Back to Workflows build report for BioC 3.8

BUILD WEB VIG report for RnaSeqGeneEdgeRQL on malbec1

This page was generated on 2018-05-18 09:51:47 -0400 (Fri, 18 May 2018).

Package 17/21HostnameOS / ArchINSTALLBUILD
RnaSeqGeneEdgeRQL 1.3.3
Yunshun Chen , Gordon Smyth
Snapshot Date: 2018-05-18 07:35:07 -0400 (Fri, 18 May 2018)
URL: https://git.bioconductor.org/packages/RnaSeqGeneEdgeRQL
Branch: master
Last Commit: 5691650
Last Changed Date: 2018-05-13 20:12:59 -0400 (Sun, 13 May 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RnaSeqGeneEdgeRQL
Version: 1.3.3
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", ".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R")'
StartedAt: 2018-05-18 08:51:25 -0400 (Fri, 18 May 2018)
EndedAt: 2018-05-18 08:52:23 -0400 (Fri, 18 May 2018)
EllapsedTime: 58.1 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", ".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R")'
###
##############################################################################
##############################################################################


> rmarkdown::render(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", output_format="BiocStyle:::html_fragment")


processing file: edgeRQL.Rmd

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |.                                                                     |   1%
   inline R code fragments


  |                                                                            
  |.                                                                     |   2%
label: setup (with options) 
List of 3
 $ echo   : logi FALSE
 $ results: chr "hide"
 $ warning: logi FALSE


  |                                                                            
  |..                                                                    |   3%
  ordinary text without R code


  |                                                                            
  |...                                                                   |   4%
label: sra

  |                                                                            
  |....                                                                  |   5%
  ordinary text without R code


  |                                                                            
  |....                                                                  |   6%
label: group

  |                                                                            
  |.....                                                                 |   7%
  ordinary text without R code


  |                                                                            
  |......                                                                |   8%
label: checkdownload (with options) 
List of 3
 $ echo   : logi FALSE
 $ results: chr "hide"
 $ message: logi FALSE

trying URL 'http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE60450&format=file&file=GSE60450_Lactation-GenewiseCounts.txt.gz'
Content type 'application/octet-stream' length 513592 bytes (501 KB)
==================================================
downloaded 501 KB


  |                                                                            
  |......                                                                |   9%
  ordinary text without R code


  |                                                                            
  |.......                                                               |  10%
label: download (with options) 
List of 1
 $ eval: logi FALSE


  |                                                                            
  |........                                                              |  11%
  ordinary text without R code


  |                                                                            
  |........                                                              |  12%
label: readcounts

  |                                                                            
  |.........                                                             |  13%
  ordinary text without R code


  |                                                                            
  |..........                                                            |  14%
label: DGEList (with options) 
List of 1
 $ message: logi FALSE


  |                                                                            
  |...........                                                           |  15%
  ordinary text without R code


  |                                                                            
  |...........                                                           |  16%
label: symbols (with options) 
List of 1
 $ message: logi FALSE

'select()' returned 1:1 mapping between keys and columns

  |                                                                            
  |............                                                          |  17%
  ordinary text without R code


  |                                                                            
  |.............                                                         |  18%
label: dropNAsymbols

  |                                                                            
  |.............                                                         |  19%
  ordinary text without R code


  |                                                                            
  |..............                                                        |  20%
label: design

  |                                                                            
  |...............                                                       |  21%
  ordinary text without R code


  |                                                                            
  |................                                                      |  22%
label: keep

  |                                                                            
  |................                                                      |  23%
  ordinary text without R code


  |                                                                            
  |.................                                                     |  24%
label: filter

  |                                                                            
  |..................                                                    |  25%
  ordinary text without R code


  |                                                                            
  |..................                                                    |  26%
label: aveLogCPM (with options) 
List of 1
 $ fig.cap: chr "Histogram of average log2 CPM."


