Message-ID: <25b589b25af628379c5a9ac502580552@mail.infomaniak.com>
Date: 2021-01-29T08:57:07Z
From: Marcel Baumgartner
Subject: Error when calling (R 4.0.x on Windows) from Python
In-Reply-To: <CAHqSRuSOYk=aWzKg9Ub4LN+hXTZ8ptZDw7gzrxt67957kNDwXQ@mail.gmail.com>
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.
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