Hi Gauthier,
I got an exception when starting your modified MZmine-2.11-EEE:
[10:30:08|INFO|MZmineCore]: Starting MZmine 2.11-EEE
[10:30:08|FINE|TmpFileCleanup]: Checking for old temporary files...
[10:30:08|FINE|MZmineCore]: Loading core classes..
[10:30:08|FINE|MZmineCore]: Initializing core classes..
[10:30:08|FINE|MZmineCore]: Loading modules
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.projectmethods.projectload.ProjectLoadModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveAsModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.projectmethods.projectclose.ProjectCloseModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.batchmode.BatchModeModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.peakpicking.msms.MsMsPeakPickerModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.filtering.datasetfilters.DataSetFiltersModule
[10:30:08|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule
[10:30:08|FINEST|RUtilities]: Checking R Engine.
[10:30:08|FINEST|RUtilities]: Creating R Engine.
[10:30:08|FINEST|RUtilities]:
[10:30:08|FINEST|RUtilities]: R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
[10:30:08|FINEST|RUtilities]: R is free software and comes with ABSOLUTELY NO
WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
[10:30:08|FINEST|RUtilities]: Natural language support but running in an
English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
[10:30:08|FINEST|RUtilities]: Type 'demo()' for some demos, 'help()' for
on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[10:30:08|FINEST|RUtilities]: Rengine created, waiting for R.
[10:30:08|FINEST|RUtilities]: Loading required package: ptw
[10:30:08|FINEST|RUtilities]: Loading required package: baseline
[10:30:08|SEVERE|MZmineCore]: Could not load module class
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule(java.lang.ExceptionInInitializerError@sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method))
java.lang.ExceptionInInitializerError
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
at java.lang.Class.newInstance(Class.java:438)
at net.sf.mzmine.main.MZmineCore.main(MZmineCore.java:138)
Caused by: java.lang.IllegalStateException: The "baseline" R package couldn't
be loaded - is it installed in R?
at
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrector.<init>(BaselineCorrector.java:84)
at
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.correctors.RollingBallCorrector.<init>(RollingBallCorrector.java:38)
at
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionParameters.<clinit>(BaselineCorrectionParameters.java:76)
... 6 more
Furher, when I tried to run the baseline correction module, I got this:
[10:30:09|WARNING|MZmineCore]: Error while loading parameter values for Batch
queue(java.lang.IllegalArgumentException: Module class
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule
does not have any parameter set
insta...@net.sf.mzmine.main.impl.MZmineConfigurationImpl.getModuleParameters(MZmineConfigurationImpl.java:73))
java.io.IOException: java.lang.IllegalArgumentException: Module class
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule
does not have any parameter set instance
at
net.sf.mzmine.main.impl.MZmineConfigurationImpl.loadConfiguration(MZmineConfigurationImpl.java:158)
at net.sf.mzmine.main.MZmineCore.main(MZmineCore.java:204)
Caused by: java.lang.IllegalArgumentException: Module class
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule
does not have any parameter set instance
at
net.sf.mzmine.main.impl.MZmineConfigurationImpl.getModuleParameters(MZmineConfigurationImpl.java:73)
at
net.sf.mzmine.main.impl.MZmineConfigurationImpl.loadConfiguration(MZmineConfigurationImpl.java:151)
... 1 more
I realized this is probably because I didn't install the prerequisities, but in
any case the errors should be reported more clearly and exceptions should be
caught in the code. Using runtime exceptions like
java.lang.IllegalStateException can be sometimes dangerous, because they are
not declared.
Best regards,
Tomas
On Nov 9, 2014, at 1:24, Gauthier Boaglio <gauthier.boag...@gmail.com> wrote:
> Fixed the main (but not the least) bugs:
>
> * Fixed baseline task issues (multi-threading was very sadly handled).
> * Fixed "PeakDetectionCorrector" (R code was leading to failures when using
> bins - "use m/z bins" checked).
>
>
> Here is the new release, available for testing:
> http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141108.zip
>
>
> Best regards
> Gauthier
>
>
>
> On 11/08/2014 11:12 AM, Gauthier Boaglio wrote:
>> Hi Tomas.
>>
>> I already posted those information on the mailing list but I did not
>> received them, so I believe those mails did not reach the list members as
>> well. That is why I am forwarding the whole stuff to your personal address.
>>
>> Test release download link:
>>
>> http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141107.zip
>>
>>
>> I'm also aware of some bugs while running the task on several file (not
>> especially the batch mode by itself). I'll keep you in touch as soon as I
>> have fixed it.
>>
>>
>> -------- Forwarded Message --------
>> Subject: Further developments on the "Baseline Correction" module.
>> Date: Fri, 07 Nov 2014 16:46:55 +0100
>> From: Gauthier Boaglio <gauthier.boag...@gmail.com>
>> To: mzmine-devel@lists.sourceforge.net
>> On 11/07/2014 04:42 PM, Gauthier Boaglio wrote:
>> > Hi all,
>> >
>> > I did some further developments on the "Baseline Correction" module.
>> > This is not yet completely "crash tested" (specially regarding the
>> > compatibility of what I made with the "batch mode" system). But still
>> > working quite well. And it might be a good candidate for integration
>> > in the trunk. Perhaps... I let you judges on this, but I'd be glad to
>> > help with this task if applicable.
>> >
>> > Here's the change log. If any of you has the irreducible need to see
>> > and test it, any comment or bug report would be greatly appreciated!
>> > Thanks.
>> >
>> > MZmine2 change log for "Baseline corrector module":
>> >
>> > --------------------------------------------------
>> >
>> >>> Modified files (package
>> >>> "net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection"):
>> >
>> > * ParameterSetupDialogWithChromatogramPreview:
>> >
>> > => Slightly modified to add the possibility for switching
>> > to TIC (versus Base Peak) preview.
