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 <jmchil...@gmail.com>To:
rbrown1...@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 <jmchil...@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:>>
$__tool_directory__/Foo.R>> -John>>> On Thu, Feb 4, 2016 at 7:05 PM,
<rbrown1...@comcast.net> wrote:>> Good morning team,>> I have an Rscript tool
that is trying to read a file I uploaded into the>> history beforehand. Galaxy
is running with the same user and privileges as>> the dataset directory.>>
<command>Rscript --slave --vanilla>> --file=$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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