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.dun...@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.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 >> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > >______________________________________________ >R-package-devel@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Sent from my phone. Please excuse my brevity. ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
