xcms 2.99.6
Steffen Neumann
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms | | Last Changed Rev: 131862 / Revision: 131943 | | Last Changed Date: 2017-08-09 05:24:08 -0400 (Wed, 09 Aug 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### chmod a+r xcms -R && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data xcms
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* checking for file 'xcms/DESCRIPTION' ... OK
* preparing 'xcms':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, 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: Rcpp
Loading required package: ProtGenerics
This is MSnbase version 2.3.9
Read '?MSnbase' and references therein for information
about the package and how 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 2.99.6
Attaching package: 'xcms'
The following object is masked from 'package:stats':
sigma
Warning: 'readMSData2' is deprecated.
Use 'readMSData(..., mode = "onDisk")' instead.
See help("Deprecated")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-tic-1.png" -trim "new_functionality_files/figure-html/faahKO-tic-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-tic-1.png" -trim "new_functionality_files/figure-html/faahKO-tic-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-bpi-1.png" -trim "new_functionality_files/figure-html/faahKO-bpi-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-bpi-1.png" -trim "new_functionality_files/figure-html/faahKO-bpi-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-bbpi-manual-1.png" -trim "new_functionality_files/figure-html/faahKO-bbpi-manual-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-bbpi-manual-1.png" -trim "new_functionality_files/figure-html/faahKO-bbpi-manual-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-tic-boxplot-1.png" -trim "new_functionality_files/figure-html/faahKO-tic-boxplot-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-tic-boxplot-1.png" -trim "new_functionality_files/figure-html/faahKO-tic-boxplot-1.png"' execution failed with error code 4
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 18718 regions of interest ... OK: 548 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 14431 regions of interest ... OK: 444 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 15209 regions of interest ... OK: 472 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 17808 regions of interest ... OK: 540 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 18651 regions of interest ... OK: 649 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 16040 regions of interest ... OK: 445 found.
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-peak-intensity-boxplot-1.png" -trim "new_functionality_files/figure-html/faahKO-peak-intensity-boxplot-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-peak-intensity-boxplot-1.png" -trim "new_functionality_files/figure-html/faahKO-peak-intensity-boxplot-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-peak-image-1.png" -trim "new_functionality_files/figure-html/faahKO-peak-image-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-peak-image-1.png" -trim "new_functionality_files/figure-html/faahKO-peak-image-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-peak-plot-1.png" -trim "new_functionality_files/figure-html/faahKO-peak-plot-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-peak-plot-1.png" -trim "new_functionality_files/figure-html/faahKO-peak-plot-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-extracted-chrom-with-peaks-1.png" -trim "new_functionality_files/figure-html/faahKO-extracted-chrom-with-peaks-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-extracted-chrom-with-peaks-1.png" -trim "new_functionality_files/figure-html/faahKO-extracted-chrom-with-peaks-1.png"' execution failed with error code 4
Sample number 3 used as center sample.
Aligning ko15.CDF against ko18.CDF ... OK
Aligning ko16.CDF against ko18.CDF ... OK
Aligning wt15.CDF against ko18.CDF ... OK
Aligning wt16.CDF against ko18.CDF ... OK
Aligning wt18.CDF against ko18.CDF ... OK
Applying retention time adjustment to the identified chromatographic peaks ... OK
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-bpi-obiwarp-1.png" -trim "new_functionality_files/figure-html/faahKO-bpi-obiwarp-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-bpi-obiwarp-1.png" -trim "new_functionality_files/figure-html/faahKO-bpi-obiwarp-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-adjusted-rtime-boxplot-1.png" -trim "new_functionality_files/figure-html/faahKO-adjusted-rtime-boxplot-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-adjusted-rtime-boxplot-1.png" -trim "new_functionality_files/figure-html/faahKO-adjusted-rtime-boxplot-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-extracted-chrom-with-peaks-aligned-1.png" -trim "new_functionality_files/figure-html/faahKO-extracted-chrom-with-peaks-aligned-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-extracted-chrom-with-peaks-aligned-1.png" -trim "new_functionality_files/figure-html/faahKO-extracted-chrom-with-peaks-aligned-1.png"' execution failed with error code 4
Processing 3196 mz slices ... OK
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-plot-peak-density-1.png" -trim "new_functionality_files/figure-html/faahKO-plot-peak-density-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-plot-peak-density-1.png" -trim "new_functionality_files/figure-html/faahKO-plot-peak-density-1.png"' execution failed with error code 4
Requesting 167 missing peaks from ko15.CDF ... got 94.
