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

Duncan Murdoch murdoch.duncan at gmail.com
Wed Jul 15 15:24:01 CEST 2015

On 15/07/2015 9:07 AM, sbihorel wrote:
> Hi,
> I saw a few recent posts on topics related to mine (eg
> https://stat.ethz.ch/pipermail/r-package-devel/2015q3/000238.html). It
> looks like I need to import more packages in my NAMESPACE, correct?
> However, I thought that imports would be recursive, ie imports would
> also get the info from dependent packages.

I haven't been following this thread, but the 2nd para above makes it
sound as though an explanation of the NAMESPACE directives would be helpful.

If you say

 importFrom(Hmisc, latex)

it acts as though you have made a copy of the Hmisc::latex function
within your package environment.  (It isn't exported, unless you ask to
export it.)

If you say


it acts as though you have made copies of every exported function from
Hmisc within your package environment.  This is why we recommend
importing only the functions you need; otherwise your package
environment gets bloated.

No recursive copies are made, unless Hmisc happens to import something
and re-exports it.

When I say "acts as though", I don't mean it literally makes copies; it
implements this in a more efficient way, basically only copying pointers
to those functions -- but from a user point of view, you shouldn't be
able to tell the difference, since you're not allowed to modify

Duncan Murdoch

> Sebastien
> On 7/13/2015 9:42 PM, sbihorel wrote:
>> 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 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]]
>>>     ______________________________________________
>>>     R-package-devel at r-project.org <javascript:;> mailing list
>>>     https://stat.ethz.ch/mailman/listinfo/r-package-devel

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