[R-pkg-devel] note

[Bernd JAGLA]

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.


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...


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...


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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