R help - Nov 2004 - Creating .Rout.save files for package subdirectory "tests"

Hi,

I added the "tests" subdirectory and a test file (say
"myTest.R") to our
"systemfit" package. Up to now I create the
"myTest.Rout.save" file with 
> R CMD BATCH --vanilla myTest.R myTest.Rout.save
However, "R CMD check" reports two differences between
myTest.Rout.save and
the output of myTest.R:
a) myTest.Rout.save contains following extra line at the beginning of the 
file:
> invisible(options(echo = TRUE))
b) myTest.Rout.save contains the following 2 extra lines at the very end of 
the file:
> proc.time()
[1] 1.80 0.07 2.00 0.01 0.00

Everytime I change myTest.R and create a new myTest.R.save file I have to 
delete these 3 lines by hand. I could do this e.g. by a script using
"sed",
but I wonder if I can start "R CMD BATCH" with an option that
suppresses any
commands that are not in the input file, i.e. "invisible(options(echo = 
TRUE))" and "proc.time()".
Or what is the easiest way to create .Rout.save files?
(I am using R 2.0.0 on a i686 PC with SuSE Linux 9.0)

Thanks,
Arne

-- 
Arne Henningsen
Department of Agricultural Economics
University of Kiel
Olshausenstr. 40
D-24098 Kiel (Germany)
Tel: +49-431-880 4445
Fax: +49-431-880 1397
ahenningsen at agric-econ.uni-kiel.de
http://www.uni-kiel.de/agrarpol/ahenningsen/

>>>>> "Arne" == Arne Henningsen <ahenningsen at
email.uni-kiel.de>
>>>>>     on Fri, 5 Nov 2004 11:56:02 +0100 writes:
    Arne> Hi, I added the "tests" subdirectory and a test file
    Arne> (say "myTest.R") to our "systemfit" package. Up
to now
    Arne> I create the "myTest.Rout.save" file with
    >> R CMD BATCH --vanilla myTest.R myTest.Rout.save

that explains everything.  
Why do you do so?

Instead: 

1) Start with no '.Rout.save'

2) R CMD check  <pkg>
   will produce one in  <pkg>.Rcheck/tests/myTest.Rout
   Copy it to the package source, i.e. typically

   cp <pkg>.Rcheck/tests/myTest.Rout <pkg>/tests/myTest.Rout.save

3) R CMD check  <pkg>  
   now *will* do the comparison and give no difference hopefully

Martin Maechler, ETH Zurich


    Arne> However, "R CMD check" reports two differences between
    Arne> myTest.Rout.save and the output of myTest.R: a)
    Arne> myTest.Rout.save contains following extra line at the
    Arne> beginning of the file:
    >> invisible(options(echo = TRUE))
    Arne> b) myTest.Rout.save contains the following 2 extra
    Arne> lines at the very end of the file:
    >> proc.time()
    Arne> [1] 1.80 0.07 2.00 0.01 0.00

    Arne> Everytime I change myTest.R and create a new
    Arne> myTest.R.save file I have to delete these 3 lines by
    Arne> hand. I could do this e.g. by a script using "sed",
    Arne> but I wonder if I can start "R CMD BATCH" with an
    Arne> option that suppresses any commands that are not in
    Arne> the input file, i.e. "invisible(options(echo = TRUE))"
    Arne> and "proc.time()".  Or what is the easiest way to
    Arne> create .Rout.save files?  (I am using R 2.0.0 on a
    Arne> i686 PC with SuSE Linux 9.0)

    Arne> Thanks, Arne

On Fri, 5 Nov 2004, Arne Henningsen wrote:
> I added the "tests" subdirectory and a test file (say
"myTest.R") to our
> "systemfit" package. Up to now I create the
"myTest.Rout.save" file with
> > R CMD BATCH --vanilla myTest.R myTest.Rout.save
> 
> However, "R CMD check" reports two differences between
myTest.Rout.save and
> the output of myTest.R:
> a) myTest.Rout.save contains following extra line at the beginning of the 
> file:
> > invisible(options(echo = TRUE))
> b) myTest.Rout.save contains the following 2 extra lines at the very end of
> the file:
> > proc.time()
> [1] 1.80 0.07 2.00 0.01 0.00
> 
> Everytime I change myTest.R and create a new myTest.R.save file I have to 
> delete these 3 lines by hand. I could do this e.g. by a script using
"sed",
> but I wonder if I can start "R CMD BATCH" with an option that
suppresses any
> commands that are not in the input file, i.e. "invisible(options(echo
=
> TRUE))" and "proc.time()".
This is not what R CMD BATCH is intended for, so on such option exists.
> Or what is the easiest way to create .Rout.save files?
> (I am using R 2.0.0 on a i686 PC with SuSE Linux 9.0)
1) Run R CMD check and copy myTest.Rout[.fail] to 
   pkg-name/tests/myTest.Rout.save.

2) R --vanilla < myTest.R > myTest.Rout.save 2>&1 if you use sh.
   R --vanilla < myTest.R >&! myTest.Rout.save    if you use csh

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595