From mtmorgan at fhcrc.org  Tue Apr  2 04:02:13 2013
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Mon, 01 Apr 2013 19:02:13 -0700
Subject: [Rd] missing exported methods when compiling vignettes in R
 3.0.0 RC
In-Reply-To: <CAFDcVCQHM+1uj1NBr1kDHbJnArRqXOqxCrbkZ3g+GPZAc0KG2g@mail.gmail.com>
References: <mailman.11.1364810408.30516.r-devel@r-project.org>
	<1B1B843261D34A409EEE3DCAE737981E@rug.nl>
	<CAFDcVCQHM+1uj1NBr1kDHbJnArRqXOqxCrbkZ3g+GPZAc0KG2g@mail.gmail.com>
Message-ID: <515A3C25.30709@fhcrc.org>

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))
## &lt;environment: namespace:base&gt;
</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(&quot;which.min&quot;)
## &lt;environment: 0x8f5b0c0&gt;
## Methods may be defined for arguments: x
## Use  showMethods(&quot;which.min&quot;)  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.morey at 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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/r-devel
>


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[Rd] missing exported methods when compiling vignettes in R 3.0.0 RC
Martin Morgan