On 04/01/2013 05:37 PM, Henrik Bengtsson 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:
Maybe to further move this along, the vignette can be replaced with
<!--
%\VignetteEngine{knitr}
%\VignetteIndexEntry{Using the BayesFactor package, version 0.9.2+}
-->
```{r}
library(BayesFactor)
which.min
```
and built with
tools:::buildVignettes(dir="~/tmp/pkg/BayesFactorPCL/")
and the output shows that which.min is not the expected S4 generic.
BayesFactorPCL/vignettes$ tail manual.html
</code></pre>
<pre><code>## function (x)
## .Internal(which.min(x))
## <environment: namespace:base>
</code></pre>
</body>
</html>
This contrasts with, e.g.,
R -e "knitr::knit2html('~/tmp/pkg/BayesFactorPCL/vignettes/manual.Rmd')"
which gives
BayesFactorPCL/vignettes$ tail manual.html
## function (x)
## standardGeneric("which.min")
## <environment: 0x8f5b0c0>
## Methods may be defined for arguments: x
## Use showMethods("which.min") for currently available ones.
</code></pre>
</body>
</html>
One (or two) other minor points -- which.min / which.max are _not_ S3 generics,
so I'm not sure it makes sense to define / export S3 methods. The implicit
generics which.min / which.max need to be documented.
Martin
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> 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
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