[R-sig-Debian] pkg/tests: how to run them with --vanilla

[mat]

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 ...
   Exécution ‘00SetarAndFriends.R’
   Comparaison ‘00SetarAndFriends.Rout’ à ‘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 ...
   Exécution ‘00SetarAndFriends.R’
   Comparaison ‘00SetarAndFriends.Rout’ à ‘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 écrit :
> 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 nécessité le package : zoo
>> | > proc.time()
>> | utilisateur système écoulé
>> | 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 écrit :
>> | > 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 précédente restaurée]
>> | > |>
>> | > |>  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
>>
>