Marcel,?I?think?the?solution?is?embarrassingly >>>>>>?????? >>>>>>???????simple: >>>>>>?????? >>>>>>???????From?the?SO?post,?where?she?showed?a?bit?more?detail?than >>>>>>??????you >>>>>>?????? >>>>>>???????show?here,?it's?clear?you?have?confused?'R.exe'?and >>>>>>?????? >>>>>>???????'Rscript.exe'?and?what?you?say?above?is?not?true: >>>>>>?????? >>>>>>???????'R.exe'?was?used?for?R?3.6.0?but?for?R?4.0.3,?you/she >>>>>>??????used >>>>>>?????? >>>>>>???????'Rscript.exe'?instead. >>>>>>?????? >>>>>>???????...?as?you've?noticed?now,?they?do?behave?differently, >>>>>>?????? >>>>>>???????indeed! >>>>>>?????? >>>>>>???????Well,?this?was?not?the?solution?to?their?--?Windows-only >>>>>>??????--?problem. >>>>>>?????? >>>>>>???????The?problem?*is*?indeed?visible?if?they?only?use?R.exe >>>>>>??????(also >>>>>>?????? >>>>>>???????for?R?4.0.3). >>>>>>?????? >>>>>>???????I've?commented?more?on?the?SO?issue?(see?above), >>>>>>?????? >>>>>>???????notably?asking?for?a?*minimal*?repr.ex.?(reproducible >>>>>>??????example), >>>>>>?????? >>>>>>???????and?one?*not*?using?"<YOUR?PATH>"?and?setwd()?.. >>>>>????? >>>>>??????Isn't?this?purely?a?Python?or?user?problem??R?shouldn't >>>>>?????process >>>>>????? >>>>>??????redirection?directives?like >>>>>????? >>>>>??????1>?"~/log.txt"?2>&1 >>>>>????? >>>>>??????because?it's?the?shell's?job?to?process?those.?If?Python?is >>>>>?????acting?as >>>>>????? >>>>>??????the?shell,?it?needs?to?handle?those?things.?If?R?was >>>>>?????handling?the >>>>>????? >>>>>??????command?via >>>>???? >>>>?????Oops,?sent?before?finishing: >>>>???? >>>>?????If?R?was?handling?the?command?via?system()?or?system2(),?it >>>>????would?handle >>>>???? >>>>?????redirection?itself.?If?it?was?using?the?Windows-only?shell(), >>>>????it?would >>>>???? >>>>?????call?cmd.exe?(by?default)?to?handle?redirection.?(This?is?a >>>>????difference >>>>???? >>>>?????between?R?on?Windows?and?R?in?Unix:?in?Unix?a?shell?is?always >>>>????used.) >>>>???? >>>>?????Duncan?Murdoch >>>>???? >>>>?????______________________________________________ >>>>???? >>>>?????R-help at r-project.org?mailing?list?--?To?UNSUBSCRIBE?and?more, >>>>????see >>>>???? >>>>?????stat.ethz.ch/mailman/listin... >>>>????[https://stat.ethz.ch/mailman/listinfo/r-help] >>>>???? >>>>?????PLEASE?do?read?the?posting?guide >>>>????www.R-project.org/posting-g... >>>>????[http://www.R-project.org/posting-guide.html] >>>>???? >>>>?????and?provide?commented,?minimal,?self-contained,?reproducible >>>>????code.[[alternative HTML version deleted]]
Duncan Murdoch
2021-Jan-29 10:19 UTC
[R] Error when calling (R 4.0.x on Windows) from Python
On 29/01/2021 3:57 a.m., Marcel Baumgartner wrote:> Dear Bill, Duncan and Martin, > > thanks for your investigation. Can you clarify on next steps? Is this > now an official bug, or have you found a workaround? For your > information: the issue showed up the first time when I called R 4.0.2 > from within a software called "IDEA" (from Caseware Analytics), using > their scripting language (similar to Visual Basic). With my colleague we > then simply reproduce the error calling R from Python, so that we could > share it more easily. When we run this command directly on the CMD in > Windows, all works fine. The issue only happens when R is called within > another software. >I would say this is a bug, with two workarounds. These are only needed (and will only work) on Windows. 