OK, so I think until we figure this out and/or the fix is on CRAN I can work around it using eval=FALSE with some hidden code blocks to hide the double colon notation. I've installed the latest revision of knitr, and it does fix the problem.
On Tuesday, 2 April 2013 at 4:40 AM, Yihui Xie wrote: > I do not know much about S4, but I figured out one possible solution > on knitr's side, which I do not really understand. In short, your S4 > methods need to be evaluated in globalenv(), but knitr uses the > parent.frame() by default, which is not the global environment when it > is called as the vignette builder. > > Now I have forced the evaluation to be in the global environment, and > pushed the changes to the knitr development version on Github: > https://github.com/yihui/knitr > > Regards, > Yihui > -- > Yihui Xie <xieyi...@gmail.com (mailto:xieyi...@gmail.com)> > Phone: 515-294-2465 Web: http://yihui.name > Department of Statistics, Iowa State University > 2215 Snedecor Hall, Ames, IA > > > On Mon, Apr 1, 2013 at 7:37 PM, Henrik Bengtsson <h...@biostat.ucsf.edu > (mailto:h...@biostat.ucsf.edu)> wrote: > > Hi, > > > > things have indeed changed on how non-Sweave vignettes are built (this > > happened around R devel 2013-03-05 r62130). However, it's not clear > > to me what changes would be behind your problems, if any. > > > > Build your vignette with the following buildVignette(), which emulates > > what R does when it builds vignettes (cf. tools::buildVignettes()). > > As you'll see, it reproduces your error: > > > > if (!exists("buildVignette", mode="function")) { > > source("http://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/R.rsp/R/buildVignette.R?root=r-dots";); > > } > > > > EXAMPLE (in a fresh R session): > > > > url <- > > "http://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/BayesFactorPCL/vignettes/manual.Rmd?root=bayesfactorpcl"; > > if (!file.exists("manual.Rmd")) download.file(url, "manual.Rmd"); > > > > output <- buildVignette("manual.Rmd", buildPkg="knitr"); > > browseURL(output); > > > > bfr <- readLines(output); > > idxs <- grep("which.max(bf)", bfr, fixed=TRUE); > > idxs <- sort(sapply(idxs, FUN=function(idx) idx+(-5:5))); > > cat(sprintf("%03d: %s\n", idxs, bfr[idxs])); > > > > > cat(sprintf("%03d: %s", idxs, bfr[idxs]), sep="\n") > > 2517: </code></pre> > > 2518: > > 2519: <pre><code>## [1] TRUE > > 2520: </code></pre> > > 2521: > > 2522: <pre><code class="r">BayesFactor::which.max(bf) > > 2523: </code></pre> > > 2524: > > 2525: <pre><code>## complaints > > 2526: ## 1 > > 2527: </code></pre> > > 2531: > > 2532: <pre><code>## critical + advance > > 2533: ## 21 > > 2534: </code></pre> > > 2535: > > 2536: <pre><code class="r">which.max(bf) > > 2537: </code></pre> > > 2538: > > 2539: <pre><code>## Error: no method for coercing this S4 class to a vector > > 2540: </code></pre> > > 2541: > > > > So, have a look at browseVignette() and how it calls the 'knitr' weave > > function. That should help you narrow down what's going on. > > > > > sessionInfo() > > R version 3.0.0 RC (2013-03-31 r62463) > > 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] tools stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] BayesFactor_0.9.3 markdown_0.5.4 coda_0.16-1 lattice_0.20-15 > > [5] knitr_1.1.7 > > > > loaded via a namespace (and not attached): > > [1] digest_0.6.3 evaluate_0.4.3 formatR_0.7 grid_3.0.0 > > [5] mvtnorm_0.9-9994 pbapply_1.0-5 stringr_0.6.2 > > > > Hope this helps > > > > /Henrik > > > > On Mon, Apr 1, 2013 at 4:52 PM, Richard D. Morey <r.d.mo...@rug.nl > > (mailto:r.d.mo...@rug.nl)> wrote: > > > A new problem has cropped up with compiling vignettes for my package > > > BayesFactor. I'm not sure when it started, but I can tell you it didn't > > > occur on R 2.15.3, and it does on 3.0.0 RC (2013-03-31 r62463) (session > > > info is at the bottom of this message). > > > > > > I have defined methods for which.min and which.max for a class (I've > > > defined both S3 and S4 methods for the class "BFBayesFactor") in my > > > package. I've exported the S4 class using exportMethods, and declared the > > > S3 method with S3method. You can see the NAMESPACE file here: > > > > > > https://r-forge.r-project.org/scm/viewvc.php/pkg/BayesFactorPCL/NAMESPACE?view=markup&root=bayesfactorpcl > > > > > > and the methods here: > > > > > > https://r-forge.r-project.org/scm/viewvc.php/pkg/BayesFactorPCL/R/methods-BFBayesFactor.R?view=markup&root=bayesfactorpcl > > > > > > I have code in a vignette that calls the which.max method on a > > > BFBayesFactor object. However, when that happens as the vignette is being > > > compiled, I get an error: > > > > > > which.max(bf) > > > ## Error: no method for coercing this S4 class to a vector > > > > > > > > > > > > This also occurs with which.min, but oddly not any other method > > > (including the is.na method, which is declared exactly the same way, as > > > far as I can tell). This seems to imply that the which.min and which.max > > > methods are not exported. > > > > > > When I use double colon notation - which as I understand, only works with > > > exported functions - it works (see below). > > > > > > When I compile the Rmd file manually, I do not see this problem; I get no > > > errors. This seems to be a problem unique to compiling the vignette. I've > > > tried it in Rstudio, R from the command line, and using Rscript and > > > calling knitr directly. It only occurs when building a vignette for the > > > source package. > > > > > > Steps to reproduce: > > > 1. Check out latest version of BayesFactor package from R-forge > > > (https://r-forge.r-project.org/scm/?group_id=554) (revision 320) > > > > > > 2. Create a source package (which compiles the vignette) > > > > > > 3. Open tar to see compiled vignette HTML (doc/manual.html - or, > > > alternatively, see > > > https://www.dropbox.com/s/6csznytp8i1akjl/manual.html). Search for second > > > occurrence of "which.max", and see the following lines: > > > > > > ## which model index is the best? > > > is(bf, "BFBayesFactor") > > > ## [1] TRUE > > > BayesFactor::which.max(bf) > > > ## complaints > > > ## 1 > > > BayesFactor::which.min(bf) > > > ## critical + advance > > > ## 21 > > > which.max(bf) > > > ## Error: no method for coercing this S4 class to a vector > > > which.min(bf) > > > ## Error: no method for coercing this S4 class to a vector > > > > > > > > > > > > I've been pulling my hair out on this, especially because something seems > > > to have changed over the past few weeks that caused this, but I didn't > > > catch exactly when, and I don't know if the issue lies with R 3.0.0 or my > > > package. > > > > > > > sessionInfo() > > > R version 3.0.0 RC (2013-03-31 r62463) > > > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > locale: > > > [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > > > [1] BayesFactor_0.9.5 markdown_0.5.4 knitr_1.1.6 coda_0.16-1 > > > lattice_0.20-15 > > > loaded via a namespace (and not attached): > > > [1] digest_0.6.3 evaluate_0.4.3 formatR_0.7 grid_3.0.0 mvtnorm_0.9-9994 > > > [6] pbapply_1.0-5 stringr_0.6.2 tools_3.0.0 > > > > > > > > > > > > > > > Any help would be greatly appreciated, > > > Richard > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
