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BUILD report for RMassBank on celaya2

This page was generated on 2019-04-09 13:05:39 -0400 (Tue, 09 Apr 2019).

Package 1361/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RMassBank 2.11.2
RMassBank at Eawag
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/RMassBank
Branch: master
Last Commit: 31f7949
Last Changed Date: 2019-04-03 14:49:54 -0400 (Wed, 03 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: RMassBank
Version: 2.11.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RMassBank
StartedAt: 2019-04-08 20:20:57 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 20:23:57 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 180.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R 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
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Loaded compoundlist successfully
msmsWorkflow: Step 1. Acquire all MSMS spectra from files

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  |================================                                |  50%
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  |================================================================| 100%msmsWorkflow: Step 2. First analysis pre recalibration

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Error: processing vignette 'RMassBank.Rnw' failed with diagnostics:
 chunk 10 
Error in .jcall(mfSet, "I", "size") : 
  RcallMethod: invalid object parameter

--- 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%
  |                                                                      
  |================================================================| 100%msmsWorkflow: Done.
msmsWorkflow: Step 2. First analysis pre recalibration

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Error: processing vignette 'RMassBankNonstandard.Rnw' failed with diagnostics:
 chunk 11 
Error in .jcall(mfSet, "I", "size") : 
  RcallMethod: invalid object parameter

--- failed re-building ‘RMassBankNonstandard.Rnw’

--- re-building ‘RMassBankXCMS.Rnw’ using Sweave
Loaded compoundlist successfully

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  |                                                                |   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, colMeans, colSums, 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, rowMeans,
    rowSums, 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

This is MSnbase version 2.9.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:stats’:

    smooth

The following object is masked from ‘package:base’:

    trimws


This is xcms version 3.5.1 


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.

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  |================================                                |  50%msmsWorkflow: Step 2. First analysis pre recalibration

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Error: processing vignette 'RMassBankXCMS.Rnw' failed with diagnostics:
 chunk 9 
Error in .jcall(mfSet, "I", "size") : 
  RcallMethod: invalid object parameter

--- failed re-building ‘RMassBankXCMS.Rnw’

SUMMARY: processing the following files failed:
  ‘RMassBank.Rnw’ ‘RMassBankNonstandard.Rnw’ ‘RMassBankXCMS.Rnw’

Error: Vignette re-building failed.
Execution halted