  |                                                                            
  |...................                                                   |  27%
  ordinary text without R code


  |                                                                            
  |....................                                                  |  28%
label: norm

  |                                                                            
  |.....................                                                 |  29%
  ordinary text without R code


  |                                                                            
  |.....................                                                 |  30%
label: mdsplot (with options) 
List of 3
 $ fig.width : num 7
 $ fig.height: num 7
 $ fig.cap   : chr "MDS plot showing distances between expression profiles. This provides a type of unsupervised clustering of the "| __truncated__


  |                                                                            
  |......................                                                |  31%
  ordinary text without R code


  |                                                                            
  |.......................                                               |  32%
label: mdplot1 (with options) 
List of 3
 $ fig.width : num 7
 $ fig.height: num 7
 $ fig.cap   : chr "Mean-difference plot of log2-expression in sample 1 versus the average log2-expression across all other samples"| __truncated__


  |                                                                            
  |.......................                                               |  33%
  ordinary text without R code


  |                                                                            
  |........................                                              |  34%
label: mdplot11 (with options) 
List of 3
 $ fig.width : num 7
 $ fig.height: num 7
 $ fig.cap   : chr "Mean-difference plot of log2-expression in sample 11 versus the average log2-expression across all other sample"| __truncated__


  |                                                                            
  |.........................                                             |  35%
  ordinary text without R code


  |                                                                            
  |.........................                                             |  36%
label: estimateDisp

  |                                                                            
  |..........................                                            |  37%
  ordinary text without R code


  |                                                                            
  |...........................                                           |  38%
label: plotBCV (with options) 
List of 3
 $ fig.width : num 7
 $ fig.height: num 7
 $ fig.cap   : chr "Scatterplot of the biological coefficient of variation (BCV) against the average abundance of each gene. The pl"| __truncated__


  |                                                                            
  |............................                                          |  39%
  ordinary text without R code


  |                                                                            
  |............................                                          |  40%
label: glmQLFit

  |                                                                            
  |.............................                                         |  41%
  ordinary text without R code


  |                                                                            
  |..............................                                        |  42%
label: QLDisp (with options) 
List of 3
 $ fig.width : num 7
 $ fig.height: num 7
 $ fig.cap   : chr "A plot of the quarter-root QL dispersion against the average abundance of each gene. Estimates are shown for th"| __truncated__


  |                                                                            
  |..............................                                        |  43%
  ordinary text without R code


  |                                                                            
  |...............................                                       |  44%
label: df.prior

  |                                                                            
  |................................                                      |  45%
  ordinary text without R code


  |                                                                            
  |.................................                                     |  46%
label: B.PvsL

  |                                                                            
  |.................................                                     |  47%
  ordinary text without R code


  |                                                                            
  |..................................                                    |  48%
label: glmQLFTest

  |                                                                            
  |...................................                                   |  49%
  ordinary text without R code


  |                                                                            
  |...................................                                   |  51%
label: topTags

  |                                                                            
  |....................................                                  |  52%
  ordinary text without R code


  |                                                                            
  |.....................................                                 |  53%
label: decideTests

  |                                                                            
  |.....................................                                 |  54%
  ordinary text without R code


  |                                                                            
  |......................................                                |  55%
label: plotMDfit (with options) 
List of 3
 $ fig.width : num 7
 $ fig.height: num 7
 $ fig.cap   : chr "MD plot showing the log-fold change and average abundance of each gene. Significantly up and down DE genes are "| __truncated__


  |                                                                            
  |.......................................                               |  56%
  ordinary text without R code


  |                                                                            
  |........................................                              |  57%
label: treat

  |                                                                            
  |........................................                              |  58%
  ordinary text without R code


  |                                                                            
  |.........................................                             |  59%
label: treatdecideTests

  |                                                                            
  |..........................................                            |  60%
  ordinary text without R code


  |                                                                            
  |..........................................                            |  61%
label: plotMDtreat (with options) 
List of 3
 $ fig.width : num 7
 $ fig.height: num 7
 $ fig.cap   : chr "MD plot showing the log-fold change and average abundance of each gene. Genes with fold-changes significantly g"| __truncated__


  |                                                                            
  |...........................................                           |  62%
  ordinary text without R code


  |                                                                            
  |............................................                          |  63%
label: cpm

  |                                                                            
  |.............................................                         |  64%
  ordinary text without R code


  |                                                                            
  |.............................................                         |  65%
label: order

  |                                                                            
  |..............................................                        |  66%
  ordinary text without R code


  |                                                                            
  |...............................................                       |  67%
label: scale

  |                                                                            
  |...............................................                       |  68%
  ordinary text without R code


  |                                                                            
  |................................................                      |  69%
label: heatmap (with options) 
List of 4
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 12
 $ fig.cap   : chr "Heat map across all the samples using the top 30 most DE genes between the basal lactating group and the basal "| __truncated__