Requesting 126 missing peaks from ko16.CDF ... got 66.
Requesting 154 missing peaks from ko18.CDF ... got 85.
Requesting 176 missing peaks from wt15.CDF ... got 101.
Requesting 163 missing peaks from wt16.CDF ... got 89.
Requesting 187 missing peaks from wt18.CDF ... got 113.
Reverting retention times of identified peaks to original values ... OK
Processing 3196 mz slices ... OK
Performing retention time correction using 20 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/faahKO-peak-groups-alignment-plot-1.png" -trim "new_functionality_files/figure-html/faahKO-peak-groups-alignment-plot-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/faahKO-peak-groups-alignment-plot-1.png" -trim "new_functionality_files/figure-html/faahKO-peak-groups-alignment-plot-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/binning-imputation-example-1.png" -trim "new_functionality_files/figure-html/binning-imputation-example-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/binning-imputation-example-1.png" -trim "new_functionality_files/figure-html/binning-imputation-example-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "new_functionality_files/figure-html/profBinLin-problems-1.png" -trim "new_functionality_files/figure-html/profBinLin-problems-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "new_functionality_files/figure-html/profBinLin-problems-1.png" -trim "new_functionality_files/figure-html/profBinLin-problems-1.png"' execution failed with error code 4
Loading required package: waveslim
waveslim: Wavelet Method for 1/2/3D Signals (version = 1.7.5)
There were 50 or more warnings (use warnings() to see the first 50)
There were 50 or more warnings (use warnings() to see the first 50)
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "xcms-direct-injection_files/figure-html/calibration-result-1.png" -trim "xcms-direct-injection_files/figure-html/calibration-result-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "xcms-direct-injection_files/figure-html/calibration-result-1.png" -trim "xcms-direct-injection_files/figure-html/calibration-result-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning: running command 'C:\Windows\system32\cmd.exe /c convert "xcms-direct-injection_files/figure-html/feature-FT01-1.png" -trim "xcms-direct-injection_files/figure-html/feature-FT01-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "xcms-direct-injection_files/figure-html/feature-FT01-1.png" -trim "xcms-direct-injection_files/figure-html/feature-FT01-1.png"' execution failed with error code 4
Requesting 10 missing peaks from HAM004_641fE_14-11-07--Exp1.extracted.mzdata ... got 10.
Requesting 11 missing peaks from HAM004_641fE_14-11-07--Exp2.extracted.mzdata ... got 11.
Requesting 11 missing peaks from HAM004_641fE_14-11-07--Exp3.extracted.mzdata ... got 11.
Requesting 11 missing peaks from HAM004_641fE_14-11-07--Exp4.extracted.mzdata ... got 11.
Requesting 12 missing peaks from HAM004_641fE_14-11-07--Exp5.extracted.mzdata ... got 12.
Requesting 8 missing peaks from HAM005_641fE_14-11-07--Exp1.extracted.mzdata ... got 8.
Requesting 8 missing peaks from HAM005_641fE_14-11-07--Exp2.extracted.mzdata ... got 8.
Requesting 9 missing peaks from HAM005_641fE_14-11-07--Exp3.extracted.mzdata ... got 9.
Requesting 9 missing peaks from HAM005_641fE_14-11-07--Exp4.extracted.mzdata ... got 9.
Requesting 9 missing peaks from HAM005_641fE_14-11-07--Exp5.extracted.mzdata ... got 9.
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Warning: running command '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf "xcmsMSn.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'xcmsMSn'. The following files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf', 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'new_functionality.R', 'new_functionality.Rmd', 'new_functionality.html', 'new_functionality.org', 'references.bib', 'xcms-direct-injection.R', 'xcms-direct-injection.Rmd', 'xcms-direct-injection.html', 'xcms.bib', 'xcms.org', 'xcmsMSn-TreePlot.pdf', 'xcmsMSn.Rnw', 'xcmsMSn.tex', 'xcmsPreprocess.Rnw-notrun'
Calls: <Anonymous> -> find_vignette_product
Execution halted