Re: [Rd] Silently loading and Depends: versus NAMESPACE imports

From: Uwe Ligges <ligges_at_statistik.tu-dortmund.de>
Date: Fri, 24 Feb 2012 12:56:37 +0100

On 24.02.2012 07:45, Hervé Pagès wrote:

> On 01/28/2012 08:15 AM, Dirk Eddelbuettel wrote:

>>
>> On 28 January 2012 at 16:52, Uwe Ligges wrote:
>> |
>> |
>> | On 27.01.2012 15:57, Dirk Eddelbuettel wrote:
>> |>
>> |> On 12 January 2012 at 12:12, Hervé Pagès wrote:
>> |> | Hi Dirk,
>> |> |
>> |> | On 01/11/2012 11:42 AM, Dirk Eddelbuettel wrote:
>> |> |>
>> |> |> R CMD check really hates it when my .onLoad() function contains
>> |> |> suppressMessages(library(foo))
>> |> |
>> |> | Note that you can always fool 'R CMD check' by doing something like:
>> |> |
>> |> | sillyname<- library
>> |> | suppressMessages(sillyname("foo"))
>> |> |
>> |> | Also isn't suppressPackageStartupMessages() more appropriate?
>> |> |
>> |> |>
>> |> |> However, _and for non-public packages not going to CRAN_ I
>> prefer doing this
>> |> |> over using explicit Depends or import statements in the
>> NAMESPACE file as the
>> |> |> latter do not give me an ability to make the loading less
>> verbose. With the
>> |> |> R universe of packages being as vast as at is, a simple
>> (non-public) package
>> |> |> I have loads about five or six other packages explicitly, each
>> of which loads
>> |> |> even more. The net result is totally intimidating _sixty lines
>> full_ of
>> |> |> verbose noise that is meaningful to me as an R programmer, but
>> not for the
>> |> |> colleagues expected to use the packages. It looks rather
>> uninviting, frankly.
>> |> |>
>> |> |> How do I use imports via NAMESPACE, and yet keep the noise level
>> down to zero?
>> |> |
>> |> | If you only need to import foo (i.e. and actually don't need to
>> attach
>> |> | it to the search path) then putting foo in Imports and using import
>> |> | statements in NAMESPACE will keep the noise level down to zero.
>> |>
>> |> I don't think so.
>> |>
>> |> I have an internal package, call it fooUtils, that (among other
>> things) needs
>> |> to figure at startup whether it runs on this or that OS.
>> |>
>> |> So that package fooUtils does
>> |>
>> |> .onLoad<- function(libname, pkgname) {
>> |>
>> |> if (.Platform$OS.type == "windows") {
>> |> packageStartupMessage("Running on Windows")
>> |> # [... more stuff here ... ]
>> |> } else if (.Platform$OS.type == "unix") {
>> |> packageStartupMessage("Running on Linux")
>> |> # [... more stuff here ... ]
>> |> } else {
>> |> warning("Platform ", .Platform$OS.type, " not recognised")
>> |> drives<- NULL
>> |> }
>> |>
>> |> # ....
>> |>
>> |> }
>> |
>> | Are you sure you want the messages in .onLoad rather than .onAttach?
>
> Yep. Since in your original post you didn't say that the package
> you import had its startup message in the wrong place (.onLoad),
> I assumed it was in the right place (.onAttach).
>

>>
>> Thanks Uwe -- looks like that was exactly the hint I needed.
>>
>> By splitting the task across onLoad and onAttach I seem to be able to get
>> want I need even if the package is "tickled" via NAMESPACE's importFrom.
>
> Are you saying you have some control over the package you import so you
> could fix it?

Yes, Dirk had control but did not mention in that message. At least, at the time of writing, I was able to guess the real name of the packages Dirk was referring to given I had seen other communication off list.

Uwe

>
> H.
>

>>
>> Dirk
>>
>> | See ?.onLoad and its "Good practice" section:
>> |
>> | "Loading a namespace should where possible be silent, with startup
>> | messages given by .onAttach. These messages (and any essential ones
>> from
>> | .onLoad) should use packageStartupMessage so they can be silenced where
>> | they would be a distraction."
>> |
>> | Best,
>> | Uwe
>> |
>> |
>> |
>> |>
>> |> and contrary to your claim, this is not silent as soon as I do
>> |>
>> |>
>> |> importFrom(fooUtils, someThing)
>> |>
>> |>
>> |> the messages above pop up. While I can suppress them for 'normal'
>> loads via
>> |>
>> |> suppressMessages(library(fooUtils))
>> |>
>> |> or
>> |>
>> |> suppressPackageStartupMessages(library(fooUtils))
>> |>
>> |>
>> |> I cannot suppress them via NAMESPACE imports.
>> |>
>> |> Dirk
>> |>
>> |> | So I guess your question is: how do we suppress package startup
>> messages
>> |> | for packages listed in Depends?
>> |> |
>> |> | Cheers,
>> |> | H.
>> |> |
>> |> |>
>> |> |> Dirk
>> |> |>
>> |> |
>> |> |
>> |> | --
>> |> | Hervé Pagès
>> |> |
>> |> | Program in Computational Biology
>> |> | Division of Public Health Sciences
>> |> | Fred Hutchinson Cancer Research Center
>> |> | 1100 Fairview Ave. N, M1-B514
>> |> | P.O. Box 19024
>> |> | Seattle, WA 98109-1024
>> |> |
>> |> | E-mail: hpages_at_fhcrc.org
>> |> | Phone: (206) 667-5791
>> |> | Fax: (206) 667-1319
>> |>
>>
>
>

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