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 | |
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### Running command:
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### /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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|================================================================| 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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|================================================================| 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