Re: [Rd] last user argument missing from Rscript --verbose
Terrific, and I appreciate your thoughts and encouragement. So, getting back on-list, I propose a backward-incompatible change, with or without --verbose, that the --args be included in the 'av' array, and passed to R, only if there are user arguments to follow it. The condition for a first argument, at the time --args is currently included, is (i0+1) < argc Scott's fix, already in the devel version, solves my original complaint and should continue to do so, as long as av[ac] continues to be the terminating NULL. That is, av[ac-1] is the last argument in the R command. On Sep 20, 2014, at 4:39 PM, Martin Maechler wrote: > > On Fri, Sep 19, 2014 at 5:26 PM, Harris A. Jaffee wrote: > I must have searched the archives badly! > > I did not suggest that, exactly. My hack was a little more complicated, > trying to honor what seemed to be the general intent of the code. So, I > only conditionally echo the argument at i=ac-1 (see attached). > > Thank you, I understand but think it's unnecessarily complicated. > Rather I think that the following issue should ideally be handled: > > There is also a more basic issue to decide, whether the "--args" should be > sent to > R when nothing follows it, but that debate should occur on-list, if at all. > > and if that is fixed (not sending '--args' if at the end), the simple fix > for verbose printing will be enough. > > Yes, please go back on saying this on R-devel ... You did take it offline > (and some say that it is not allowed to put something private suddenly back > online, so I did not ... but do not care if you do it here). > > > Martin > > > > > On Sep 19, 2014, at 9:14 AM, Scott Kostyshak wrote: > > > On Fri, Sep 19, 2014 at 8:12 AM, Martin Maechler > > > wrote: > >>> Harris A Jaffee > >>>on Thu, 18 Sep 2014 19:32:29 +0200 writes: > >> > >> (using HTML, please don't ) > >> > >>> The loop that echoes the arguments almost always stops too soon. It > >>> apparently does that to avoid > >>> echoing the "--args" (that had been inserted) when there are no user > >>> arguments. However, when there > >>> are user arguments, the next element of the 'av' array is the last > >>> argument and usually not "--args", > >>> although it can be. > >>> ?Rscript is a little sketchy: > >>> `--verbose' gives details of what `Rscript' is doing. Also passed > >>> on to R. > >>> What is passed to R is correct, but the diagnostic is not: > >>> $ Rscript --verbose /dev/null 1 2 > >>> running > >>> '/path_to_R --slave --no-restore --file=/dev/null --args 1' > >>> Fixed (only tested on Mac): > >>> $ Rscript --verbose /dev/null 1 2 > >>> running > >>> '/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R --slave > >>> --no-restore --file=/dev/null --args 1 2' > >> > >> You are right about the problem, also reproducible on Linux. > >> You mention a 'fix'. > >> It looks to me that is just > >> > >> - for(i = 1; i < ac-1; i++) fprintf(stderr, " %s", av[i]); > >> + for(i = 1; i < ac; i++) fprintf(stderr, " %s", av[i]); > >> > >> in unix/Rscript.c, right ? > > > > Yes, I suggested the same patch here: > > http://r.789695.n4.nabble.com/patch-Rscript-off-by-one-error-in-output-td4693780.html > > > > Scott > > > >> BTW: If one use -e 'commandArgs()' instead of /dev/null one > >> sees that Rscript's "lying" about the last argument is not > >> helpful anyway : > >> > >> Rscript --verbose -e 'commandArgs()' > >> > >> running > >>'/usr/local64.sfs/app/R/R-3.1.1-inst/bin/R --slave --no-restore -e > >> commandArgs()' > >> > >> [1] "/usr/local64.sfs/app/R/R-3.1.1-inst/bin/exec/R" > >> [2] "--slave" > >> [3] "--no-restore" > >> [4] "-e" > >> [5] "commandArgs()" > >> [6] "--args" > >> > >> because the '--args' appears anyway and indeed *is* passed to 'R'... > >> > >> A better fix would rather suppress that; but I will commit the > >> above change. > > > > > > -- > > Scott Kostyshak > > Economics PhD Candidate > > Princeton University > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Bug in new behaviour for all.equal and environments?
Hi R-devel, The following code: all.equal(baseenv(), baseenv()) gives the error when run in a clean R session with latest R-devel (r66650): kevin:~$ R --vanilla --slave -e "all.equal(baseenv(), baseenv())" Error in all.equal.envRefClass(target[[i]], current[[i]], check.attributes = check.attributes, : attempt to apply non-function Calls: all.equal ... all.equal.list -> all.equal -> all.equal.envRefClass Execution halted Although I don't know if it's helpful -- it appears that packages that include some S4 machinery will effect the outcome of this error, e.g. if we load 'Biobase' first: kevin:~$ R --vanilla --slave -e "suppressPackageStartupMessages(library(Biobase)); all.equal(baseenv(), baseenv())" Error in target$getClass() : object '.refClassDef' not found Calls: all.equal ... all.equal.list -> all.equal -> all.equal.envRefClass -> Execution halted We were bumping into an error with this in Rcpp -- we used all.equal (through RUnit) to confirm that baseenv(), and a function returning the base environment, would return TRUE. For completeness: kevin:~$ R --vanilla --slave -e "sessionInfo()" R Under development (unstable) (2014-09-20 r66650) Platform: x86_64-apple-darwin13.3.0 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks, Kevin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Bug in new behaviour for all.equal and environments?
