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

2015-07-21 Thread Duncan Murdoch
On 21/07/2015 2:08 PM, Jennifer Bryan wrote: > Sebastien: thanks for sharing the definitive solution! > > To the people on this list with the power to edit "Writing R Extensions": > > When a discussion here suggests a specific improvement, what is the best way > for the community to propose a re

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

2015-07-21 Thread Jennifer Bryan
Sebastien: thanks for sharing the definitive solution! To the people on this list with the power to edit "Writing R Extensions": When a discussion here suggests a specific improvement, what is the best way for the community to propose a revision? So that knowledge gets transferred from this lis

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

2015-07-21 Thread sbihorel
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[latti

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

2015-07-20 Thread Jennifer Bryan
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: \

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

2015-07-20 Thread Hadley Wickham
On Mon, Jul 13, 2015 at 5:38 PM, Duncan Murdoch wrote: > On 13/07/2015 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

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

2015-07-20 Thread sbihorel
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_functio

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

2015-07-15 Thread Dirk Eddelbuettel
On 15 July 2015 at 09:07, sbihorel wrote: | 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? Yes. | However, I thought that imports would be rec

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

2015-07-15 Thread sbihorel
Hi Duncan, So if the NAMESPACE of a package contains exportPattern("^[^\\.]"), does this mean that only the functions created within the package are exported and that the functions that were imported are not exported? On 7/15/2015 9:24 AM, Duncan Murdoch wrote: On 15/07/2015 9:07 AM, sbihore

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

2015-07-15 Thread Duncan Murdoch
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 recur

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

2015-07-15 Thread sbihorel
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 depe

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

2015-07-13 Thread sbihorel
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

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

2015-07-13 Thread Duncan Murdoch
On 13/07/2015 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(){.

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

2015-07-13 Thread Seth Wenchel
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 NAMESP

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

2015-07-13 Thread sbihorel
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