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

Hi,

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

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

Regarding the export, pkgA, pkgB, and pkgC NAMESPACE files include: 
exportPattern("^[^\\.]").

Sebastien


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.

HTH
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.

    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 ?kiwixposedev?
         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]]