1. If you want to include redirection in the command line, then call cmd.exe yourself, and have it call Rterm.exe. I think your original command R.exe -f code.R --args "~/file.txt" 1> "~/log.txt" 2>&1" could be written as cmd.exe 1>log.txt 2>&1 /C R.exe -f code.R --args "~/file.txt" (but I haven't tested it). You could also use the slightly more efficient cmd.exe 1>log.txt 2>&1 /C Rterm.exe -f code.R --args "~/file.txt" if Rterm.exe is on your path; by default I don't think it will be. 2. Change the Python code to a different function call than subprocess.call. It should be one that's equivalent to the C system() function; I believe os.system() is what you want, so you'd use os.system("R.exe -f code.R --args "~/file.txt" 1> "~/log.txt" 2>&1") and the redirection would be handled by the implicit shell that is called by os.system. Again, replacing R.exe by Rterm.exe would be a tiny bit more efficient, but it might not be on the path. Duncan Murdoch> Best regards > > Marcel > > > Le 2021-01-27T23:14:36.000+01:00, Bill Dunlap <williamwdunlap at gmail.com> > a ?crit : > > I tried the following change, that adds quotes if the argument does > not include ">". > Index: front-ends/rcmdfn.c > ==================================================================> --- front-ends/rcmdfn.c (revision 79883) > +++ front-ends/rcmdfn.c (working copy) > @@ -173,9 +173,13 @@ > fprintf(stderr, "command line too long\n"); > return(27); > } > - strcat(cmd, "\""); > + if (!strchr(argv[i], '>')) { > + strcat(cmd, "\""); > + } > strcat(cmd, argv[i]); > - strcat(cmd, "\""); > + if (!strchr(argv[i], '>')) { > + strcat(cmd, "\""); > + } > } > /* the outermost double quotes are needed for cmd.exe */ > strcat(cmd, "\""); > > It lets the python example work. I am not sure that quoting all the > arguments buys you much, as shQuote() is still needed for arguments > that include spaces. E.g., with 3.6.3, 4.0.3, and my development > build with the above patch we get > > stopifnot(dir.create(dirname <- file.path(tempfile(), "A > SPACE"), recursive=TRUE)) > logname <- file.path(dirname, "log.txt") > unlink(logname) > system(paste( "C:\\R\\R-3.6.3\\bin\\R.exe --quiet --vanilla -e > \"commandArgs()\" 1>", logname)) > > ARGUMENT 'SPACE/log.txt' __ignored__ > > [1] 0 > > tryCatch(readLines(logname), error=function(e)conditionMessage(e)) > > [1] "cannot open the connection" > Warning message: > In file(con, "r") : > cannot open file > 'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A > SPACE/log.txt': No such file or directory > > > system(paste( "C:\\R\\R-4.0.3\\bin\\R.exe --quiet --vanilla -e > \"commandArgs()\" 1>", logname)) > commandArgs() > > [1] "C:\\R\\R-40~1.3/bin/x64/Rterm.exe" > [2] "--quiet" > [3] "--vanilla" > [4] "-e" > [5] "commandArgs()" > [6] "1>" > [7] > "C:\\Users\\willi\\AppData\\Local\\Temp\\RtmpM5tsC7\\file1a1068734a49/A" > [8] "SPACE/log.txt" > > > [1] 0 > > tryCatch(readLines(logname), error=function(e)conditionMessage(e)) > > [1] "cannot open the connection" > Warning message: > In file(con, "r") : > cannot open file > 'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A > SPACE/log.txt': No such file or directory > > > unlink(logname) > system(paste( > "C:\\msys64\\home\\willi\\ucrt3\\r\\trunk\\bin\\R.exe --quiet > --vanilla -e \"commandArgs()\" 1>", logname)) > > [1] 0 > > tryCatch(readLines(logname), error=function(e)conditionMessage(e)) > > [1] "cannot open the connection" > Warning message: > In file(con, "r") : > cannot open file > 'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A > SPACE/log.txt': No such file or directory > > tryCatch(readLines(sub(" .