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 [[alternative HTML version deleted]]
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]] > > > > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
> > ---------- Forwarded message ---------- > From: Duncan Murdoch <murdoch.duncan@gmail.com> > To: Amos Folarin <amosfolarin@gmail.com> > Date: Sun, 13 Mar 2011 20:53:57 -0400 > Subject: Re: [R] Problems getting html files out of R CMD check > 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 >Thanks Duncan, I guess much of the documentation "out there" still indicate this functionality. [[alternative HTML version deleted]]