R SIG Debian - Jul 2010 - pkg/tests: how to run them with --vanilla

Hello

I recently submitted an update of a package, and received error reports 
from CRAN maintainers concerning the pkg/tests section:
> Next time you update, can you please ensure that the .Rout.save files 
> are generated in English (with LANGUAGE=en set).  R 2.12.x will ensure 
> that the tests are run in English, and it saves a lot of unnecessary 
> chatter if the reference results also are.
>
> As a further point,
>
>> [Sauvegarde de la session pr?c?dente restaur?e]
>
> indicates that they were not generated in a vanilla session, and they 
> should be (as the tests are run with --vanilla --slave).
>
> Brian Ripley 
  I always used to run the .Rout.save files with R CMD BATCH xxx.R So it 
seems I should rather do it with R --vanilla... I tried:
cat xxx.R| R --vanilla --slave > xxx.Rout.save

But this gives files without the ">", and then it gets reported in
the R
CMD check... What would be the good way to do?

Secondly, I always got this error that the R CMD BATCH run in french, 
but the R CMD check in english. I have been told I should change to 
language=EN. But how do I do this in Linux? I just added:
Sys.setlocale("LC_ALL","en_US.UTF8")
Sys.setlocale("LC_CTYPE","en_US.UTF8")
Sys.setlocale("LC_MESSAGES","en_US.UTF8")

in the .Rprofile... it this right?

Thanks!!

Matthieu

On 3 July 2010 at 11:07, mat wrote:
| Hello
| 
| I recently submitted an update of a package, and received error reports 
| from CRAN maintainers concerning the pkg/tests section:
| 
| > Next time you update, can you please ensure that the .Rout.save files 
| > are generated in English (with LANGUAGE=en set).  R 2.12.x will ensure 
| > that the tests are run in English, and it saves a lot of unnecessary 
| > chatter if the reference results also are.
| >
| > As a further point,
| >
| >> [Sauvegarde de la session pr?c?dente restaur?e]
| >
| > indicates that they were not generated in a vanilla session, and they 
| > should be (as the tests are run with --vanilla --slave).
| >
| > Brian Ripley 
|   I always used to run the .Rout.save files with R CMD BATCH xxx.R So it 
| seems I should rather do it with R --vanilla... I tried:
| cat xxx.R| R --vanilla --slave > xxx.Rout.save

See 'R CMD BATCH --help' --- you can pass further options along:

edd at ron:/tmp$ echo "cat(4)" > foo.R
edd at ron:/tmp$ R CMD BATCH --vanilla --slave /tmp/foo.R
edd at ron:/tmp$ cat foo.Rout 
4> proc.time()
   user  system elapsed 
  0.352   0.036   0.373 
edd at ron:/tmp$ R CMD BATCH --vanilla /tmp/foo.R
edd at ron:/tmp$ cat foo.Rout 

R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> cat(4)
4> 
> proc.time()
   user  system elapsed 
   0.34    0.04    0.38 
edd at ron:/tmp$ 

| But this gives files without the ">", and then it gets reported
in the R
| CMD check... What would be the good way to do?
| 
| Secondly, I always got this error that the R CMD BATCH run in french, 
| but the R CMD check in english. I have been told I should change to 
| language=EN. But how do I do this in Linux? I just added:
| Sys.setlocale("LC_ALL","en_US.UTF8")
| Sys.setlocale("LC_CTYPE","en_US.UTF8")
| Sys.setlocale("LC_MESSAGES","en_US.UTF8")
| 
| in the .Rprofile... it this right?

Defaults work for me, so I never changed them. Sorry.

-- 
  Regards, Dirk

Thanks a lot for your answers!

Actually, I am still a little bit confused, as running R CMD BATCH with 
the --vanilla --slave options produces a .Rout.save without the > at 
each code line, and this is then reported in the R CMD check:

checking tests ...
   Ex?cution ?00SetarAndFriends.R?
   Comparaison ?00SetarAndFriends.Rout? ? ?00SetarAndFriends.Rout.save? 
...1,3d0
<
<
< > library(tsDyn)
12,18d8
< >
< > data(zeroyld)
< > dat<-zeroyld

While if I do just R CMD BATCH, I get another diff report, concerning 
the startup message:
checking tests ...
   Ex?cution ?00SetarAndFriends.R?
   Comparaison ?00SetarAndFriends.Rout? ? ?00SetarAndFriends.Rout.save? 
...1a2,19
 > R version 2.11.1 (2010-05-31)
 > Copyright (C) 2010 The R Foundation for Statistical Computing
 > ISBN 3-900051-07-0

So I did not find a way to have a clean R CMD check output... How do you 
do usually? DOn't you have one of those issues?

Thanks a lot!

