Re: [Open-ms-general] InternalRecalibration in KNIME, Rscript issue

[Julianus P. <pfe...@in...>]

Dear David,

unfortunately the 2.0.1 binaries have not yet completely been tested with KNIME. This is definitely an issue that was introduced since 2.0.0 and that we will address in our next full binary release.

Until then, if you need to use the 2.0.1 release, you can try to manually edit the path that our binaries will have access to (which is a different one from the systemwide path).
It is usually specified in
C:\Program Files (x86)\Knime\plugins\de.openms.win32.$arch.$version\payload\binaries.ini 
(or similar. I do not have a Windows machine with KNIME at hand).
Add the path to your RScript executable to the second entry (i.e. PATH=…) separated with a colon (:). You do not need to use the $ROOT variable but start with your drive letter (e.g. C:\ )

Let us know if this solves it.

Kind regards,
Julianus

> Am 22 Jul 2016 um 15:54 schrieb David Potesil <dav...@ce...>:
> 
> Dear all,
> 
> InternalCalibration node (2.0.1) in KNIME (3.2.0) on Windows returns me this error message (I removed log part preceding info about running R script):
> 
> ERROR InternalCalibration  0:98       .... Running R script 'C:/Program Files/KNIME/plugins/de.openms.win32.x86_64_2.0.1.201606281051/payload/share/OpenMS/SCRIPTS/InternalCalibration_Models.R' ...InternalCalibration took 53.00 s (wall), 01:20 m (CPU), 22.46 s (system), 58.14 s (user).]
> ERROR InternalCalibration  0:98       Failing process stderr: [ Could not find 'Rscript' executable. Make sure it's in your system path and try again., , Calibration failed. See error message above!]
> ERROR InternalCalibration  0:98       Execute failed: Failed to execute node InternalCalibration
> 
> 
> I have R installed within KNIME and tried to install it also independently. rscript command works and if I run this command "rscript 'C:/Program Files/KNIME/plugins/de.openms.win32.x86_64_2.0.1.201606281051/payload/share/OpenMS/SCRIPTS/InternalCalibration_Models.R'" it seems to be working and the output is:
> 
> Loading required package: methods
> Reading file 'NA' to plot model parameters ...Error in file(file, "rt") : cannot
> open the connection
> Calls: read.csv -> read.table -> file
> In addition: Warning message:
> In file(file, "rt") : cannot open file 'NA': No such file or directory
> Execution halted
> 
> Could anyone please give me info how should I set R correctly to be recognized e.g. by InternalCalibration node correctly? Or is the problem actually elsewhere?
> 
> Thanks a lot in advance for any hint.
> 
> Best regards,
> 
> David
> 
> -- 
> Mgr. David Potesil, PhD.
> Proteomics Core Facility and Research Group Proteomics
> CEITEC-MU
> Masaryk University
> Kamenice 5, A26
> CZ-625 00
> Brno, Czech Republic
> phone: +420 54949 8426
> fax: +420 54949 2640
> 
> 
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