Dear support! We strictly followed the instructions given at "[Mzmine-devel] Configuring MZmine to use R (Baseline correction requires R but it couldn't be loaded (Could not start R. Please check if R is installed and path to the libraries is set properly in the startMZmine script.)". However, the application still fails to process chromatogram deconvolution with the wavelets (XCMS) Algorithm. The error reads "XCMS requires R but it couldn't be loaded"
Please find below the output of our environment.
Could you please comment on what is wrong with our setup.
Thank you very much for your time and effort!
Best regards,
Florian
Output
> .libPaths()
[1] "C:/Users/florian.schroeder.TARGENOMIX/Documents/R/R-3.1.3/library"
> packageDescription("xcms")
Package: xcms
Version: 1.42.0
Date: 2014-10-11
Title: LC/MS and GC/MS Data Analysis
Author: Colin A. Smith <[email protected]>, Ralf Tautenhahn
<[email protected]>, Steffen Neumann <[email protected]>, Paul Benton
<[email protected]>, Christopher Conley
<[email protected]>
Maintainer: Ralf Tautenhahn <[email protected]>
Depends: R (>= 2.14.0), methods, mzR (>= 1.1.6), BiocGenerics, Biobase
Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>= 1.5.2),
RANN, RUnit
Enhances: Rgraphviz, Rmpi, XML
Description: Framework for processing and visualization of
chromatographically separated and single-spectra mass spectral data. Imports
from AIA/ANDI
NetCDF, mzXML, mzData and mzML files. Preprocesses data for
high-throughput, untargeted analyte profiling.
License: GPL (>= 2) + file LICENSE
URL: http://metlin.scripps.edu/download/ and
https://github.com/sneumann/xcms
BugReports: https://github.com/sneumann/xcms/issues/new
biocViews: MassSpectrometry, Metabolomics
Packaged: 2014-10-14 02:08:49 UTC; biocbuild
Built: R 3.1.1; i386-w64-mingw32; 2014-10-14 14:24:49 UTC; windows
-- File:
C:/Users/florian.schroeder.TARGENOMIX/Documents/R/R-3.1.3/library/xcms/Meta/
package.rds
> packageDescription("ptw")
Package: ptw
Type: Package
Title: Parametric Time Warping
Version: 1.9-10
Author: Jan Gerretzen <[email protected]>, Paul Eilers
<[email protected]>, Hans Wouters, Tom Bloemberg
<[email protected]>, Ron
Wehrens <[email protected]>
Maintainer: Ron Wehrens <[email protected]>
Description: Parametric Time Warping aligns patterns, i.e. it aims to put
corresponding features at the same locations. The algorithm searches for an
optimal polynomial describing the warping. It is possible
to align one sample to a reference, several samples to the same reference,
or
several samples to several references. One can choose
between calculating individual warpings, or one global warping for a set of
samples and one reference. Two optimization criteria are
implemented: RMS (Root Mean Square error) and WCC (Weighted Cross
Correlation). Both warping of peak profiles and of peak
lists are supported.
License: GPL (>= 2)
Imports: nloptr, graphics, grDevices, stats
NeedsCompilation: yes
Packaged: 2015-06-30 13:39:55 UTC; ron
Repository: CRAN
Date/Publication: 2015-07-01 06:11:39
Built: R 3.1.3; x86_64-w64-mingw32; 2015-07-20 18:49:38 UTC; windows
-- File:
C:/Users/florian.schroeder.TARGENOMIX/Documents/R/R-3.1.3/library/ptw/Meta/p
ackage.rds
> packageDescription("rJava")
Package: rJava
Version: 0.9-6
Title: Low-level R to Java interface
Author: Simon Urbanek <[email protected]>
Maintainer: Simon Urbanek <[email protected]>
Depends: R (>= 2.5.0), methods
Description: Low-level interface to Java VM very much like .C/.Call and
friends. Allows creation of objects, calling methods and accessing fields.
License: GPL-2
URL: http://www.rforge.net/rJava/
SystemRequirements: java
Packaged: 2013-12-23 15:17:13 UTC; svnuser
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-12-24 00:16:48
Built: R 3.1.3; i386-w64-mingw32; 2015-03-10 11:07:52 UTC; windows
-- File:
C:/Users/florian.schroeder.TARGENOMIX/Documents/R/R-3.1.3/library/rJava/Meta
/package.rds
>
smime.p7s
Description: S/MIME cryptographic signature
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