specL 1.17.3
Christian Panse
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/specL |
| Branch: master |
| Last Commit: c2d4a0a |
| Last Changed Date: 2019-01-26 09:58:52 -0400 (Sat, 26 Jan 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### chmod a+r specL -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data specL
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* checking for file 'specL/DESCRIPTION' ... OK
* preparing 'specL':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'cdsw.Rmd' using rmarkdown
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "cdsw_files/figure-html/unnamed-chunk-3-1.png" -trim "cdsw_files/figure-html/unnamed-chunk-3-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "cdsw_files/figure-html/unnamed-chunk-6-1.png" -trim "cdsw_files/figure-html/unnamed-chunk-6-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "cdsw_files/figure-html/unnamed-chunk-6-2.png" -trim "cdsw_files/figure-html/unnamed-chunk-6-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "cdsw_files/figure-html/unnamed-chunk-7-1.png" -trim "cdsw_files/figure-html/unnamed-chunk-7-1.png"' execution failed with error code 4
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "cdsw_files/figure-html/unnamed-chunk-8-1.png" -trim "cdsw_files/figure-html/unnamed-chunk-8-1.png"' execution failed with error code 4
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Warning in plot.histogram(r, freq = freq1, col = col, border = border, angle = angle, :
the AREAS in the plot are wrong -- rather use 'freq = FALSE'
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "cdsw_files/figure-html/unnamed-chunk-9-1.png" -trim "cdsw_files/figure-html/unnamed-chunk-9-1.png"' execution failed with error code 4
pandoc.exe: Out of memory
Error: processing vignette 'cdsw.Rmd' failed with diagnostics:
pandoc document conversion failed with error 251
--- failed re-building 'cdsw.Rmd'
--- re-building 'report.Rmd' using rmarkdown
Warning: All arguments to RSQLite Driver are ignored.
Warning: RSQLite::dbGetException() is deprecated, please switch to using standard error handling via tryCatch().
Warning: Closing open result set, pending rows
Warning in connection_release(conn@ptr) :
There are 1 result in use. The connection will be released when they are closed
Warning: All arguments to RSQLite Driver are ignored.
Warning: Closing open result set, pending rows
Warning in connection_release(conn@ptr) :
There are 1 result in use. The connection will be released when they are closed
normalizing RT ...
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw
building model ...
generating ion library ...
start generating specLSet object ...
length of findNN idx 137
length of genSwathIonLibSpecL 137
time taken: 0.250027894973755 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 131
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "report_files/figure-html/unnamed-chunk-10-1.png" -trim "report_files/figure-html/unnamed-chunk-10-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "report_files/figure-html/unnamed-chunk-11-1.png" -trim "report_files/figure-html/unnamed-chunk-11-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "report_files/figure-html/unnamed-chunk-11-2.png" -trim "report_files/figure-html/unnamed-chunk-11-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "report_files/figure-html/unnamed-chunk-11-3.png" -trim "report_files/figure-html/unnamed-chunk-11-3.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "report_files/figure-html/unnamed-chunk-11-4.png" -trim "report_files/figure-html/unnamed-chunk-11-4.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "report_files/figure-html/unnamed-chunk-11-5.png" -trim "report_files/figure-html/unnamed-chunk-11-5.png"' execution failed with error code 4
--- finished re-building 'report.Rmd'
--- re-building 'ssrc.Rmd' using rmarkdown
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "ssrc_files/figure-html/unnamed-chunk-4-1.png" -trim "ssrc_files/figure-html/unnamed-chunk-4-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "ssrc_files/figure-html/unnamed-chunk-8-1.png" -trim "ssrc_files/figure-html/unnamed-chunk-8-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "ssrc_files/figure-html/unnamed-chunk-9-1.png" -trim "ssrc_files/figure-html/unnamed-chunk-9-1.png"' execution failed with error code 4
--- finished re-building 'ssrc.Rmd'
--- re-building 'specL.Rnw' using Sweave
start protein annotation ...
time taken: 0 minutes
normalizing RT ...
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw
building model ...
generating ion library ...
start generating specLSet object ...
length of findNN idx 137
length of genSwathIonLibSpecL 137
time taken: 0.359408855438232 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 137
normalizing RT ...
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_01_fetuin_400amol_1.raw
found 7 iRT peptide(s) in s:\p1239\Proteomics\QEXACTIVE_3\ctrachse_20140910_Nuclei_diff_extraction_methods\20140910_07_fetuin_400amol_2.raw
building model ...
generating ion library ...
start generating specLSet object ...
length of findNN idx 137
length of genSwathIonLibSpecL 137
time taken: 0.234377861022949 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 137
normalizing RT ...
no iRT peptides found for building the model.
=> no iRT regression applied, using orgiginal rt instead!
generating ion library ...
start generating specLSet object ...
length of findNN idx 129
length of genSwathIonLibSpecL 129
time taken: 0.250009059906006 secs
length of genSwathIonLibSpecL after fragmentIonRange filtering 129
writting specL object (including header) to file 'specL-Spectronaut.txt' ...
--- finished re-building 'specL.Rnw'
SUMMARY: processing the following file failed:
'cdsw.Rmd'
Error: Vignette re-building failed.
Execution halted