  |                                                                            
  |.................................................                     |  70%
  ordinary text without R code


  |                                                                            
  |.................................................                     |  71%
label: makeContrasts

  |                                                                            
  |..................................................                    |  72%
  ordinary text without R code


  |                                                                            
  |...................................................                   |  73%
label: anovaQLFtest

  |                                                                            
  |....................................................                  |  74%
  ordinary text without R code


  |                                                                            
  |....................................................                  |  75%
label: complicatedContrasts

  |                                                                            
  |.....................................................                 |  76%
  ordinary text without R code


  |                                                                            
  |......................................................                |  77%
label: complicatedQLTest

  |                                                                            
  |......................................................                |  78%
  ordinary text without R code


  |                                                                            
  |.......................................................               |  79%
label: goana

  |                                                                            
  |........................................................              |  80%
  ordinary text without R code


  |                                                                            
  |.........................................................             |  81%
label: kegga

  |                                                                            
  |.........................................................             |  82%
  ordinary text without R code


  |                                                                            
  |..........................................................            |  83%
label: select (with options) 
List of 1
 $ message: logi FALSE

'select()' returned 1:1 mapping between keys and columns

  |                                                                            
  |...........................................................           |  84%
  ordinary text without R code


  |                                                                            
  |...........................................................           |  85%
label: GO2ALLEGS

  |                                                                            
  |............................................................          |  86%
  ordinary text without R code


  |                                                                            
  |.............................................................         |  87%
label: fry

  |                                                                            
  |..............................................................        |  88%
  ordinary text without R code


  |                                                                            
  |..............................................................        |  89%
label: barcode (with options) 
List of 3
 $ fig.width : num 8
 $ fig.height: num 5
 $ fig.cap   : chr "Barcode plot showing enrichment of the GO term GO:0032465 in the basal virgin group compared to the basal lacta"| __truncated__


  |                                                                            
  |...............................................................       |  90%
  ordinary text without R code


  |                                                                            
  |................................................................      |  91%
label: camera

  |                                                                            
  |................................................................      |  92%
  ordinary text without R code


  |                                                                            
  |.................................................................     |  93%
label: id2indices.Mm.c2

  |                                                                            
  |..................................................................    |  94%
  ordinary text without R code


  |                                                                            
  |..................................................................    |  95%
label: cam.BVvsLV

  |                                                                            
  |...................................................................   |  96%
  ordinary text without R code


  |                                                                            
  |....................................................................  |  97%
label: barcode2 (with options) 
List of 3
 $ fig.width : num 8
 $ fig.height: num 6.4
 $ fig.cap   : chr "Barcode plot showing strong enrichment of mammary stem cell signature in the stem cell vs luminal cell comparis"| __truncated__


  |                                                                            
  |..................................................................... |  98%
  ordinary text without R code


  |                                                                            
  |..................................................................... |  99%
label: info

  |                                                                            
  |......................................................................| 100%
  ordinary text without R code


output file: edgeRQL.knit.md

/usr/bin/pandoc +RTS -K512m -RTS edgeRQL.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output edgeRQL.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' --filter /usr/bin/pandoc-citeproc 

Output created: edgeRQL.html
> 
> 
> knitr::purl(".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd", ".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R")