*$", "", logname)), > error=function(e)conditionMessage(e)) > > [1] "> commandArgs()" > "[1] > \"C:\\\\msys64\\\\home\\\\willi\\\\ucrt3\\\\r\\\\trunk/bin/x64/Rterm.exe\"" > [3] "[2] \"--quiet\" > " "[3] \"--vanilla\" > " > [5] "[4] \"-e\" > " "[5] \"commandArgs()\" > " > [7] "[6] \"SPACE/log.txt\" > " "> " > [9] "> " > > > unlink(logname) > system(paste( > "C:\\msys64\\home\\willi\\ucrt3\\r\\trunk\\bin\\R.exe --quiet > --vanilla -e \"commandArgs()\" 1>", shQuote(logname))) > > [1] 0 > > tryCatch(readLines(logname), error=function(e)conditionMessage(e)) > > [1] "> commandArgs()" > "[1] > \"C:\\\\msys64\\\\home\\\\willi\\\\ucrt3\\\\r\\\\trunk/bin/x64/Rterm.exe\"" > [3] "[2] \"--quiet\" > " "[3] \"--vanilla\" > " > [5] "[4] \"-e\" > " "[5] \"commandArgs()\" > " > [7] "> " > "> " > > -Bill > > On Wed, Jan 27, 2021 at 1:25 PM Duncan Murdoch > <murdoch.duncan at gmail.com <mailto:murdoch.duncan at gmail.com>> wrote: > > > On 27/01/2021 3:40 p.m., Bill Dunlap wrote: > > I believe the problem is from svn 77925 in > gnuwin/front-ends/rcmdfn.c, > which was committed a few days after 3.6.3 was released. > Rterm used > to put double quotes around a command line argument only if it > contained a space, now it double quotes all arguments. It > sees shell > constructs like "1>" and the following file name as > arguments and > double quoting them hides them from the shell, leading to this > problem. I think we may have to rely on the user supplying > quotes as > needed instead of blindly adding them. > > > Okay, now I see what you mean. > > If you invoke R using R.exe, it asks cmd.exe to run Rterm.exe, > so it is > possible that redirection would be handled. > > If you invoke R directly using Rterm.exe, then my description > down below > would be correct. > > Duncan Murdoch > > > > -Bill > > On Wed, Jan 27, 2021 at 12:28 PM Duncan Murdoch > <murdoch.duncan at gmail.com <mailto:murdoch.duncan at gmail.com>> > wrote: > > > On 27/01/2021 3:17 p.m., Duncan Murdoch wrote: > > On 27/01/2021 3:38 a.m., Martin Maechler wrote: > > Martin Maechler > on Tue, 26 Jan 2021 12:37:58 > +0100 writes: > > > Marcel Baumgartner > on Tue, 26 Jan 2021 08:55:48 > +0100 writes: > > > Dear all, my colleague posted our issue on > stackoverflow: > > Calling R script from Python does not save log > file in > version 4 - Stack Overflow > [stackoverflow.com/questions... > <https://stackoverflow.com/questions/65887485/calling-r-script-from-python-does-not-save-log-file-in-version-4>] > > It is about this kind of call to R: > > R.exe -f code.R --args "~/file.txt" 1> > "~/log.txt" 2>&1". > > The issue is that the log.txt file is not > created when > running R 4.x.x. The same code works perfectly > fine with > R 3.6.x. > > Any idea what's going wrong as of version 4? Regards > Marcel > > Dear Marcel, I think the solution is embarrassingly > simple: > > From the SO post, where she showed a bit more > detail than you > show here, it's clear you have confused 'R.exe' and > 'Rscript.exe' and what you say above is not true: > > 'R.exe' was used for R 3.6.0 but for R 4.0.3, > you/she used > 'Rscript.exe' instead. > > > ... as you've noticed now, they do behave > differently, > indeed! > > Well, this was not the solution to their -- > Windows-only -- problem. > The problem *is* indeed visible if they only use > R.exe (also > for R 4.0.3). > > I've commented more on the SO issue (see above), > notably asking for a *minimal* repr.ex. > (reproducible example), > and one *not* using "<YOUR PATH>" and setwd() .. > > > Isn't this purely a Python or user problem? R > shouldn't process > redirection directives like > > 1> "~/log.txt" 2>&1 > > because it's the shell's job to process those. If > Python is acting as > the shell, it needs to handle those things. If R was > handling the > command via > > > Oops, sent before finishing: > > If R was handling the command via system() or system2(), > it would handle > redirection itself. If it was using the Windows-only > shell(), it would > call cmd.exe (by default) to handle redirection. (This > is a difference > between R on Windows and R in Unix: in Unix a shell is > always used.) > > Duncan Murdoch > > ______________________________________________ > R-help at r-project.org <mailto:R-help at r-project.org> > mailing list -- To UNSUBSCRIBE and more, see > stat.ethz.ch/mailman/listin... > <https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide > www.R-project.org/posting-g... > <http://www.R-project.org/posting-guide.html> > and provide commented, minimal, self-contained, > reproducible code. > > >
