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.dun...@gmail.com <mailto:murdoch.dun...@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.chalm...@gmail.com <mailto:rphilip.chalm...@gmail.com> <mailto:rphilip.chalm...@gmail.com <mailto:rphilip.chalm...@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.dun...@gmail.com <mailto:murdoch.dun...@gmail.com> <mailto:murdoch.dun...@gmail.com <mailto:murdoch.dun...@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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