[R-pkg-devel] note

[Duncan Murdoch]

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
> 
> 
> 
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> 
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