Tomas Kalibera
2021-Feb-02 13:49 UTC
[R] Error when calling (R 4.0.x on Windows) from Python
A reproducible example:
system("\"C:\\Program Files\\R\\R-4.0.3\\bin\\R.exe\" -e
commandArgs()
>out")? # does not create "out"
system("\"C:\\Program Files\\R\\R-3.6.3\\bin\\R.exe\" -e
commandArgs()
>out")? # creates "out"
Note that this does not create "out", either:
system("\"C:\\Program Files\\R\\R-3.6.3\\bin\\x64\\Rterm.exe\" -e
commandArgs() >out")
I think redirections should be left to the shell, so e.g. those calls
from Python should use "os.system" if they needed redirection, as
Duncan
suggested.
I see that both R.exe and Rterm.exe give "Usage: Rterm [options] [<
infile] [> outfile] [EnvVars]", which may be confusing to programmers
invoking R without a shell, but then talking there about invocation via
shell could confuse typical users, instead.
My best guess is that the redirection in R.exe in 3.6 worked rather by
accident, as a consequence of that R.exe internally invoked (and still
invokes) Rterm.exe via the shell, but R.exe did not protect all
arguments from expansions from that internal shell invocation. If
redirection was meant to work without external shell, it would have
instead been implemented explicitly also in Rterm.exe.
My change 77926 made sure that all arguments to that internal shell
invocation were protected, following bug reports such as PR#17709, where
users had "&" in their file names. Therefore, this works,
executing file
code&.r
system("\"C:\\Program Files\\R\\R-4.0.3\\bin\\R.exe\" -f
code&.r")
but not with 3.6.3, and I would not be surprised if even more special
characters became popular, soon.
After all, what if someone wanted to pass an argument to R including
">", that should work, too:
---- t.r ----
cat("Header: ", commandArgs(TRUE)[1], "\n")
-------------
system("\"C:\\Program Files\\R\\R-4.0.3\\bin\\R.exe\" -f t.r
--args
<html>") # prints Header:? <html>
system("\"C:\\Program Files\\R\\R-3.6.3\\bin\\R.exe\" -f t.r
--args
<html>") # fails with? The syntax of the command is incorrect.
So in summary, I don't agree this is a bug.
Best
Tomas
On 1/29/21 11:19 AM, Duncan Murdoch wrote:> On 29/01/2021 3:57 a.m., Marcel Baumgartner wrote:
>> Dear Bill, Duncan and Martin,
>>
>> thanks for your investigation. Can you clarify on next steps? Is this
>> now an official bug, or have you found a workaround? For your
>> information: the issue showed up the first time when I called R 4.0.2
>> from within a software called "IDEA" (from Caseware
Analytics), using
>> their scripting language (similar to Visual Basic). With my colleague
>> we then simply reproduce the error calling R from Python, so that we
>> could share it more easily. When we run this command directly on the
>> CMD in Windows, all works fine. The issue only happens when R is
>> called within another software.
>>
>
> I would say this is a bug, with two workarounds.? These are only
> needed (and will only work) on Windows.
>
> 1.? If you want to include redirection in the command line, then call
> cmd.exe yourself, and have it call Rterm.exe.? I think your original
> command
>
> R.exe -f code.R --args "~/file.txt" 1> "~/log.txt"
2>&1"
>
> could be written as
>
> cmd.exe 1>log.txt 2>&1 /C R.exe -f code.R --args
"~/file.txt"
>
> (but I haven't tested it).? You could also use the slightly more
> efficient
>
> cmd.exe 1>log.txt 2>&1 /C Rterm.exe -f code.R --args
"~/file.txt"
>
> if Rterm.exe is on your path; by default I don't think it will be.
