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.
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.biho...@cognigencorp.com
>> <mailto:sebastien.biho...@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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>>
>
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