[R-pkg-devel] \Sexpr{} expressions but no 'build/partial.rdb' file
Duncan Murdoch
murdoch.duncan at gmail.com
Thu Jul 27 14:34:22 CEST 2017
On 26/07/2017 12:23 PM, Phil Chalmers wrote:
> 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.
For the rest of the list: This claim is incorrect. The tarball that
was submitted to CRAN did not contain the partial.rdb file. The CRAN
message was correct.
Phil, it would be helpful if you explained how you really produced that
tarball, so people know how not to do it.
Duncan Murdoch
>
> Phil
>
> On Wed, Jul 26, 2017 at 10:30 AM, Duncan Murdoch
> <murdoch.duncan at gmail.com <mailto: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>
> <mailto: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>
> <mailto: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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