>> >
>> >
>> > * TICPlot:
>> >
>> > => Added the possibility to switch to TIC plot type from a
>> > "non-TICVisualizerWindow" context.
>> >
>> >
>> > * TICDataSet:
>> >
>> > => Added the possibility to switch to TIC plot type from a
>> > "non-TICVisualizerWindow" context.
>> >
>> >
>> > * BaselineCorrectionTask:
>> >
>> > => Adding more baseline algorithms.
>> >
>> > Deeply modified to delegate baseline correction to
>> > various correctors (whose implement specific methods by them-selves).
>> >
>> > Those correctors all share a common behavior by
>> > inheriting from the base class "BaselineCorrector", and apply there
>> > specific way of building the baselines via the various algorithms
>> > implemented in the sub-package
>> > "net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.correctors".
>> >
>> >
>> > * BaselineCorrectionParameters:
>> >
>> > => Adding more baseline algorithms.
>> >
>> > Holds baseline correction module COMMON parameters.
>> >
>> > Reduced strictly to the parameters common to all the
>> > BaselineCorrectors.
>> >
>> > See
>> > "net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.correctors"
>> >
>> > sub-package for method specific parameters.
>> >
>> >
>> >>> Added files (package
>> >>> "net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.correctors"):
>> >
>> > > Adding more baseline algorithms. Deeply refactored the baseline
>> > correction module design. Added preview feature.
>> >
>> > * BaselineCorrector
>> >
>> > * BaselineCorrectorSetupDialog
>> >
>> > * BaselineProvider
>> >
>> > * InstantUpdateSetupDialog
>> >
>> > > Correctors:
>> >
>> > * AsymmetryCorrector / AsymmetryCorrectorParameters:
>> >
>> > => Adding more baseline algorithms.
>> >
>> > Asymmetric baseline corrector (same as before).
>> > Estimates a trend based on asymmetric least squares.
>> >
>> > Uses "asysm" feature from "ptw" R-package
>> > (
>> http://cran.r-project.org/web/packages/ptw/ptw.pdf
>> ).
>> >
>> >
>> > * RollingBallCorrector / RollingBallCorrectorParameters:
>> >
>> > => Adding more baseline algorithms.
>> >
>> > Rolling Ball baseline corrector. Estimates a trend
>> > based on Rolling Ball algorithm.
>> >
>> > Uses "rollingBall" feature from "baseline"
>> > R-package (
>> http://cran.r-project.org/web/packages/baseline/baseline.pdf
>> ).
>> >
>> > (Ideas from Rolling Ball algorithm for X-ray
>> > spectra by M.A.Kneen and H.J. Annegarn. Variable window width has been
>> > left out).
>> >
>> >
>> > * PeakDetectionCorrector / PeakDetectionCorrectorParameters:
>> >
>> > => Adding more baseline algorithms.
>> >
>> > Peak detection is done in several steps sorting
>> > out real peaks through different criteria. Peaks are removed from
>> >
>> > spectra and minimums and medians are used to
>> > smooth the remaining parts of the spectra.
>> >
>> > Uses "peakDetection" feature from "baseline"
>> > R-package (
>> http://cran.r-project.org/web/packages/baseline/baseline.pdf
>> ).
>> >
>> > (A translation from Kevin R. Coombes et al.'s
>> > MATLAB code for detecting peaks and removing baselines).
>> >
>> >
>> > * RubberBandCorrector / RubberBandCorrectorParameters:
>> >
>> > => Adding more baseline algorithms.
>> >
>> > Rubber Band baseline corrector.
>> >
>> > Estimates a trend based on Rubber Band algorithm
>> > (which determines a convex envelope for the spectra).
>> >
>> > Uses "spc.rubberband" feature from "hyperSpec"
>> > R-package
>> > (
>> http://cran.r-project.org/web/packages/hyperSpec/vignettes/introduction.pdf
>> ).
>> >
>> >
>> > * LocMinLoessCorrector / LocMinLoessCorrectorParameters:
>> >
>> > => Adding more baseline algorithms.
>> >
>> > Local Minima + LOESS (smoothed low-percentile
>> > intensity) baseline corrector.
>> >
>> > Uses "bslnoff" feature from "PROcess"
>> > R/Bioconductor package
>> > (
>> http://bioconductor.org/packages/release/bioc/manuals/PROcess/man/PROcess.pdf
>> ).
>> >
>>
>> Preview of what it does:
>>
>>
>> New Baseline correction setup:
>>
>>
>>
>>
>> <Mail Attachment.png>
>>
>>
>>
>>
>>
>>
>> With baseline preview enabled:
>>
>>
>>
>>
>> <Mail Attachment.png>
>>
>>
>>
>>
>>
>> >
>> > Regards
>> > Gauthier
>> >
>>
>>
>> --
>> Gauthier BOAGLIO
>> CEFE - UMR 5175
>> 1919 route de Mende
>> F-34293 Montpellier cedex 5
>>
>> Tel: +33/0 4 67 61 32 15
>> Fax: +33/0 4 67 61 33 36
>>
>> email:
>> gauthier.boag...@cefe.cnrs.fr
>>
>> www:
>> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio
>>
>>
>> http://www.evolepid.org/people.php?name=boaglio
>>
>>
>>
>>
>>
>
>
> --
> Gauthier BOAGLIO
> CEFE - UMR 5175
> 1919 route de Mende
> F-34293 Montpellier cedex 5
>
> Tel: +33/0 4 67 61 32 15
> Fax: +33/0 4 67 61 33 36
>
> email:
> gauthier.boag...@cefe.cnrs.fr
>
> www:
> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio
>
>
> http://www.evolepid.org/people.php?name=boaglio
>
>
>
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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