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.comTo: rbrown1422@comcast.net, galaxy-dev@lists.galaxyproject.orgSent: 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>>>>>> ___________________________________________________________>> Please keep all replies on the list by using "reply all">> in your mail client. To manage your subscriptions to this>> and other Galaxy lists, please use the interface at:>> https://lists.galaxyproject.org/%3E%3E%3E%3E To search Galaxy mailing lists use the unified search at:>> http://galaxyproject.org/search/mailinglists/