Rterm.exe crash

[Giuseppe Martano]

Since 2 days I have problem to use mz.

 

If I use for example batches.runCentwave() eMZed will search for R again and than will crash.

 

Regards

Giuseppe

[Uwe Schmitt]

Sorry, my first answer is obsolete.

Looks like your R version is not up to date. mzR requires R 2.15 and seems

to crash when loaded.

Which R version do you use ?

Cheers, Uwe

[Giuseppe Martano]

R version 2.15.0 (2012-03-30)

It is strange because is loaded 2. Once during the start up and the second time after calling "runCentwave", but Rterm crash only the 2° time.

 

Regards

Giuseppe

[Uwe Schmitt]

Do you use a locally installed version, or the application bubble ?

Cheers, Uwe

[Giuseppe Martano]

Its from the bubble.

[Uwe Schmitt]

Am 12.09.2012 12:43, schrieb Giuseppe Martano:

Its from the bubble.

--
 
 
 

ok. maybe the bubble uses an older version of R,
I contacted Jacques.

Uwe

-- 
Dr. rer. nat. Uwe Schmitt
Leitung F/E Mathematik

mineway GmbH
Gebäude 4
Im Helmerswald 2
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Telefon: +49 (0)681 8390 5334
Telefax: +49 (0)681 830 4376

usch...@mineway.de
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[Giuseppe Martano]

After the update to R 2.15.1 the problem is not solved.

[quote]

In [1]: x = batches.runCentwave()
read  //volvox/spectro/Orbitrap/martanog/2012-09-03-GM-Dinamic_labeling2/MZXML/2012-09-03-GM-016-Inf_pool_id19-mr1.mzXML
"Q:\R2x.32a\R/bin/R.exe" --vanilla --silent < c:\users\martanog.d\appdata\local\temp\tmpqvib2_\script.R
>
>                         if (require("xcms") == FALSE)
+                         {
+                             source("http://bioconductor.org/biocLite.R")
+                             biocLite("xcms", dep=T)
+                         }
Lade nötiges Paket: xcms
Lade nötiges Paket: mzR
Failed with error:  'Paket 'Rcpp' benötigt von 'mzR' nicht gefunden'
BiocInstaller version 1.4.7, ?biocLite for help
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.7.
Installing package(s) 'xcms'
Warnung in install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  'lib = "\\gram/OMICS/gr_vorholt/emzed/r_libs"' is not writable
Fehler in install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  unable to install packages
Calls: biocLite -> biocLiteInstall -> install.packages
Ausführung angehalten
------------------------------------------------------------
Traceback (most recent call last):
  File "<ipython console>", line 1, in <module>
  File "Q:\eMZed_1.x\eMZed\batches\feature_detector.py", line 94, in runCentwave
    return P(configs.centwaveConfig, True).run(pattern, destination, configid, **params)
  File "Q:\eMZed_1.x\eMZed\batches\_BatchRunner.py", line 68, in run
    result = self.process(path)
  File "Q:\eMZed_1.x\eMZed\batches\feature_detector.py", line 21, in process
    table = self.det.process(ds)
  File "Q:\eMZed_1.x\eMZed\libms\RConnect\XCMSConnector.py", line 141, in process
    raise Exception("R operation failed")
Exception: R operation failed

[/quote]

[Uwe Schmitt]

If you read the error messages carefully you see the cause of the problem:

  'lib = "\\gram/OMICS/gr_vorholt/emzed/r_libs"' is not writable 

Regards, Uwe

[Giuseppe Martano]

Tnx alot