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

[Phil Chalmers]

Yes, I can see the partial.rdb file in the list, also in entry 28. So I
believe the problem is on the CRAN build.

Phil

On Wed, Jul 26, 2017 at 10:30 AM, Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

> 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
>>
>>
>>
>

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