>
> 2.? Change the Python code to a different function call than
> subprocess.call.? It should be one that's equivalent to the C system()
> function; I believe os.system() is what you want, so you'd use
>
> os.system("R.exe -f code.R --args "~/file.txt" 1>
"~/log.txt" 2>&1")
>
> and the redirection would be handled by the implicit shell that is
> called by os.system.? Again, replacing R.exe by Rterm.exe would be a
> tiny bit more efficient, but it might not be on the path.
>
> Duncan Murdoch
>
>> Best regards
>>
>> Marcel
>>
>>
>> Le 2021-01-27T23:14:36.000+01:00, Bill Dunlap
>> <williamwdunlap at gmail.com> a ?crit :
>>
>> ??? I tried the following change, that adds quotes if the argument does
>> ??? not include ">".
>> ??? Index: front-ends/rcmdfn.c
>>
==================================================================>> ???
--- front-ends/rcmdfn.c (revision 79883)
>> ??? +++ front-ends/rcmdfn.c (working copy)
>> ??? @@ -173,9 +173,13 @@
>> ??? fprintf(stderr, "command line too long\n");
>> ??? return(27);
>> ??? }
>> ??? - strcat(cmd, "\"");
>> ??? + if (!strchr(argv[i], '>')) {
>> ??? + strcat(cmd, "\"");
>> ??? + }
>> ??? strcat(cmd, argv[i]);
>> ??? - strcat(cmd, "\"");
>> ??? + if (!strchr(argv[i], '>')) {
>> ??? + strcat(cmd, "\"");
>> ??? + }
>> ??? }
>> ??? /* the outermost double quotes are needed for cmd.exe */
>> ??? strcat(cmd, "\"");
>>
>> ??? It lets the python example work. I am not sure that quoting all the
>> ??? arguments buys you much, as shQuote() is still needed for arguments
>> ??? that include spaces. E.g., with 3.6.3, 4.0.3, and my development
>> ??? build with the above patch we get
>>
>> ??????? stopifnot(dir.create(dirname <- file.path(tempfile(),
"A
>> ??????? SPACE"), recursive=TRUE))
>> ??????? logname <- file.path(dirname, "log.txt")
>> ??????? unlink(logname)
>> ??????? system(paste( "C:\\R\\R-3.6.3\\bin\\R.exe --quiet
--vanilla -e
>> ??????? \"commandArgs()\" 1>", logname))
>>
>> ??? ARGUMENT 'SPACE/log.txt' __ignored__
>>
>> ??? [1] 0
>>
>> ??????? tryCatch(readLines(logname),
>> error=function(e)conditionMessage(e))
>>
>> ??? [1] "cannot open the connection"
>> ??? Warning message:
>> ??? In file(con, "r") :
>> ??? cannot open file
>> 'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A
>> ??? SPACE/log.txt': No such file or directory
>>
>>
>> ??????? system(paste( "C:\\R\\R-4.0.3\\bin\\R.exe --quiet
--vanilla -e
>> ??????? \"commandArgs()\" 1>", logname))
>> ??????? commandArgs()
>>
>> ??? [1] "C:\\R\\R-40~1.3/bin/x64/Rterm.exe"
>> ??? [2] "--quiet"
>> ??? [3] "--vanilla"
>> ??? [4] "-e"
>> ??? [5] "commandArgs()"
>> ??? [6] "1>"
>> ??? [7]
>>
"C:\\Users\\willi\\AppData\\Local\\Temp\\RtmpM5tsC7\\file1a1068734a49/A"
>> ??? [8] "SPACE/log.txt"
>>
>>
>> ??? [1] 0
>>
>> ??????? tryCatch(readLines(logname),
>> error=function(e)conditionMessage(e))
>>
>> ??? [1] "cannot open the connection"
>> ??? Warning message:
>> ??? In file(con, "r") :
>> ??? cannot open file
>> 'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A
>> ??? SPACE/log.txt': No such file or directory
>>
>>
>> ??????? unlink(logname)
>> ??????? system(paste(
>> ??????? "C:\\msys64\\home\\willi\\ucrt3\\r\\trunk\\bin\\R.exe
--quiet
>> ??????? --vanilla -e \"commandArgs()\" 1>", logname))
>>
>> ??? [1] 0
>>
>> ??????? tryCatch(readLines(logname),
>> error=function(e)conditionMessage(e))
>>
>> ??? [1] "cannot open the connection"
>> ??? Warning message:
>> ??? In file(con, "r") :
>> ??? cannot open file
