On Jul 21, 2015, at 5:59 AM, sbihorel <Sebastien.Bihorel at cognigencorp.com> wrote:
Hi Jennifer,
Following your suggestions and after a couple of trial-and-error steps, I believe the syntax is the following:
\code{\link[name_of_package:name_of_Rd_file]{alias_or_text}}
For instance, to link to panel.abline or strip.custom from the lattice package, I used:
\code{\link[lattice:panel.functions]{panel.abline}}
\code{\link[lattice:strip.default]{panel.custom}}
Using this notation I was able to make all warnings disappear upon installation of my package.
Typically, you can extract the name of the Rd file from the ? help page (upper left corner info). But this is not 100% reliable if the maintainer of the package is not consistent in the way (s)he documents the package.
Thanks a lot for your help.
Sebastien
On 7/20/2015 5:45 PM, Jennifer Bryan wrote:
Hi Sebastien,
This note about Rd warnings reminded me that I recently had the same problem. So I recreated it and, I think, have found a solution.
I will explain in my specific example to be clear.
I need to link to the docs for the Token2.0 class from the httr package. First thing you try:
\code{\link[httr]{Token2.0}}
but then you get the warnings you describe upon installation. As in your case, the Token2.0 class doesn?t have it?s own .Rd file but is, rather, documented in the topic titled ?Token-class?.
Next thing you try:
\code{\link[httr]{Token-class}}
which works, but I don?t like this display text ? it doesn?t really make sense in the context of *my* documentation.
Finally you do this:
\code{\link[=Token-class]{Token2.0}}
to link to the correct topic but get the desired display text. However, I am no longer specifying that this topic is from the httr package, but it seems to work.
Maybe someone else can weigh in with more insight about the need / desirability of specifying the associated package.
? Jenny
On Jul 20, 2015, at 2:05 PM, sbihorel <Sebastien.Bihorel at cognigencorp.com> wrote:
Hi,
Thanks to your suggestions and those of other responders, I was able to get rid of the warning messages returned during R CMD check.
However I am still confused by the .Rd file-related warnings I get when we install the packages. For instance:
Rd warning: /tmp/some/path/man/pkgC_function_009.Rd:21: missing file link "panel.abline"
I typed: \code{\link[lattice]{panel.abline}} on line 21 for the Rd file.
My NAMESPACE file includes:
importFrom(lattice,panel.abline)
Surprisingly, other cross-references to lattice functions also imported using importFrom do not generate warning upon installation.
When I consider the full list of function links that generate warnings, it looks like all of them are associated with alias rather than name tags in the target .Rd file (for instance, panel.abline is documented in a .Rd file with \name{panel.functions}).
The CRAN manual is not clear on this point. Is there a specific syntax to use to document this types of links?
Thank you again for your time
Sebastien
On 7/15/2015 9:24 AM, Duncan Murdoch wrote:
On 15/07/2015 9:07 AM, sbihorel wrote:
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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