[R-pkg-devel] note

[Jeff Newmiller]

Regarding the global variables... I found [1] illuminating, in particular the comments on the solution.

[1] https://stackoverflow.com/questions/41954302/where-to-create-package-environment-variables

On June 4, 2019 11:07:20 AM PDT, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>On 04/06/2019 8:36 a.m., Bernd  JAGLA wrote:
>> Hi,
>> 
>> 
>> I am trying to submit a package with a shiny app to cran.
>> 
>> I get 2 notes that I don't know how to resolve. I would appreciate
>very much any suggestions/help.
>> 
>> 
>> Thanks a lot.
>> 
>> 
>> It seems the first note is on possibly misspelled words. I am using
>camel-case to "explain" the name of the app, the app's name itself is
>mostly capitalized, and the others are either names of objects or the
>title (Transcriptomics), which I believe should be capitalized... So, I
>don't really know how to overcome this.
>
>Explain in your submission note why you spelled things the way you did.
>
>Generally non-English words should be in single quotes; see 
>https://cloud.r-project.org/web/packages/submission_checklist.html. 
>But 
>"sHiny" looks wrong in any case if it is not quoted.
>> 
>> 
>> With respect to the TRONCO license, I believe the reason for the
>message is that they included a custom file, but they are also using
>GPL3 (which I am required to use by my company) I don't see a
>solution...
>
>TRONCO is a Bioconductor package, and isn't declaring its GPL-3 license
>
>in the format that CRAN wants.  Explain this in your submission note.
>> 
>> 
>> Then, there are some global variables and things that are only
>defined under the inst directory. I came about the solution of putting
>the main part of my app /inst by finding similar solutions on google. I
>ran into a whole bunch of problems with putting everything under /R and
>I can create a package etc on GitHub and locally and install them
>through GitHub or locally. The only caveat is that I had to define
>these variables to pass the arguments as there are different
>environments involved... I think I chose the variable names in a way
>that shouldn't interfere with anything...
>
>Don't create global variables. The global environment is off limits to 
>you. You can have an environment in your package that contains those 
>variables.  This one you'll have to change, not just explain like the 
>others.
>
>Duncan Murdoch
>> 
>> 
>> As you can imagine by now, this is the first package I am submitting
>and it is quite a daunting task, so I am very sorry to haven't
>understood by now all the documentation and I am still hoping that the
>approach I took is viable. 😉
>> 
>> 
>> Thanks for taking the time to look into this.
>> 
>> 
>> Here is the log:
>> 
>> * using log directory
>'d:/RCompile/CRANincoming/R-devel/SCHNAPPs.Rcheck'
>> * using R Under development (unstable) (2019-06-03 r76654)
>> * using platform: x86_64-w64-mingw32 (64-bit)
>> * using session charset: ISO8859-1
>> * checking for file 'SCHNAPPs/DESCRIPTION' ... OK
>> * checking extension type ... Package
>> * this is package 'SCHNAPPs' version '0.1.2'
>> * package encoding: UTF-8
>> * checking CRAN incoming feasibility ... NOTE
>> Maintainer: 'Bernd Jagla <bernd.jagla using pasteur.fr>'
>> 
>> New submission
>> 
>> Possibly mis-spelled words in DESCRIPTION:
>>    APPlication (8:32)
>>    SCHNAPPs (8:45)
>>    SingleCellExperiment (11:5)
>>    Transcriptomics (4:9)
>>    sHiny (8:26)
>> 
>> Package has a FOSS license but eventually depends on the following
>> package which may restrict use:
>>    TRONCO
>> 
>> Size of tarball: 14400839 bytes
>> * 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 hidden files and directories ... OK
>> * checking for portable file names ... OK
>> * checking whether package 'SCHNAPPs' can be installed ... OK
>> * checking installed package size ... OK
>> * checking package directory ... OK
>> * checking for future file timestamps ... 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
>> * loading checks for arch 'i386'
>> ** 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
>> * loading checks for arch 'x64'
>> ** 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 ... [10s] NOTE
>> schnapps: no visible global function definition for 'shinyApp'
>> schnapps: no visible binding for global variable 'scShinyUI'
>> schnapps: no visible binding for global variable 'scShinyServer'
>> schnapps: no visible global function definition for 'runApp'
>> Undefined global functions or variables:
>>    runApp scShinyServer scShinyUI shinyApp
>> 
>> Found the following assignments to the global environment:
>> File 'SCHNAPPs/R/schnapps-Main.R':
>>    assign(".SCHNAPPs_locContributionDir", localContributionDir,
>>      envir = globalenv())
>>    assign(".SCHNAPPs_defaultValueSingleGene", defaultValueSingleGene,
>>      envir = globalenv())
>>    assign(".SCHNAPPs_defaultValueMultiGenes", defaultValueMultiGenes,
>>      envir = globalenv())
>>    assign(".SCHNAPPs_defaultValueRegExGene", defaultValueRegExGene,
>>      envir = globalenv())
>>    assign(".SCHNAPPs_DEBUG", DEBUG, envir = globalenv())
>>    assign(".SCHNAPPs_DEBUGSAVE", DEBUGSAVE, envir = globalenv())
>> * 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 R/sysdata.rda ... OK
>> * checking installed files from 'inst/doc' ... OK
>> * checking files in 'vignettes' ... OK
>> * checking examples ... NONE
>> * checking for unstated dependencies in 'tests' ... OK
>> * checking tests ...
>> ** running tests for arch 'i386' ... [4s] OK
>>    Running 'testthat.R' [3s]
>> ** running tests for arch 'x64' ... [4s] OK
>>    Running 'testthat.R' [3s]
>> * checking for unstated dependencies in vignettes ... OK
>> * checking package vignettes in 'inst/doc' ... OK
>> * checking re-building of vignette outputs ... [9s] OK
>> * checking PDF version of manual ... OK
>> * DONE
>> Status: 2 NOTEs
>> 
>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
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