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

sbihorel Sebastien.Bihorel at cognigencorp.com
Tue Jul 14 03:42:55 CEST 2015


Sorry about the table. It looked good when displayed using a fixed width 
font. Let me try to linearize it:

  * pkgA
          + Depends: methods, lattice, grid, gam
          + Imports: Hmisc, survival
      o NAMESPACE:
          + import: lattice, grid, gam, methods
          + importFrom: Hmisc (one function)
  * pkgB
          + Depends: pkgA
          + Imports: <nothing>
      o NAMESPACE:
          + import: pkgA
          + importFrom: <nothing
  * pkgC
          + Depends: methods, pkgB
          + Imports: <nothing>
      o NAMESPACE:
          + import: methods, pkgB
          + importFrom: <nothing

Regarding the export, pkgA, pkgB, and pkgC NAMESPACE files include: 


On 7/13/2015 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.
> Seth
> On Monday, July 13, 2015, sbihorel <Sebastien.Bihorel at cognigencorp.com 
> <mailto: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.
>                 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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