RMassBank 2.16.0
RMassBank at Eawag
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/RMassBank |
| Branch: RELEASE_3_11 |
| Last Commit: f1c64de |
| Last Changed Date: 2020-04-27 14:30:41 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK |  |
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###
### Running command:
###
### chmod a+r RMassBank -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RMassBank
###
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* checking for file 'RMassBank/DESCRIPTION' ... OK
* preparing 'RMassBank':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'RMassBank.Rnw' using Sweave
Loading required package: Rcpp
Loaded compoundlist successfully
msmsWorkflow: Step 1. Acquire all MSMS spectra from files
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| | 0%
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|================================ | 50%
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|================================================================| 100%msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.08532641193125
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.50309679767344
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6891014363453
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77395556232187
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 203.74409411212656
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 205.2540123250172
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.08926317950937
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.69079516193125
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68998644611094
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7714226033375
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 200.82116625568125
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68850634357187
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.606749751775
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.689757564275
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6059410359547
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68862841388437
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 198.4196617390797
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60507128497812
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68888781329844
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60710070392344
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.66349718829844
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.67318651935312
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68072436115
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6895897175953
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7728874470875
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 204.59658739825937
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 204.59921190997812
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 208.6405632283375
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6806785847828
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6896812703297
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.70170519611094
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7074577595875
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7729637410328
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60757372638437
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6737205769703
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6811363484547
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.69038317462656
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7095329549
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6175377156422
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6812584187672
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.69076464435312
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.70486376544687
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77462694904062
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60656664630625
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6691276814625
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68086169025156
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6893913533375
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.69924853107187
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.70706103107187
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7727196004078
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 203.90058825275156
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 205.19137499591562
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 207.19570849200937
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 197.0926353718922
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.1486198689625
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.39372179767344
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60690233966562
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68327257892344
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68991015216562
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.70637438556406
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7114403035328
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77304003497812
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 204.13021776935312
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 206.14556811115
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 197.0906822468922
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60650561115
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6815330769703
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68991015216562
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.699034908025
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77316210529062
|
|================================ | 50%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12310717365
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 239.1308433797047
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 233.36604235431406
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 235.8847038533375
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12345812579844
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 233.19302294513437
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 234.91227648517344
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 235.28958056232187
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12544176837656
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 237.3259422566578
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.1198875691578
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 238.14855883380625
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12287829181406
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12780688068125
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 244.1047203328297
|
|================================================================| 100%
msmsWorkflow: Step 3. Aggregate all spectra
msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
msmsWorkflow: Done.
msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
msmsWorkflow: Done.
msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
msmsWorkflow: Done.
msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.08511280918157
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.50287283994427
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68887667177927
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77373041930085
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 203.74386051535262
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 205.253772166202
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.08904955994265
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.690570389814
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68976167759956
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77119747161862
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 200.82094516393445
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68828158165934
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6065253533324
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.689532796784
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60571664111555
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6884036514271
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 198.41945097380105
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60484689401363
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68866304968464
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60687630391675
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.66327253787102
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.67296182573583
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68049963393042
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68936495085234
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7726623088327
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 204.59634998267984
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 204.5989744837591
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 208.6403082220632
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6804538577675
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68945650317917
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.70148037535074
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7072329131775
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7727386024373
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6073493242702
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.67349588097213
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68091161939876
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.69015840434685
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.709308099236
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.61731327003264
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68103368916658
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6905398723721
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.70463893060307
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77440180302415
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60634224867917
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6689030059375
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68063696242018
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6891665874797
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.69902372126538
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7068361864305
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77249446290162
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 203.90035395402396
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 205.19113511566042
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 207.19546001067434
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 197.0924302793647
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.14840599579054
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.39350687685376
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60667794054353
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6830478403434
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68968538399474
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.70614954398428
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.71121543936385
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7728148960419
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 204.1299824402567
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 206.14532415513884
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 197.09047716248853
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6062812137951
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68130834614516
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68968538399474
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.69881009917088
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7729369658102
|
|================================ | 50%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12273740351918
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 239.13042988346382
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 233.3656613776574
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 235.88430956133993
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.123088353972
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 233.19264282876597
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 234.91188747426693
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 235.28918951471957
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12507198696946
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 237.32553970971833
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.11951781457853
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 238.14815136068998
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.11530640913904
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.1225085227887
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12743708784916
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 244.10427504859163
|
|================================================================| 100%
msmsWorkflow: Step 6. Aggregate recalibrated results
msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
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msmsWorkflow: Step 8. Peak multiplicity filtering
msmsWorkflow: Done.
mbWorkflow: Step 1. Gather info from several databases
The string does not look like a valid InChIKey: NA
:1: parser error : Start tag expected, '<' not found
The string does not look like a valid InChIKey: NA
^
Warning in xmlRoot.XMLInternalDocument(x, addFinalizer = FALSE) :
empty XML document
Warning in getCompTox(inchikey_split) :
EPA web service is currently offline
Error: processing vignette 'RMassBank.Rnw' failed with diagnostics:
chunk 22
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'unique': error in evaluating the argument 'X' in selecting a method for function 'lapply': $ operator is invalid for atomic vectors
--- failed re-building 'RMassBank.Rnw'
--- re-building 'RMassBankNonstandard.Rnw' using Sweave
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
msmsWorkflow: Done.
