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

[Duncan Murdoch]

On 13/07/2015 5:36 PM, Seth Wenchel wrote:
> 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.

That's very dangerous advice.  roxygen stomps on all kinds of things
besides the things you want it to touch.

Duncan Murdoch
> 
> 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
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
> 
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