[R] Problems getting html files out of R CMD check

[Duncan Murdoch]

On 11-03-13 7:14 PM, Amos Folarin wrote:
> Hi,
>
> I'm trying to R CMD check a package, however I have hit a snag. There seems
> to be a problem with the creation of the /html files (the only file that's
> constructed here is the 00Index.html). I've tested each of the .Rd files
> independently with R CMD Rdconv, they all happily create html files without
> complaint.

R doesn't build .html files any more unless you ask it to explicitly, 
e.g. using R CMD Rdconv.

Duncan Murdoch

>
>
> R CMD check<package>  gives the no warnings. I'm therefore curious why this
> hasn't created the html files for the package, I think I must be missing
> something.
>
> * using log directory ‘/home/me/scratch/CellProfileR.Rcheck’
> * using R version 2.12.2 (2011-02-25)
> * using platform: i686-pc-linux-gnu (32-bit)
> * using session charset: UTF-8
> * checking for file ‘CellProfileR/DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘CellProfileR’ version ‘1.0’
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking for executable files ... OK
> * checking whether package ‘CellProfileR’ can be installed ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies ... OK
> * checking whether the package can be unloaded cleanly ... OK
> * checking for unstated dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... NOTE
> prepare_Rd: CellProfile-R-internal.Rd:10: Dropping empty section \usage
> prepare_Rd: CellProfile-R-internal.Rd:12: Dropping empty section \arguments
> prepare_Rd: CellProfile-R-internal.Rd:22: Dropping empty section \value
> prepare_Rd: CellProfile-R-internal.Rd:25: Dropping empty section \note
> prepare_Rd: CellProfile-R-internal.Rd:23: Dropping empty section \references
> prepare_Rd: CellProfile-R-internal.Rd:29: Dropping empty section \seealso
> prepare_Rd: CellProfile-R-internal.Rd:30: Dropping empty section \examples
> prepare_Rd: CellProfile-R-package.Rd:43: Dropping empty section \seealso
> prepare_Rd: CellProfile-R-package.Rd:44: Dropping empty section \examples
> prepare_Rd: createUnifiedTable.Rd:59-61: Dropping empty section \note
> prepare_Rd: createUnifiedTable.Rd:53-55: Dropping empty section \references
> prepare_Rd: fileConnect.Rd:47-49: Dropping empty section \note
> prepare_Rd: fileConnect.Rd:41-43: Dropping empty section \references
> prepare_Rd: fileConnect.Rd:53-55: Dropping empty section \seealso
> prepare_Rd: loadTable.Rd:29-31: Dropping empty section \details
> prepare_Rd: loadTable.Rd:41-43: Dropping empty section \note
> prepare_Rd: loadTable.Rd:35-37: Dropping empty section \references
> prepare_Rd: mapMetadataToTable.Rd:53-55: Dropping empty section \note
> prepare_Rd: mapMetadataToTable.Rd:47-49: Dropping empty section \references
> prepare_Rd: mapMetadataToTable.Rd:59-61: Dropping empty section \seealso
> prepare_Rd: mySqlConnect.Rd:27-29: Dropping empty section \details
> prepare_Rd: mySqlConnect.Rd:39-41: Dropping empty section \note
> prepare_Rd: mySqlConnect.Rd:33-35: Dropping empty section \references
> prepare_Rd: mySqlConnect.Rd:43-45: Dropping empty section \seealso
> prepare_Rd: mySqlConnect.Rd:46: Dropping empty section \examples
> prepare_Rd: recastDatabaseTable.Rd:39-41: Dropping empty section \note
> prepare_Rd: recastDatabaseTable.Rd:36-38: Dropping empty section \author
> prepare_Rd: recastDatabaseTable.Rd:33-35: Dropping empty section \references
> prepare_Rd: recastDatabaseTable.Rd:45-47: Dropping empty section \seealso
> prepare_Rd: saveTable.Rd:20-22: Dropping empty section \details
> prepare_Rd: saveTable.Rd:30-32: Dropping empty section \note
> prepare_Rd: saveTable.Rd:24-26: Dropping empty section \references
> prepare_Rd: saveTable.Rd:36-38: Dropping empty section \seealso
> prepare_Rd: saveTable.Rd:39: Dropping empty section \examples
> prepare_Rd: splitTableOnVariable.Rd:18: Dropping empty section \details
> prepare_Rd: splitTableOnVariable.Rd:24-26: Dropping empty section \note
> prepare_Rd: splitTableOnVariable.Rd:20-22: Dropping empty section
> \references
> prepare_Rd: splitTableOnVariable.Rd:30-32: Dropping empty section \seealso
> prepare_Rd: sqLiteConnect.Rd:34-36: Dropping empty section \note
> prepare_Rd: sqLiteConnect.Rd:28-30: Dropping empty section \references
> prepare_Rd: sqLiteConnect.Rd:40-42: Dropping empty section \seealso
> * checking Rd metadata ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * checking Rd contents ... OK
> * checking for unstated dependencies in examples ... OK
> * checking data for non-ASCII characters ... OK
> * checking examples ... OK
> * checking PDF version of manual ... OK
>
>
>
>
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>   [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
>   [7] LC_PAPER=en_GB.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] MASS_7.3-7
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.2
>
> 	[[alternative HTML version deleted]]
>
>
>
>
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