Loaded compoundlist successfully
msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
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|================================ | 50%
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|================================================================| 100%msmsWorkflow: Done.
msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.08532641193125
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.50309679767344
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6891014363453
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77395556232187
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 203.74409411212656
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 205.2540123250172
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.69079516193125
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68998644611094
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.7714226033375
|
|================================ | 50%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12310717365
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 239.1308433797047
|
|================================================================| 100%
msmsWorkflow: Step 3. Aggregate all spectra
msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.08489620049465
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.50266071817381
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68866672167587
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77352153024776
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 203.74368047321417
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 205.25355892447052
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 199.0888330315445
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6903604605198
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68955173836753
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77098855034583
|
|================================ | 50%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.1226132377211
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 239.13038436435494
|
|================================================================| 100%
msmsWorkflow: Step 6. Aggregate recalibrated results
msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
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msmsWorkflow: Done.
msmsWorkflow: Step 1. Acquire all MSMS spectra from files
|
| | 0%
|
|================================ | 50%
|
|================================================================| 100%msmsWorkflow: Done.
msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68864367267344
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68844530841562
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68899462482187
|
|================================ | 50%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12280199786875
|
|================================================================| 100%
msmsWorkflow: Step 3. Aggregate all spectra
msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6047902732138
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.68827575098237
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 203.38481590002917
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 197.86321021045717
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 197.86772670524695
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6078116750497
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6880773752584
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.77307393038495
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.60573636868617
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 201.6886267234241
|
|================================ | 50%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 231.12219961593556
|
|================================================================| 100%
msmsWorkflow: Step 6. Aggregate recalibrated results
msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
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|================================================================| 100%
msmsWorkflow: Done.
msmsWorkflow: Step 8. Peak multiplicity filtering
msmsWorkflow: Done.
--- finished re-building 'RMassBankNonstandard.Rnw'
--- re-building 'RMassBankXCMS.Rnw' using Sweave
Loaded compoundlist successfully
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
|
| | 0%Provided scanrange was adjusted to 1 - 0
Loading required package: xcms
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect,
is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages
'citation("pkgname")'.
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:gplots':
space
The following object is masked from 'package:base':
expand.grid
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.14.2
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
This is xcms version 3.10.2
Attaching package: 'xcms'
The following object is masked from 'package:RMassBank':
ppm
The following object is masked from 'package:stats':
sigma
Provided scanrange was adjusted to 1 - 0
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 40 regions of interest ... OK: 29 found.
Provided scanrange was adjusted to 1 - 0
Provided scanrange was adjusted to 1 - 0
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 32 regions of interest ... OK: 29 found.
|
|================================ | 50%msmsWorkflow: Step 2. First analysis pre recalibration
|
| | 0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 449.07854770915293
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 450.0730023992753
|
|================================================================| 100%
msmsWorkflow: Step 3. Aggregate all spectra
msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
msmsWorkflow: Step 5. Reanalyze recalibrated spectra
|
| | 0%org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 449.078547709153
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 450.073002399275
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 451.0761138169945
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 452.0734818929621
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 449.0777674629694
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 450.0733055213719
org.openscience.cdk.formula.MassToFormulaTool ERROR: Proposed mass is out of the range: 451.0749247359002
|
|================================================================| 100%
msmsWorkflow: Step 6. Aggregate recalibrated results
msmsWorkflow: Step 7. Reanalyze fail peaks for N2 + O
|
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|================================================================| 100%
msmsWorkflow: Step 8. Peak multiplicity filtering
msmsWorkflow: Done.
mbWorkflow: Step 1. Gather info from several databases
mbWorkflow: Step 2. Export infolist (if required)
No new data added.
mbWorkflow: Step 3. Data reformatting
mbWorkflow: Step 4. Spectra compilation
Compiling: Glucolesquerellin
mbWorkflow: Step 5. Flattening records
mbWorkflow: Step 6. Generate molfiles
Error: processing vignette 'RMassBankXCMS.Rnw' failed with diagnostics:
chunk 10
Error in createMolfile(as.numeric(c[[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]])) :
Pubchem and Cactus both seem to be down.
--- failed re-building 'RMassBankXCMS.Rnw'
SUMMARY: processing the following files failed:
'RMassBank.Rnw' 'RMassBankXCMS.Rnw'
Error: Vignette re-building failed.
Execution halted