Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread John Fox
Dear Duncan, Further to my last message, and in case it's relevant, with the development version of the Rcmdr package loaded, I get > getAnywhere("data") A single object matching 'data' was found It was found in the following places package:utils namespace:utils with value . . . Best, John

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] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread John Fox
Dear Duncan, On Mon, 13 Jul 2015 20:00:02 -0400 Duncan Murdoch wrote: > On 13/07/2015 7:35 PM, John Fox wrote: > > Dear Duncan, > > > >> -Original Message- > >> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] > >> Sent: July-13-15 7:01 PM > >> To: John Fox; 'peter dalgaard' > >>

Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread Duncan Murdoch
On 13/07/2015 7:35 PM, John Fox wrote: > Dear Duncan, > >> -Original Message- >> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] >> Sent: July-13-15 7:01 PM >> To: John Fox; 'peter dalgaard' >> Cc: r-package-devel@r-project.org >> Subject: Re: [R-pkg-devel] "invalid 'envir' argument

Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread John Fox
Dear Duncan, > -Original Message- > From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] > Sent: July-13-15 7:01 PM > To: John Fox; 'peter dalgaard' > Cc: r-package-devel@r-project.org > Subject: Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel > > It happened in r68597.

Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread Duncan Murdoch
It happened in r68597. In my example, I hadn't imported the data() function from utils; when I did that, it was fixed. Not sure why the error is complaining about the envir argument. Duncan Murdoch On 13/07/2015 6:47 PM, John Fox wrote: > Dear Duncan and Peter, > > I've just arrived at more or

Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread John Fox
Dear Duncan and Peter, I've just arrived at more or less the same thing: foo <- function() data(package="MASS") bar <- function() data(package="MASS", envir=.GlobalEnv) baz <- function() data(package="MASS", envir=globalenv()) all trigger the note when included with the

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] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread Duncan Murdoch
On 13/07/2015 5:23 PM, John Fox wrote: > Dear Peter, > >> -Original Message- >> From: peter dalgaard [mailto:pda...@gmail.com] >> Sent: July-13-15 4:52 PM >> To: John Fox >> Cc: r-package-devel@r-project.org >> Subject: Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel >> >> Y

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

Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread John Fox
Dear Peter, > -Original Message- > From: peter dalgaard [mailto:pda...@gmail.com] > Sent: July-13-15 4:52 PM > To: John Fox > Cc: r-package-devel@r-project.org > Subject: Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel > > Yes, there was a similar note from Alexandra Kuznet

Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread peter dalgaard
Yes, there was a similar note from Alexandra Kuznetsova a couple of days ago. Look unintentional, but it is not easy to spot what triggers it. If someone could cook up a minimal example, or - maybe easier given the relatively short timeframe - bisect their way to the exact svn revision that trig

[R-pkg-devel] "invalid 'envir' argument" note from R-devel

2015-07-13 Thread John Fox
Dear list members, I'm getting a new note from R-devel that I haven't seen before when checking the development version of the Rcmdr package: * checking R code for possible problems ... NOTE readDataFromPackage: Error while checking: invalid 'envir' argument This note doesn't app

[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

Re: [R-pkg-devel] invalid URL status 391

2015-07-13 Thread Gavin Simpson
Note the "(possibly)"; just explain the URL is correct when/if you submitted to CRAN. I think this is may be an issue with the function used to test the URL not being able to follow the redirect. Status codes in the 3xx block relate to redirects but I couldn't find what code 391 means... but the UR

[R-pkg-devel] invalid URL status 391

2015-07-13 Thread Berry Boessenkool
Good evening (or, depending on your time zone, good morning, night or any favorite time of the day), I get the following NOTE with Rdevel 2015-07-12 r68650  CMD check --as-cran: Found the following (possibly) invalid URLs:   URL: http://www.jstor.org/stable/view/2983411     From: man/ci.Rd    

[R-pkg-devel] recommendation: codetoolsBioC

2015-07-13 Thread Kasper Daniel Hansen
With the new NAMESPACE requirements of importing everything in the bundled packages I would like to recommend using writeNamespaceImports from codetoolsBioC. This analyzes your code and produces a NAMESPACE file with all imports. Of course, you might benefit from checking it manually. This pac