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.ja...@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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