[R-pkg-devel] data.frame compression and no visible global function

[Iñaki Ucar]

On Tue, 14 May 2019 at 12:08, Christian Peikert
<christian.peikert using t-online.de> wrote:
>
> Dear all,
> I have tried to upload my R-package to CRAN but this package was sadly
> reject due to a Warning and a Note. I already know this warning/note but
> I could find out to solve this.
>
> * checking data for ASCII and uncompressed saves ... WARNING
>    Warning: large data files saved inefficiently:
>          size         ASCII     compress
>    cellr_morgenstern_et_al_2017.rda       544Kb    TRUE        xz
>    mcp_reimann_et_al_2017.rda               154Kb    TRUE        xz
>
> These two data frames are required example datasets. I have used the
> following save function:
>
> save(cellr_morgenstern_et_al_2017,
> file="cellr_morgenstern_et_al_2017.rda",compress='xz',
> compression_level=9 ,ascii = TRUE)
> save(mcp_reimann_et_al_2017,
> file="mcp_reimann_et_al_2017.rda",compress='xz', compression_level=9
> ,ascii = TRUE)

Try tools::resaveRdaFiles instead.

> * checking R code for possible problems ... [40s] NOTE
> runExample03: no visible global function definition for 'shinyClustPro'
>
> shinyApp is a function defined in a source R file which is loaded by the
> source function. Because this is an example function, it should not be a
> “visible” function in the package.
>
> appDir <- system.file("shiny-examples", "03", package = "clustpro")
> moduleDir <- system.file("shiny_module", package = "clustpro")
> source(file.path(moduleDir,"module_shiny_clustpro.R"))
> ….
> …..
> shinyClustPro(df_proteomics, data_columns = data_columns, info_columns =
> info_columns)

You can add a simple shinyClustPro <- NULL before sourcing the file
(and therefore, that variable is rewritten). If showing that line
annoys you, put it inside a \dontshow{} block (but not sure if this
could raise another NOTE).

Iñaki