Hello, In R 3.1.1 on Windows 7 it's ok. > all.equal(baseenv(), baseenv()) [1] TRUE > sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252 [3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C [5] LC_TIME=Portuguese_Portugal.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Rui Barradas Em 21-09-2014 18:06, Kevin Ushey escreveu: Hi R-devel, The following code: all.equal(baseenv(), baseenv()) gives the error when run in a clean R session with latest R-devel (r66650): kevin:~$ R --vanilla --slave -e "all.equal(baseenv(), baseenv())" Error in all.equal.envRefClass(target[[i]], current[[i]], check.attributes = check.attributes, : attempt to apply non-function Calls: all.equal ... all.equal.list -> all.equal -> all.equal.envRefClass Execution halted Although I don't know if it's helpful -- it appears that packages that include some S4 machinery will effect the outcome of this error, e.g. if we load 'Biobase' first: kevin:~$ R --vanilla --slave -e "suppressPackageStartupMessages(library(Biobase)); all.equal(baseenv(), baseenv())" Error in target$getClass() : object '.refClassDef' not found Calls: all.equal ... all.equal.list -> all.equal -> all.equal.envRefClass -> Execution halted We were bumping into an error with this in Rcpp -- we used all.equal (through RUnit) to confirm that baseenv(), and a function returning the base environment, would return TRUE. For completeness: kevin:~$ R --vanilla --slave -e "sessionInfo()" R Under development (unstable) (2014-09-20 r66650) Platform: x86_64-apple-darwin13.3.0 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks, Kevin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] last user argument missing from Rscript --verbose
On 20 September 2014 at 19:55, Harris A. Jaffee wrote: | Terrific, and I appreciate your thoughts and encouragement. | | So, getting back on-list, I propose a backward-incompatible change, with | or without --verbose, that the --args be included in the 'av' array, and | passed to R, only if there are user arguments to follow it. The condition | for a first argument, at the time --args is currently included, is | | (i0+1) < argc | | Scott's fix, already in the devel version, solves my original complaint and | should continue to do so, as long as av[ac] continues to be the terminating | NULL. That is, av[ac-1] is the last argument in the R command. In case you were unaware of it, r from littler (which has been around even longer than Rscript) has always propagated its arguments into argv: edd@max:~$ r -e'print(argv)' foo bar biz x=42 [1] "foo" "bar" "biz" "x=42" edd@max:~$ See http://dirk.eddelbuettel.com/code/littler.html and my blog pages on littler at http://dirk.eddelbuettel.com/blog/code/littler/ for more about 'r' and littler; pre-built binaries exist at CRAN for Debian and Ubuntu; and it builds easily on a lot of other OSs. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Bug in new behaviour for all.equal and environments?
On 21/09/2014, 1:38 PM, Rui Barradas wrote: > Hello, > > In R 3.1.1 on Windows 7 it's ok. > > > all.equal(baseenv(), baseenv()) > [1] TRUE > > sessionInfo() > R version 3.1.1 (2014-07-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) I'm not sure if that's really "ok", since it returns TRUE for any pair of environments, e.g. all.equal(baseenv(), emptyenv()) The current R-devel behaviour is temporary and certain to change. Duncan Murdoch > > locale: > [1] LC_COLLATE=Portuguese_Portugal.1252 > LC_CTYPE=Portuguese_Portugal.1252 > [3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C > > [5] LC_TIME=Portuguese_Portugal.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > Rui Barradas > > Em 21-09-2014 18:06, Kevin Ushey escreveu: >> Hi R-devel, >> >> The following code: >> >> all.equal(baseenv(), baseenv()) >> >> gives the error when run in a clean R session with latest R-devel (r66650): >> >> kevin:~$ R --vanilla --slave -e "all.equal(baseenv(), baseenv())" >> Error in all.equal.envRefClass(target[[i]], current[[i]], >> check.attributes = check.attributes, : >>attempt to apply non-function >> Calls: all.equal ... all.equal.list -> all.equal -> >> all.equal.envRefClass >> Execution halted >> >> Although I don't know if it's helpful -- it appears that packages that >> include some S4 machinery will effect the outcome of this error, e.g. >> if we load 'Biobase' first: >> >> kevin:~$ R --vanilla --slave -e >> "suppressPackageStartupMessages(library(Biobase)); >> all.equal(baseenv(), baseenv())" >> Error in target$getClass() : object '.refClassDef' not found >> Calls: all.equal ... all.equal.list -> all.equal -> >> all.equal.envRefClass -> >> Execution halted >> >> We were bumping into an error with this in Rcpp -- we used all.equal >> (through RUnit) to confirm that baseenv(), and a function returning >> the base environment, would return TRUE. >> >> For completeness: >> >> kevin:~$ R --vanilla --slave -e "sessionInfo()" >> R Under development (unstable) (2014-09-20 r66650) >> Platform: x86_64-apple-darwin13.3.0 (64-bit) >> >> locale: >> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> Thanks, >> Kevin >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
