R help - Aug 2004 - R CMD check testing environment

I can't tell from the docs  ("Writing R Extensions" 1.9.1) exactly
what
environment the tests, examples, and vignettes that R CMD check tries to
run are in.

In particular:
1) how do I get the package loaded?
2) how do I access data in the data/ directory?
3) where is the material in the other directories?  (e.g., has inst/
material been installed?  where?)

Apparently (section 1.3) stuff in demo/ is not checked, which seems odd.

By inspecting some other packages, it seems the answer to 1) is that the
package is already loaded, so I don't need to say library(...).  In
particular, I don't need to figure out what lib.loc is.

I have some C code as part of the package, so that (well the .so file)
needs to be loaded too.

2) Others seem to just say data(..), but this doesn't work for me.
I created the data with
save(gold, e2, q2, file="mspath/data/inputs", compress=TRUE)
and later renamed the file to inputs.RData.  (check didn't think the
file counted without the extension).

I have tried to access it in my test script (under tests/) with both
load and data (e.g., data("inputs"), data("inputs.RData"),
data(inputs)).  I get
> data(inputs)
Warning message: 
Data set 'inputs' not found in: data(inputs) 

For that matter, my assumed answer to 1) doesn't seem to be working out,
because when I try to access one of my functions it tells me it can't
find it.  The function name is the same as the package name.

Perhaps the problem is I have inferred answers from \example{}, and the
story for tests/ is different.

Although I'm currently focussed on running a script in tests/, I'd like
to know what the story is for \examples in documentation or vignettes.

Thanks.

P.S. Is there a typical way to produce the .Rout.save file used in
tests/?  What I'm doing is a slightly awkward 2-step process.
-- 
Ross Boylan                                      wk:  (415) 502-4031
530 Parnassus Avenue (Library) rm 115-4          ross at biostat.ucsf.edu
Dept of Epidemiology and Biostatistics           fax: (415) 476-9856
University of California, San Francisco
San Francisco, CA 94143-0840                     hm:  (415) 550-1062

Ross Boylan wrote:
> I can't tell from the docs  ("Writing R Extensions" 1.9.1)
exactly what
> environment the tests, examples, and vignettes that R CMD check tries to
> run are in.
> 
> In particular:
> 1) how do I get the package loaded?
> 2) how do I access data in the data/ directory?
> 3) where is the material in the other directories?  (e.g., has inst/
> material been installed?  where?)
> 
> Apparently (section 1.3) stuff in demo/ is not checked, which seems odd.
> 
> By inspecting some other packages, it seems the answer to 1) is that the
> package is already loaded, so I don't need to say library(...).  In
> particular, I don't need to figure out what lib.loc is.
> 
> I have some C code as part of the package, so that (well the .so file)
> needs to be loaded too.
Yes. You don't need library() in the the help pages' exmaples, but you 
need it in tests.

> 2) Others seem to just say data(..), but this doesn't work for me.
> I created the data with
> save(gold, e2, q2, file="mspath/data/inputs", compress=TRUE)
> and later renamed the file to inputs.RData.  (check didn't think the
> file counted without the extension).
Indeed, the manuals tells us that saved images have to be called either
*.RData (note the capitalization) or *.rda.

> I have tried to access it in my test script (under tests/) with both
> load and data (e.g., data("inputs"),
data("inputs.RData"),
> data(inputs)).  I get
> 
>>data(inputs)
> 
> Warning message: 
> Data set 'inputs' not found in: data(inputs) 
Works for me as "Mytests.R" in "Mypackage":

  library(Mypackage)
  data(MydataInMypackage)
  print(MydataInMypackage)


> For that matter, my assumed answer to 1) doesn't seem to be working
out,
> because when I try to access one of my functions it tells me it can't
> find it.  The function name is the same as the package name.
> 
> Perhaps the problem is I have inferred answers from \example{}, and the
> story for tests/ is different.
Right, see above.

> Although I'm currently focussed on running a script in tests/, I'd
like
> to know what the story is for \examples in documentation or vignettes.
You won't need library() in the examples ...

> Thanks.
> 
> P.S. Is there a typical way to produce the .Rout.save file used in
> tests/?  What I'm doing is a slightly awkward 2-step process.

Running R CMD check once, looking whether the Rout looks fine (this 
should be the step that takes most of the time, and R can't do it for 
you), rename the file it, finished.


Uwe Ligges