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:
|
| m...@cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$ echo
| "library(sandwich)" > foo.R
| m...@cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$ R CMD BATCH foo.R
| m...@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
| m...@cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$
| m...@cunix:~/Dropbox/Documents/tsDyn/tsDyn/tests$ R CMD BATCH --vanilla
| --slave foo.R
| m...@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:
| >
| > e...@ron:/tmp$ echo "cat(4)"> foo.R
| > e...@ron:/tmp$ R CMD BATCH --vanilla --slave /tmp/foo.R
| > e...@ron:/tmp$ cat foo.Rout
| > 4> proc.time()
| > user system elapsed
| > 0.352 0.036 0.373
| > e...@ron:/tmp$ R CMD BATCH --vanilla /tmp/foo.R
| > e...@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
| > e...@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
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