[R-pkg-devel] \Sexpr{} expressions but no 'build/partial.rdb' file

[Duncan Murdoch]

On 26/07/2017 9:05 AM, Phil Chalmers wrote:
> Hi Duncan,
>
> I use the standard R CMD build/check --as-cran combo. Here's my output
> from my Win 10 64-bit box:
>
> C:\Users\Phil\Desktop>C:/PROGRA~1/R/R-devel/bin/x64/R CMD build mirtCAT
> * checking for file 'mirtCAT/DESCRIPTION' ... OK
> * preparing 'mirtCAT':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to process help pages
> * saving partial Rd database
> * creating vignettes ... OK
> * cleaning src
> * checking for LF line-endings in source and make files and shell scripts
> * checking for empty or unneeded directories
> * building 'mirtCAT_1.6.tar.gz'
>
>
> C:\Users\Phil\Desktop>C:/PROGRA~1/R/R-devel/bin/x64/R CMD check
> mirtCAT_1.6.tar.gz --as-cran
> * using log directory 'C:/Users/Phil/Desktop/mirtCAT.Rcheck'
> * using R Under development (unstable) (2017-07-25 r72968)
> * using platform: x86_64-w64-mingw32 (64-bit)
> * using session charset: ISO8859-1
> * using option '--as-cran'
> * checking for file 'mirtCAT/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'mirtCAT' version '1.6'
> * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
> Maintainer: 'Phil Chalmers <rphilip.chalmers at gmail.com
> <mailto:rphilip.chalmers at gmail.com>>'
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking whether package 'mirtCAT' can be installed ... OK
> * checking installed package size ... OK
> * checking package directory ... OK
> * checking 'build' directory ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking for left-over 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 whether the namespace can be loaded with stated dependencies
> ... OK
> * checking whether the namespace can be unloaded cleanly ... OK
> * checking loading without being on the library search path ... OK
> * checking use of S3 registration ... OK
> * checking 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 ... OK
> * checking Rd metadata ... OK
> * checking Rd line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
> * checking line endings in Makefiles ... OK
> * checking compilation flags in Makevars ... OK
> * checking for GNU extensions in Makefiles ... OK
> * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
> * checking compiled code ... OK
> * checking installed files from 'inst/doc' ... OK
> * checking files in 'vignettes' ... OK
> * checking examples ... OK
> * checking for unstated dependencies in vignettes ... OK
> * checking package vignettes in 'inst/doc' ... OK
> * checking re-building of vignette outputs ... OK
> * checking PDF version of manual ... OK
> * DONE
>
> Status: OK
>
> --------------------------------------------------------
>
> Exactly the same thing occurs on my Ubuntu 64-bit box. So again, I'm
> still unsure how to proceed, particularly if only some OS's/versions are
> detecting this error other than mine.

Sounds like a bug somewhere.  Does the file you submitted to CRAN 
contain the build/partial.rdb file?  If so, the bug is in the check code 
being run by CRAN.  If not, the bug is in the build code that you ran.

You can get a listing of the contents from within R using

untar("mirtCAT_1.6.tar.gz", list = TRUE)

When I do that, the partial.rdb file is entry 28.

Duncan Murdoch

>
> Phil
>
> On Wed, Jul 26, 2017 at 7:06 AM, Duncan Murdoch
> <murdoch.duncan at gmail.com <mailto:murdoch.duncan at gmail.com>> wrote:
>
>     On 25/07/2017 4:42 PM, Phil Chalmers wrote:
>
>         Hi all,
>
>         First time posting here, so hopefully I'm following the correct
>         etiquette.
>
>         I recently received the error:
>
>         "Package has help file(s) containing build-stage \Sexpr{}
>         expressions but
>         no 'build/partial.rdb' file."
>
>         when submitting a package to CRAN (source code: https://github.com/
>         philchalmers/mirtCAT). However, I'm having difficulty
>         reproducing the exact
>         problem on my Windows and Linux computers with the latest R dev
>         version
>         (2017-07-25 r72968). Moreover, I don't really understand the
>         issue, as I do
>         not use \Sexpr{} anywhere in the package.
>
>         After a quick search, I found a link on SO
>         (https://stackoverflow.com/
>         questions/32357637/two-note-messages-from-r-cmd-check-as-cran),
>         but it does
>         not appear too helpful as far as I can tell (I don't explicitly use
>         \package_____() commands anywhere). Can anyone shed some light
>         on this
>         warning and my difficulty in reproducing the message? Thank you
>         in advance.
>
>
>     How did you produce the tar.gz file?  If you did it in some way
>     other than running "R CMD build ...", don't do that.   When I run R
>     CMD build, I do get the build/partial.rdb file in the tarball.
>
>     Duncan Murdoch
>
>