recycle rep to pass data.table 1.12.2

[mattdowle]

Dear Venelin,
As discussed on email.
Hope ok.
Thanks, Matt

[venelin]

Dear Matt,

Thanks for this. I've now added you as a ctb to the authors list of the package.

I've merged the pull request into the master branch and fixed the failing vignette-build. The second problematic line was correctly coded, so I've rolled-back your change on it. To clarify, group (or column) 13 in your commented block had .N=2 due to a different issue (which is now solved). Therefore, all but one column should have .N=1 in this case and recycling should be as usual here. I think, I am ready to submit this updated version to CRAN. Let me know if you know of another possible issue with that.

Best,
Venelin

[mattdowle]

Dear Venelin,
Great - thanks! It was very kind of you to add me as contributor, thank you.
I have just cloned master and rerun, to double-check. I still see the following 3 warnings. I don't think it is data.table related? It helps me a lot in revdep checking if this can pass without warnings (notes are ok). If there's something I need to do differently on my side, that's fine too if you let me know.

$ git clone https://github.com/venelin/POUMM.git
Cloning into 'POUMM'...
remote: Enumerating objects: 791, done.
remote: Counting objects: 100% (791/791), done.
remote: Compressing objects: 100% (320/320), done.
remote: Total 1466 (delta 574), reused 655 (delta 451), pack-reused 675
Receiving objects: 100% (1466/1466), 13.68 MiB | 5.73 MiB/s, done.
Resolving deltas: 100% (953/953), done.

$ R CMD build POUMM 
* checking for file ‘POUMM/DESCRIPTION’ ... OK
* preparing ‘POUMM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Quitting from lines 33-41 (InterpretingPOUMM.Rmd) 
Error: processing vignette 'InterpretingPOUMM.Rmd' failed with diagnostics:
bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted

$ R CMD build POUMM --no-build-vignettes 
* checking for file ‘POUMM/DESCRIPTION’ ... OK
* preparing ‘POUMM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘POUMM_2.1.4.02.tar.gz’

$ R CMD check POUMM_2.1.4.02.tar.gz 
* using log directory ‘/home/mdowle/GitHub/forks/POUMM.Rcheck’
* using R version 3.5.2 (2018-12-20)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘POUMM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘POUMM’ version ‘2.1.4.02’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘POUMM’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
* checking package 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 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 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘InterpretingPOUMM.Rmd’, ‘REFERENCES.bib’, ‘UserGuide.Rmd’, ‘UserGuideCache.RData’
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignettes without corresponding PDF/HTML:
   ‘InterpretingPOUMM.Rmd’
   ‘UserGuide.Rmd’

* checking running R code from vignettes ...
   ‘InterpretingPOUMM.Rmd’ using ‘UTF-8’ ... OK
   ‘UserGuide.Rmd’ using ‘UTF-8’ ... OK
 NONE
* checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Quitting from lines 33-41 (InterpretingPOUMM.Rmd) 
Error: processing vignette 'InterpretingPOUMM.Rmd' failed with diagnostics:
bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  ‘/home/mdowle/GitHub/forks/POUMM.Rcheck/00check.log’
for details.

[venelin]

Dear Matt,

Thanks for double-checking.

The "magic number" error should be due to the use of git lfs for .RData files in the POUMM repository. To speed-up the build of vignettes, I was using some cached objects stored in a .RData file in the vignettes directory. If you do a normal clone of the POUMM repository, it would not pull the .RData file itself, but a text file containing a symbolic link to the binary file on the lfs system. To solve the issue (and because I was never satisfied with having this .RData file in the vignettes directory), I've now stored these cache objects as a data object - a .rda file in the package's data directory. Your test should pass now, because lfs tracking for .rda files is not enabled.

Cheers,
Venelin

[mattdowle]

Dear Venelin,
Many thanks! I just retried and it's all good now: no errors or warnings, just 2 notes.
Yes would be great if you can submit to CRAN please. Maybe those 2 notes need addressing to be accepted on CRAN but they're fine by me.
Best, Matt

[venelin]

Dear Matt,

Are the two notes you see the following:

• checking for unstated dependencies in vignettes ... NOTE
  '::' or ':::' import not declared from: ‘usethis’
• checking installed package size ... NOTE
  installed size is 6.1Mb
  sub-directories of 1Mb or more:
  libs 4.6Mbchecking for unstated dependencies in vignettes ... NOTE

Cheers,
Venelin

[mattdowle]

Yes those are the two.