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
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