>> 'C:\Users\willi\AppData\Local\Temp\RtmpM5tsC7\file1a1068734a49/A
>> ??? SPACE/log.txt': No such file or directory
>>
>> ??????? tryCatch(readLines(sub(" .*$", "",
logname)),
>> ??????? error=function(e)conditionMessage(e))
>>
>> ??? [1] "> commandArgs()"
>> ??? "[1]
>>
\"C:\\\\msys64\\\\home\\\\willi\\\\ucrt3\\\\r\\\\trunk/bin/x64/Rterm.exe\""
>> ??? [3] "[2] \"--quiet\"
>> ??? " "[3] \"--vanilla\"
>> ??? "
>> ??? [5] "[4] \"-e\"
>> ??? " "[5] \"commandArgs()\"
>> ??? "
>> ??? [7] "[6] \"SPACE/log.txt\"
>> ??? " "> "
>> ??? [9] "> "
>>
>>
>> ??????? unlink(logname)
>> ??????? system(paste(
>> ??????? "C:\\msys64\\home\\willi\\ucrt3\\r\\trunk\\bin\\R.exe
--quiet
>> ??????? --vanilla -e \"commandArgs()\" 1>",
shQuote(logname)))
>>
>> ??? [1] 0
>>
>> ??????? tryCatch(readLines(logname),
>> error=function(e)conditionMessage(e))
>>
>> ??? [1] "> commandArgs()"
>> ??? "[1]
>>
\"C:\\\\msys64\\\\home\\\\willi\\\\ucrt3\\\\r\\\\trunk/bin/x64/Rterm.exe\""
>> ??? [3] "[2] \"--quiet\"
>> ??? " "[3] \"--vanilla\"
>> ??? "
>> ??? [5] "[4] \"-e\"
>> ??? " "[5] \"commandArgs()\"
>> ??? "
>> ??? [7] "> "
>> ??? "> "
>>
>> ??? -Bill
>>
>> ??? On Wed, Jan 27, 2021 at 1:25 PM Duncan Murdoch
>> ??? <murdoch.duncan at gmail.com <mailto:murdoch.duncan at
gmail.com>> wrote:
>>
>>
>> ??????? On 27/01/2021 3:40 p.m., Bill Dunlap wrote:
>>
>> ??????????? I believe the problem is from svn 77925 in
>> ??????????? gnuwin/front-ends/rcmdfn.c,
>> ??????????? which was committed a few days after 3.6.3 was released.
>> ??????????? Rterm used
>> ??????????? to put double quotes around a command line argument only
>> if it
>> ??????????? contained a space, now it double quotes all arguments. It
>> ??????????? sees shell
>> ??????????? constructs like "1>" and the following file
name as
>> ??????????? arguments and
>> ??????????? double quoting them hides them from the shell, leading to
>> this
>> ??????????? problem. I think we may have to rely on the user supplying
>> ??????????? quotes as
>> ??????????? needed instead of blindly adding them.
>>
>>
>> ??????? Okay, now I see what you mean.
>>
>> ??????? If you invoke R using R.exe, it asks cmd.exe to run Rterm.exe,
>> ??????? so it is
>> ??????? possible that redirection would be handled.
>>
>> ??????? If you invoke R directly using Rterm.exe, then my description
>> ??????? down below
>> ??????? would be correct.
>>
>> ??????? Duncan Murdoch
>>
>>
>>
>> ??????????? -Bill
>>
>> ??????????? On Wed, Jan 27, 2021 at 12:28 PM Duncan Murdoch
>> ??????????? <murdoch.duncan at gmail.com <mailto:murdoch.duncan
at gmail.com>>
>> ??????????? wrote:
>>
>>
>> ??????????????? On 27/01/2021 3:17 p.m., Duncan Murdoch wrote:
>>
>> ??????????????????? On 27/01/2021 3:38 a.m., Martin Maechler wrote:
>>
>> ??????????????????????????????????????????? Martin Maechler
>> ??????????????????????????????????????????? on Tue, 26 Jan 2021
12:37:58
>> ??????????????????????????????????????????? +0100 writes:
>>
>>
>> ??????????????????????????????????????????? Marcel Baumgartner
>> ??????????????????????????????????????????? on Tue, 26 Jan 2021
08:55:48
>> ??????????????????????????????????????????? +0100 writes:
>>
>>
>> ??????????????????????? Dear all, my colleague posted our issue on
>> ??????????????????????? stackoverflow:
>>
>> ??????????????????????? Calling R script from Python does not save log
>> ??????????????????????? file in
>> ??????????????????????? version 4 - Stack Overflow
>> ??????????????????????? [stackoverflow.com/questions...
