Good morning Gildas,
After moving  my <command R ....    outside of the <stdio />  block below -- this fixed worked
FYI   the Rscript  in the same tool dir has issues with reading a dataset from the directory.   Seems like permissions but isn't.
Thank you
Bob Brown
----- Original Message -----
From: Gildas Le Corguillé <lecorguille@sb-roscoff.fr>
To: rbrown1422@comcast.net
Cc: John Chilton <jmchilton@gmail.com>, galaxy-dev@lists.galaxyproject.org
Sent: Fri, 05 Feb 2016 08:27:07 -0000 (UTC)
Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size
Hi,
Because R always return blabla in the standard error output (stderr), by default Galaxy thinks that there is a problem. You need this following lines in your wrapper xml : 
<stdio>
      <exit_code range="1:" level="fatal" />
</stdio>
With that, Galaxy will use the code error (echo  $?) instead of the stderr to detect an error.
Another thing, you can use 
<command interpreter="Rscript">Foo.R $inputFile1 ..... </command>
If your script is in the same folder as your xml

Gildas
-----------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
------------------------------------------------------------------


Le 4 févr. 2016 à 21:25, rbrown1422@comcast.net a écrit :

John,
Thanks for the great info.  I got the R to work not the Rscript.
However, my data files return RED even though there is data in them
I am still getting R warning but no errors
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C"
Is there a flag I can set to igrore these warning and have Galaxy return GREEN?
thanks.
bob
----- Original Message -----
From: John Chilton <jmchilton@gmail.com>
To: rbrown1422@comcast.net, galaxy-dev@lists.galaxyproject.org
Sent: Thu, 04 Feb 2016 20:11:53 -0000 (UTC)
Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size
Forgot to cc the mailing list.
-John
On Thu, Feb 4, 2016 at 8:11 PM, John Chilton <jmchilton@gmail.com> wrote:
> Are you sure about the --file when calling Rscript?
>
> Here is the usage for my local version which does not expect an
> argument named --file:
>
> Usage: /path/to/Rscript [--options] [-e expr] file [args]
>
> --options accepted are
> --help Print usage and exit
> --version Print version and exit
> --verbose Print information on progress
> --default-packages=list
> Where 'list' is a comma-separated set
> of package names, or 'NULL'
> or options to R, in addition to --slave --no-restore, such as
> --save Do save workspace at the end of the session
> --no-environ Don't read the site and user environment files
> --no-site-file Don't read the site-wide Rprofile
> --no-init-file Don't read the user R profile
> --restore Do restore previously saved objects at startup
> --vanilla Combine --no-save, --no-restore, --no-site-file
> --no-init-file and --no-environ
>
> 'file' may contain spaces but not shell metacharacters
>
> Also, instead of using $GALAXY_ROOT - I would use $__tool_directory__
> if the tool XML file is located next to the RScript, like this:
>
> $__tool_directory__/Foo.R
>
> -John
>
>
> On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1422@comcast.net> wrote:
>> Good morning team,
>> I have an Rscript tool that is trying to read a file I uploaded into the
>> history beforehand. Galaxy is running with the same user and privileges as
>> the dataset directory.
>> <command>Rscript --slave --vanilla
>> --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R --args $inputFile1 ..... </command>
>> Why would this be?
>>
>> Error in file(file, "rt") : cannot open the connection
>> Calls: performDataOrdering -> read.table -> file
>> In addition: Warning message:
>> In file(file, "rt") :
>> cannot open file
>> '--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such
>> file or directory
>> Execution halted
>>
>> When I try to run as R versus Rscript - I get a syntax error about
>> unexpected '(' on function call that works fine in R window.
>>
>> Thanks
>> Bob
>>
>>
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