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 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

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