On Mon, Dec 15, 2014 at 9:44 AM, Jeff Hansen <dsche...@gmail.com> wrote:
> Thanks Henrik! Adding the line
>
> library("methods")
>
> to the list of required libraries did indeed solve the problem. My next
> comment will show my naivety when it comes to R dependency management, but I
> noticed that including `library("rJava")` in place of methods also solves
> the problem. This confuses me because I would think that RWeka depends on
> rJava so I don't understand why transitive dependencies wouldn't
> automatically be loaded -- something for me to research more when I have the
> chance.The naming of field "Depends" in DESCRIPTION is a bit unfortunate and misleading, since the package depends all all packages under "Depends" and "Imports" on order for it to be loaded. The reason for the name is historical - it predates namespaces and was coined at a time when "Imports" didn't exists. If you look at http://cran.r-project.org/web/packages/RWeka/index.html, or packageDescription("RWeka"), you'll find that RWeka *imports* rJava, but it does not *attach* it. A package listed under "Depends" will be *loaded* and *attached* whereas a package under "Imports" will only be *loaded*. An attached package makes its API available via search() and therefore also to the user at the R prompt, whereas a package that is only loaded, will not be available this way. Next, since RWeka only lists rJava under Imports, rJava is only *loaded*. In turn, whatever package rJava depends on ("Depends" or "Imports" etc) will only be *loaded*. In other words, it does not matter that rJava has "methods" under "Depends" - the latter will still only be *loaded*. EXAMPLE: $ Rscript -e "library('RWeka'); sessionInfo()" R Under development (unstable) (2014-12-10 r67152) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets base other attached packages: [1] RWeka_0.4-23 loaded via a namespace (and not attached): [1] grid_3.2.0 methods_3.2.0 rJava_0.9-6 RWekajars_3.7.11-1 [5] tools_3.2.0 You can explicitly load (the namespace of a) package (emulating what happens with Imports) by: $: Rscript -e "loadNamespace('rJava'); sessionInfo()" <environment: namespace:rJava> R Under development (unstable) (2014-12-10 r67152) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets base loaded via a namespace (and not attached): [1] methods_3.2.0 rJava_0.9-6 tools_3.2.0 and compare it to when you attach a package: Rscript -e "library('rJava'); sessionInfo()" [HB-X201]{hb}: Rscript -e "library('rJava'); sessionInfo()" Loading required package: methods R Under development (unstable) (2014-12-10 r67152) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] methods stats graphics grDevices utils datasets base other attached packages: [1] rJava_0.9-6 loaded via a namespace (and not attached): [1] tools_3.2.0 Look at where 'methods' ends up. /Henrik > > Thanks for the help -- sadly it took me a month to see it as these responses > were automatically diverted to a folder using filter logic I set up a few > years ago and forgot about... > > On Wed, Nov 19, 2014 at 2:57 PM, Henrik Bengtsson <h...@biostat.ucsf.edu> > wrote: >> >> When using Rscript, the 'methods' package is not loaded/attached by >> default, which it is when you use R. See ?Rscript for details. For >> any scripts intended for batch usage, the safest is to only assume >> that 'base' is attached, but nothing else. >> >> /Henrik >> >> On Wed, Nov 19, 2014 at 10:03 AM, Ben Tupper <ben.bigh...@gmail.com> >> wrote: >> > Hi, >> > >> > On Nov 19, 2014, at 11:48 AM, Jeff Hansen <dsche...@gmail.com> wrote: >> > >> >> I have a script that uses RWeka (and consequently rJava). When I run >> >> it in Rstudio everything works fine. When I run it with `R CMD BATCH`, >> >> everything also works fine. However, when I run it with Rscript, I get >> >> the following error: >> >> >> >> Error in FUN(X[[1L]], ...) : >> >> object is not a Java object reference (jobjRef/jarrayRef). >> >> Calls: evaluate_Weka_classifier -> t -> sapply -> lapply -> FUN >> >> Execution halted >> >> >> >> The following is a very simple toy script that you can run to produce >> >> the results: >> >> >> >> library("RWeka") >> >> result <- c(TRUE,FALSE,TRUE,FALSE,TRUE) >> >> observation <- c(TRUE,FALSE,TRUE,FALSE,TRUE) >> >> df <- data.frame(result,observation) >> >> j48 <- J48(result ~ .,data=df) >> >> evaluate_Weka_classifier(j48) >> >> >> >> Save that to a file called help.R and run >> >> >> >> R CMD BATCH help.R >> >> >> >> Check the output file help.Rout and you should see no errors. Now try >> >> running it from: >> >> >> >> Rscript help.R >> >> >> > >> > You might try using the the --vanilla option for each. At least then >> > you can rule out that something is being restored in the session of one but >> > not the other. >> > >> > R --vanilla CMD BATCH help.R >> > Rscript --vanilla help.R >> > >> > Cheers, >> > Ben >> > >> > >> >> And you should see the error I've pasted above. >> >> >> >> I have consulted (and will continue to consult) the literature, but >> >> the manuals tend to answer how usage differs between the two commands >> >> rather than going into implementation details. I imagine there's a >> >> difference in how environments get loaded and I just need to adjust >> >> something on the Rscript side. >> >> >> >> I'm working on a Mac (OSX) running R 3.1.0, but I get the same results >> >> when I run everything from a Centos 6.4 virtual machine (headless) >> >> with R 3.1.1 installed. >> >> >> >> Thanks for any help! >> >> >> >> ______________________________________________ >> >> R-help@r-project.org mailing list >> >> 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@r-project.org mailing list >> > 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@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.
