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pkg/tests: how to run them with --vanilla

5 messages · Matthieu Stigler, Dirk Eddelbuettel, Chirag Anand

Original
Matthieu Stigler
# 
Hello

I recently submitted an update of a package, and received error reports 
from CRAN maintainers concerning the pkg/tests section:
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
Dirk Eddelbuettel
#
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.
4>
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.
Matthieu Stigler
# 
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?

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 :
Dirk Eddelbuettel
#
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.

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.
| >
| >    
|