Bioconductor Package Maintainer
| Snapshot Date: 2018-05-18 07:35:07 -0400 (Fri, 18 May 2018) |
| URL: https://git.bioconductor.org/packages/proteomics |
| Branch: master |
| Last Commit: 4db7a5e |
| Last Changed Date: 2018-04-30 10:10:33 -0400 (Mon, 30 Apr 2018) |
| Back to Workflows build report for BioC 3.8 |
This page was generated on 2018-05-18 09:51:46 -0400 (Fri, 18 May 2018).
| Package 13/21 | Hostname | OS / Arch | INSTALL | BUILD | ||||||
| proteomics 1.3.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | |
| Package: proteomics |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/proteomics/proteomics.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/proteomics/proteomics.Rmd", ".buildwebvig/proteomics/proteomics.R")' |
| StartedAt: 2018-05-18 08:44:39 -0400 (Fri, 18 May 2018) |
| EndedAt: 2018-05-18 08:51:21 -0400 (Fri, 18 May 2018) |
| EllapsedTime: 401.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/proteomics/proteomics.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/proteomics/proteomics.Rmd", ".buildwebvig/proteomics/proteomics.R")'
###
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> rmarkdown::render(".buildwebvig/proteomics/proteomics.Rmd", output_format="BiocStyle:::html_fragment")
processing file: proteomics.Rmd
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Bioconductor version 3.8 (BiocInstaller 1.31.1), ?biocLite for help
This is the 'RforProteomics' version 1.19.0.
To get started, visit
http://lgatto.github.com/RforProteomics/
or, in R, open package vignettes by typing
RforProteomics() # R/Bioc for proteomics overview
RProtVis() # R/Bioc for proteomics visualisation
For a full list of available documents:
vignette(package='RforProteomics')
Attaching package: 'RforProteomics'
The following object is masked from 'package:stats':
spectrum
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trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta'
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MS-GF+ Beta (v10072) (6/30/2014)
Loading database files...
Creating /home/biocbuild/bbs-3.8-workflows/meat/.buildwebvig/proteomics/erwinia_carotovora.revCat.fasta.
Creating the suffix array indexed file... Size: 2920847
AlphabetSize: 28
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Loading database finished (elapsed time: 6.67 sec)
Reading spectra...
Ignoring 0 profile spectra.
Ignoring 0 spectra having less than 10 peaks.
Reading spectra finished (elapsed time: 62.99 sec)
Using 6 threads.
Search Parameters:
PrecursorMassTolerance: 20.0ppm
IsotopeError: 0,1
TargetDecoyAnalysis: true
FragmentationMethod: As written in the spectrum or CID if no info
Instrument: HighRes
Enzyme: Tryp
Protocol: iTRAQ
NumTolerableTermini: 2
MinPeptideLength: 6
MaxPeptideLength: 40
NumMatchesPerSpec: 1
Spectrum 0-6102 (total: 6103)
pool-1-thread-2: Preprocessing spectra...
Loading built-in param file: HCD_HighRes_Tryp_iTRAQ.param
pool-1-thread-6: Preprocessing spectra...
Loading built-in param file: HCD_HighRes_Tryp_iTRAQ.param
pool-1-thread-4: Preprocessing spectra...
pool-1-thread-1: Preprocessing spectra...
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pool-1-thread-6: Database search...
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pool-1-thread-1: Database search progress... 68.5% complete
pool-1-thread-2: Database search finished (elapsed time: 14.00 sec)
pool-1-thread-2: Computing spectral E-values...
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Computing q-values...
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Writing results...
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MS-GF+ complete (total elapsed time: 176.96 sec)
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output file: proteomics.knit.md
/usr/bin/pandoc +RTS -K512m -RTS proteomics.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output proteomics.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.8-bioc/R/library/BiocStyle/resources/fragment.html --no-highlight --number-sections --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
Output created: proteomics.html
There were 50 or more warnings (use warnings() to see the first 50)
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> knitr::purl(".buildwebvig/proteomics/proteomics.Rmd", ".buildwebvig/proteomics/proteomics.R")
processing file: .buildwebvig/proteomics/proteomics.Rmd
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output file: .buildwebvig/proteomics/proteomics.R
[1] ".buildwebvig/proteomics/proteomics.R"
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