>>
<https://stackoverflow.com/questions/65887485/calling-r-script-from-python-does-not-save-log-file-in-version-4>]
>>
>> ??????????????????????? It is about this kind of call to R:
>>
>> ??????????????????????? R.exe -f code.R --args "~/file.txt"
1>
>> ??????????????????????? "~/log.txt" 2>&1".
>>
>> ??????????????????????? The issue is that the log.txt file is not
>> ??????????????????????? created when
>> ??????????????????????? running R 4.x.x. The same code works perfectly
>> ??????????????????????? fine with
>> ??????????????????????? R 3.6.x.
>>
>> ??????????????????????? Any idea what's going wrong as of version
4?
>> Regards
>> ??????????????????????? Marcel
>>
>> ??????????????????????? Dear Marcel, I think the solution is
>> embarrassingly
>> ??????????????????????? simple:
>>
>> ???????????????????????? From the SO post, where she showed a bit more
>> ??????????????????????? detail than you
>> ??????????????????????? show here, it's clear you have confused
>> 'R.exe' and
>> ??????????????????????? 'Rscript.exe' and what you say above is
not
>> true:
>>
>> ??????????????????????? 'R.exe' was used for R 3.6.0 but for R
4.0.3,
>> ??????????????????????? you/she used
>> ??????????????????????? 'Rscript.exe' instead.
>>
>>
>> ??????????????????????? ... as you've noticed now, they do behave
>> ??????????????????????? differently,
>> ??????????????????????? indeed!
>>
>> ??????????????????????? Well, this was not the solution to their --
>> ??????????????????????? Windows-only -- problem.
>> ??????????????????????? The problem *is* indeed visible if they only
use
>> ??????????????????????? R.exe (also
>> ??????????????????????? for R 4.0.3).
>>
>> ??????????????????????? I've commented more on the SO issue (see
above),
>> ??????????????????????? notably asking for a *minimal* repr.ex.
>> ??????????????????????? (reproducible example),
>> ??????????????????????? and one *not* using "<YOUR
PATH>" and setwd() ..
>>
>>
>> ??????????????????? Isn't this purely a Python or user problem? R
>> ??????????????????? shouldn't process
>> ??????????????????? redirection directives like
>>
>> ??????????????????? 1> "~/log.txt" 2>&1
>>
>> ??????????????????? because it's the shell's job to process
those. If
>> ??????????????????? Python is acting as
>> ??????????????????? the shell, it needs to handle those things. If R
was
>> ??????????????????? handling the
>> ??????????????????? command via
>>
>>
>> ??????????????? Oops, sent before finishing:
>>
>> ??????????????? If R was handling the command via system() or
system2(),
>> ??????????????? it would handle
>> ??????????????? redirection itself. If it was using the Windows-only
>> ??????????????? shell(), it would
>> ??????????????? call cmd.exe (by default) to handle redirection. (This
>> ??????????????? is a difference
>> ??????????????? between R on Windows and R in Unix: in Unix a shell is
>> ??????????????? always used.)
>>
>> ??????????????? Duncan Murdoch
>>
>> ??????????????? ______________________________________________
>> ??????????????? R-help at r-project.org <mailto:R-help at
r-project.org>
>> ??????????????? mailing list -- To UNSUBSCRIBE and more, see
>> ??????????????? stat.ethz.ch/mailman/listin...
>> <https://stat.ethz.ch/mailman/listinfo/r-help>
>> ??????????????? PLEASE do read the posting guide
>> ??????????????? www.R-project.org/posting-g...
>> <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
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> and provide commented, minimal, self-contained, reproducible code.