[R-pkg-devel] Help needed to setting custom packages for R 3.1.2
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 import(Hmisc) 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 Hmisc::latex. 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 ?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
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