Matthieu



Le 04. 07. 10 15:00, Prof Brian Ripley a ?crit :
> On Sun, 4 Jul 2010, Dirk Eddelbuettel wrote:
>
>>
>> On 4 July 2010 at 10:36, mat wrote:
>> | Thanks! But I have then a strange problem:
>> | -running R CMD BATCH will read in english
>> | -running R CMD BATCH --vanilla --slave will read in french!
>> |
>> | I guess it comes from the fact that R CMD BATCH reads my .Rprofile
>> | settings but --vanilla --slave not?
>>
>> Yes, and by design as --vanilla means ignore my ~/.R* files.
>>
>> So you must change your language in another place, for example in the 
>> shell
>> in which you are calling R CMD BATCH.  You could just create a
'worker
>> script' that sets those variables and then calls R CMD BATCH.
>
> And as the R-admin manual says and I said, you set the environment 
> variable LANGUAGE to en: this overrides any other settings for the 
> language.  So in any shell
>
> env LANGUAGE=en R CMD BATCH --vanilla --slave foo.R foo.Rout.save
>
> or in bash
>
> LANGUAGE=en R CMD BATCH --vanilla --slave foo.R foo.Rout.save
>
> How to set environment variables is covered in the rw-FAQ, but Linux 
> users are expected to know how to use them!
>
>>
>> Dirk
>>
>> | See:
>> |
>> | mat at cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$ echo
>> | "library(sandwich)" > foo.R
>> | mat at cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$ R CMD BATCH foo.R
>> | mat at cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$ cat foo.Rout
>> |
>> | R version 2.11.1 (2010-05-31)
>> | [...]
>> | [Previously saved workspace restored]
>> |
>> | > library(sandwich)
>> | Loading required package: zoo
>> | >
>> | > proc.time()
>> | user system elapsed
>> | 0.630 0.010 0.632
>> | mat at cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$
>> | mat at cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$ R CMD BATCH
--vanilla
>> | --slave foo.R
>> | mat at cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$ cat foo.Rout
>> | Le chargement a n?cessit? le package : zoo
>> | > proc.time()
>> | utilisateur syst?me ?coul?
>> | 0.38 0.02 0.38
>> |
>> | So it seems I should change the language differently... probably 
>> setting
>> | the global environment variable? I don't know if this is possible
just
>> | within the R CMD BATCH? I read from ?BATCH
>> |
>> | Additional options can be set by the environment variable
>> | ?R_BATCH_OPTIONS?: these come after ?--restore --save
>> | --no-readline? and before any options given on the command line
>> |
>> | But I did not find any example how to run them...
>> |
>> | Thanks!!
>> |
>> | Matthieu
>> |
>> |
>> |
>> | Le 03. 07. 10 23:13, Dirk Eddelbuettel a ?crit :
>> | > On 3 July 2010 at 11:07, mat wrote:
>> | > | Hello
>> | > |
>> | > | I recently submitted an update of a package, and received
error
>> reports
>> | > | from CRAN maintainers concerning the pkg/tests section:
>> | > |
>> | > |>  Next time you update, can you please ensure that the 
>> .Rout.save files
>> | > |>  are generated in English (with LANGUAGE=en set).  R
2.12.x
>> will ensure
>> | > |>  that the tests are run in English, and it saves a lot of 
>> unnecessary
>> | > |>  chatter if the reference results also are.
>> | > |>
>> | > |>  As a further point,
>> | > |>
>> | > |>>  [Sauvegarde de la session pr?c?dente restaur?e]
>> | > |>
>> | > |>  indicates that they were not generated in a vanilla
session,
>> and they
>> | > |>  should be (as the tests are run with --vanilla --slave).
>> | > |>
>> | > |>  Brian Ripley
>> | > |   I always used to run the .Rout.save files with R CMD BATCH 
>> xxx.R So it
>> | > | seems I should rather do it with R --vanilla... I tried:
>> | > | cat xxx.R| R --vanilla --slave>  xxx.Rout.save
>> | >
>> | > See 'R CMD BATCH --help' --- you can pass further
options along:
>> | >
>> | > edd at ron:/tmp$ echo "cat(4)">  foo.R
>> | > edd at ron:/tmp$ R CMD BATCH --vanilla --slave /tmp/foo.R
>> | > edd at ron:/tmp$ cat foo.Rout
>> | > 4>  proc.time()
>> | >     user  system elapsed
>> | >    0.352   0.036   0.373
>> | > edd at ron:/tmp$ R CMD BATCH --vanilla /tmp/foo.R
>> | > edd at ron:/tmp$ cat foo.Rout
>> | >
>> | > R version 2.11.1 (2010-05-31)
>> | > Copyright (C) 2010 The R Foundation for Statistical Computing
>> | > ISBN 3-900051-07-0
>> | >
>> | > R is free software and comes with ABSOLUTELY NO WARRANTY.
>> | > You are welcome to redistribute it under certain conditions.
>> | > Type 'license()' or 'licence()' for distribution
details.
>> | >
>> | >    Natural language support but running in an English locale
>> | >
>> | > R is a collaborative project with many contributors.
>> | > Type 'contributors()' for more information and
>> | > 'citation()' on how to cite R or R packages in
publications.
>> | >
>> | > Type 'demo()' for some demos, 'help()' for
on-line help, or
>> | > 'help.start()' for an HTML browser interface to help.
>> | > Type 'q()' to quit R.
>> | >
>> | >
>> | >> cat(4)
>> | >>
>> | > 4>
>> | >
>> | >> proc.time()
>> | >>
>> | >     user  system elapsed
>> | >     0.34    0.04    0.38
>> | > edd at ron:/tmp$
>> | >
>> | > | But this gives files without the ">", and then it
gets reported
>> in the R
>> | > | CMD check... What would be the good way to do?
>> | > |
>> | > | Secondly, I always got this error that the R CMD BATCH run in 
>> french,
>> | > | but the R CMD check in english. I have been told I should 
>> change to
>> | > | language=EN. But how do I do this in Linux? I just added:
>> | > | Sys.setlocale("LC_ALL","en_US.UTF8")
>> | > | Sys.setlocale("LC_CTYPE","en_US.UTF8")
>> | > | Sys.setlocale("LC_MESSAGES","en_US.UTF8")
>> | > |
>> | > | in the .Rprofile... it this right?
>> | >
>> | > Defaults work for me, so I never changed them. Sorry.
>> | >
>> | >
>> |
>>
>> -- 
>>  Regards, Dirk
>>
>