Back to Workflows build report for BioC 3.7

BUILD WEB VIG report for rnaseqGene on malbec2

This page was generated on 2018-05-18 12:48:07 -0400 (Fri, 18 May 2018).

Package 16/21HostnameOS / ArchINSTALLBUILDBUILD WEB VIG
rnaseqGene 1.2.0
Michael Love
Snapshot Date: 2018-05-18 07:35:08 -0400 (Fri, 18 May 2018)
URL: https://git.bioconductor.org/packages/rnaseqGene
Branch: RELEASE_3_7
Last Commit: d1689af
Last Changed Date: 2018-04-30 10:07:09 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: rnaseqGene
Version: 1.2.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/rnaseqGene/rnaseqGene.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/rnaseqGene/rnaseqGene.Rmd", ".buildwebvig/rnaseqGene/rnaseqGene.R")'
StartedAt: 2018-05-18 08:49:35 -0400 (Fri, 18 May 2018)
EndedAt: 2018-05-18 08:52:22 -0400 (Fri, 18 May 2018)
EllapsedTime: 167.1 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/rnaseqGene/rnaseqGene.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/rnaseqGene/rnaseqGene.Rmd", ".buildwebvig/rnaseqGene/rnaseqGene.R")'
###
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> rmarkdown::render(".buildwebvig/rnaseqGene/rnaseqGene.Rmd", output_format="BiocStyle:::html_fragment")


processing file: rnaseqGene.Rmd

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label: style (with options) 
List of 4
 $ echo   : logi FALSE
 $ message: logi FALSE
 $ warning: logi FALSE
 $ results: chr "asis"


Attaching package: 'rmarkdown'

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label: loadairway
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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Import genomic features from the file as a GRanges object ... OK
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Make the TxDb object ... OK

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Attaching package: 'dplyr'

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label: airwayDE
using pre-existing size factors
estimating dispersions
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label: plotma
using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    bioRxiv. https://doi.org/10.1101/303255

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Attaching package: 'genefilter'

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label: fissionDE
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Session info ------------------------------------------------------------------
Packages ----------------------------------------------------------------------

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output file: rnaseqGene.knit.md

/usr/bin/pandoc +RTS -K512m -RTS rnaseqGene.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output rnaseqGene.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.7-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' --filter /usr/bin/pandoc-citeproc 

Output created: rnaseqGene.html
Warning message:
In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
> 
> 
> knitr::purl(".buildwebvig/rnaseqGene/rnaseqGene.Rmd", ".buildwebvig/rnaseqGene/rnaseqGene.R")


processing file: .buildwebvig/rnaseqGene/rnaseqGene.Rmd

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output file: .buildwebvig/rnaseqGene/rnaseqGene.R

[1] ".buildwebvig/rnaseqGene/rnaseqGene.R"
> 
>