[R-pkg-devel] Help needed to setting custom packages for R 3.1.2

[Seth Wenchel]

Are you exporting the functions from pkgB and pkgC? It's hard to tell from
your table below. The easiest way is to add a comment before each of the
functions in pkgB and pkgC that you want to expose to the users.

#' @export
foo <- function(){...}

Then run roxygen::roxygenise() to build the NAMESPACE file.

HTH
Seth

On Monday, July 13, 2015, sbihorel <Sebastien.Bihorel at cognigencorp.com>
wrote:

> Hi,
>
> My group has recently upgraded from a fairly old R version (2.12) to the
> R version 3.1.2. In parallel to this upgrade, I am updating our custom
> packages to add functionality and also make them compliant to the
> requirements of the new version of R. I would like to ask your help with
> respect to warning messages I get when I check and install the packages.
> I read the latest version of the manual on writing R extensions, try to
> apply the recommendations, but somehow I am not getting things right.
> Hopefully, with your suggestions, I could setup my package correctly to
> make these messages stop.
>
> I apologize but, for confidentiality purpose, I will have to partially
> anonymize the information.
>
> So here is the situation: we have 2 custom packages (let's call them
> pkgB and pkgC). The pkgB package depends on a 3rd package (let's call it
> pkgA) that is available on CRAN. The pkgC package depends on pkgB, make
> new function available,  and "overwrites" some of the functions
> distributed as part of pkgA. The following table summarizes the content
> of the DESCRIPTION and NAMESPACE files of each of these packages.
>
> package    DESCRIPTION NAMESPACE
>             Depends                       Imports
> import                         importFrom
> pkgA       methods, lattice, grid, gam   Hmisc, survival lattice, grid,
> gam, methods    Hmisc
> pkgB       pkgA pkgA
> pkgC       methods, pkgB methods, pkgB
>
> I do not get any warning when I build, check or install pkgB in our
> linux openSuse environment.
>
> After successful building pkgC, I run R CMD check on my built for pkgC
> but I get a ton of messages under the "checking R code for possible
> problems" section. These notes are related to actual calls to pkgA
> functions (or to one of the function provided by its dependencies). Here
> is a subset for illustration and hopefully information.
>
> * checking R code for possible problems: NOTE
> pkgC_function_001: no visible global function definition
> for"pkgA_function_AAA"
> pkgC_function_001: no visible global function definition
> for"pkgA_function_AAB"
> ...
> pkgC_function_010: no visible global function definition for"xyplot"
> pkgC_function_010: no visible global function definition for"panel.xyplot"
> pkgC_function_010: no visible global function definition for"panel.abline"
> pkgC_function_010: no visible global function definition for"grid.polygon"
> pkgC_function_010: no visible global function definition for"gpar"
> ...
>
> Now when I try to install the pkgC_0.0.1.tar.gz package, I get the
> following warnings about the content of my documentation Rd files. The
> Rd files of pkgC includes links to lattice, grid, or pkgA functions.
>
> *** installing help indices
>    converting help for package âkiwixposedevâ
>      finding HTML links ... done
> pkgC_function_001                    html
>      pkgC_function_002                    html
> ...
> Rd warning: /tmp/some/path/man/pkgC_function_009.Rd:21: missing file
> link "panel.abline"
> ...
> Rd warning: /tmp/some/path/man/pkgC_function_015.Rd:64: missing file
> link "pkA_function_AAC"
> ...
>
> I think I need to somehow modify the content of the DESCRIPTION and
> NAMESPACE files for pkgC... but adding various combinations of pkA and
> its dependencies gave me others errors about redundancies and multiple
> loading of the same packages. So in short, I am kind of lost with the
> new requirements of R 3.1.2 and would greatly appreciate any help or
> suggestions
>
> Thank you in advance for your time.
>
> Sebastien Bihorel
>
>
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>
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