processing file: .buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.Rmd

  |                                                                       
  |                                                                 |   0%
  |                                                                       
  |.                                                                |   1%
  |                                                                       
  |.                                                                |   2%
  |                                                                       
  |..                                                               |   3%
  |                                                                       
  |...                                                              |   4%
  |                                                                       
  |...                                                              |   5%
  |                                                                       
  |....                                                             |   6%
  |                                                                       
  |.....                                                            |   7%
  |                                                                       
  |.....                                                            |   8%
  |                                                                       
  |......                                                           |   9%
  |                                                                       
  |.......                                                          |  10%
  |                                                                       
  |.......                                                          |  11%
  |                                                                       
  |........                                                         |  12%
  |                                                                       
  |.........                                                        |  13%
  |                                                                       
  |.........                                                        |  14%
  |                                                                       
  |..........                                                       |  15%
  |                                                                       
  |...........                                                      |  16%
  |                                                                       
  |...........                                                      |  17%
  |                                                                       
  |............                                                     |  18%
  |                                                                       
  |............                                                     |  19%
  |                                                                       
  |.............                                                    |  20%
  |                                                                       
  |..............                                                   |  21%
  |                                                                       
  |..............                                                   |  22%
  |                                                                       
  |...............                                                  |  23%
  |                                                                       
  |................                                                 |  24%
  |                                                                       
  |................                                                 |  25%
  |                                                                       
  |.................                                                |  26%
  |                                                                       
  |..................                                               |  27%
  |                                                                       
  |..................                                               |  28%
  |                                                                       
  |...................                                              |  29%
  |                                                                       
  |....................                                             |  30%
  |                                                                       
  |....................                                             |  31%
  |                                                                       
  |.....................                                            |  32%
  |                                                                       
  |......................                                           |  33%
  |                                                                       
  |......................                                           |  34%
  |                                                                       
  |.......................                                          |  35%
  |                                                                       
  |........................                                         |  36%
  |                                                                       
  |........................                                         |  37%
  |                                                                       
  |.........................                                        |  38%
  |                                                                       
  |..........................                                       |  39%
  |                                                                       
  |..........................                                       |  40%
  |                                                                       
  |...........................                                      |  41%
  |                                                                       
  |............................                                     |  42%
  |                                                                       
  |............................                                     |  43%
  |                                                                       
  |.............................                                    |  44%
  |                                                                       
  |..............................                                   |  45%
  |                                                                       
  |..............................                                   |  46%
  |                                                                       
  |...............................                                  |  47%
  |                                                                       
  |................................                                 |  48%
  |                                                                       
  |................................                                 |  49%
  |                                                                       
  |.................................                                |  51%
  |                                                                       
  |.................................                                |  52%
  |                                                                       
  |..................................                               |  53%
  |                                                                       
  |...................................                              |  54%
  |                                                                       
  |...................................                              |  55%
  |                                                                       
  |....................................                             |  56%
  |                                                                       
  |.....................................                            |  57%
  |                                                                       
  |.....................................                            |  58%
  |                                                                       
  |......................................                           |  59%
  |                                                                       
  |.......................................                          |  60%
  |                                                                       
  |.......................................                          |  61%
  |                                                                       
  |........................................                         |  62%
  |                                                                       
  |.........................................                        |  63%
  |                                                                       
  |.........................................                        |  64%
  |                                                                       
  |..........................................                       |  65%
  |                                                                       
  |...........................................                      |  66%
  |                                                                       
  |...........................................                      |  67%
  |                                                                       
  |............................................                     |  68%
  |                                                                       
  |.............................................                    |  69%
  |                                                                       
  |.............................................                    |  70%
  |                                                                       
  |..............................................                   |  71%
  |                                                                       
  |...............................................                  |  72%
  |                                                                       
  |...............................................                  |  73%
  |                                                                       
  |................................................                 |  74%
  |                                                                       
  |.................................................                |  75%
  |                                                                       
  |.................................................                |  76%
  |                                                                       
  |..................................................               |  77%
  |                                                                       
  |...................................................              |  78%
  |                                                                       
  |...................................................              |  79%
  |                                                                       
  |....................................................             |  80%
  |                                                                       
  |.....................................................            |  81%
  |                                                                       
  |.....................................................            |  82%
  |                                                                       
  |......................................................           |  83%
  |                                                                       
  |......................................................           |  84%
  |                                                                       
  |.......................................................          |  85%
  |                                                                       
  |........................................................         |  86%
  |                                                                       
  |........................................................         |  87%
  |                                                                       
  |.........................................................        |  88%
  |                                                                       
  |..........................................................       |  89%
  |                                                                       
  |..........................................................       |  90%
  |                                                                       
  |...........................................................      |  91%
  |                                                                       
  |............................................................     |  92%
  |                                                                       
  |............................................................     |  93%
  |                                                                       
  |.............................................................    |  94%
  |                                                                       
  |..............................................................   |  95%
  |                                                                       
  |..............................................................   |  96%
  |                                                                       
  |...............................................................  |  97%
  |                                                                       
  |................................................................ |  98%
  |                                                                       
  |................................................................ |  99%
  |                                                                       
  |.................................................................| 100%
output file: .buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R

[1] ".buildwebvig/RnaSeqGeneEdgeRQL/edgeRQL.R"
> 
>