Back to Workflows build report for BioC 3.8

BUILD WEB VIG report for chipseqDB on malbec1

This page was generated on 2018-05-18 09:51:44 -0400 (Fri, 18 May 2018).

Package 4/21HostnameOS / ArchINSTALLBUILD
chipseqDB 1.3.0
Aaron Lun
Snapshot Date: 2018-05-18 07:35:07 -0400 (Fri, 18 May 2018)
URL: https://git.bioconductor.org/packages/chipseqDB
Branch: master
Last Commit: 78bb70e
Last Changed Date: 2018-04-30 10:10:33 -0400 (Mon, 30 Apr 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chipseqDB
Version: 1.3.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-1-intro.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-1-intro.Rmd", ".buildwebvig/chipseqDB/work-1-intro.R")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", ".buildwebvig/chipseqDB/work-3-h3k9ac.R")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-4-cbp.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-4-cbp.Rmd", ".buildwebvig/chipseqDB/work-4-cbp.R")'
StartedAt: 2018-05-18 08:43:42 -0400 (Fri, 18 May 2018)
EndedAt: 2018-05-18 09:15:19 -0400 (Fri, 18 May 2018)
EllapsedTime: 1897.5 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-1-intro.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-1-intro.Rmd", ".buildwebvig/chipseqDB/work-1-intro.R")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", ".buildwebvig/chipseqDB/work-3-h3k9ac.R")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/chipseqDB/work-4-cbp.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.8-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/chipseqDB/work-4-cbp.Rmd", ".buildwebvig/chipseqDB/work-4-cbp.R")'
###
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> rmarkdown::render(".buildwebvig/chipseqDB/work-1-intro.Rmd", output_format="BiocStyle:::html_fragment")


processing file: work-1-intro.Rmd

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output file: work-1-intro.knit.md

/usr/bin/pandoc +RTS -K512m -RTS work-1-intro.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output work-1-intro.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: work-1-intro.html
> 
> 
> knitr::purl(".buildwebvig/chipseqDB/work-1-intro.Rmd", ".buildwebvig/chipseqDB/work-1-intro.R")


processing file: .buildwebvig/chipseqDB/work-1-intro.Rmd

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output file: .buildwebvig/chipseqDB/work-1-intro.R

[1] ".buildwebvig/chipseqDB/work-1-intro.R"
> 
> 
> rmarkdown::render(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", output_format="BiocStyle:::html_fragment")


processing file: work-3-h3k9ac.Rmd

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 $ eval   : language !remap
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Loading required package: GenomeInfoDb
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

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    IQR, mad, sd, var, xtabs

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    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
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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
Loading required package: stats4

Attaching package: 'S4Vectors'

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Loading required package: IRanges
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 $ eval   : symbol redownload
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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/matureB-8059.bam'
Content type 'binary/octet-stream' length 617154673 bytes (588.6 MB)
==================================================
downloaded 588.6 MB

trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/matureB-8059.bam.bai'
Content type 'binary/octet-stream' length 5321936 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/matureB-8086.bam'
Content type 'binary/octet-stream' length 243983790 bytes (232.7 MB)
==================================================
downloaded 232.7 MB

trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/matureB-8086.bam.bai'
Content type 'binary/octet-stream' length 5276984 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/proB-8108.bam'
Content type 'binary/octet-stream' length 343361633 bytes (327.5 MB)
==================================================
downloaded 327.5 MB

trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/proB-8108.bam.bai'
Content type 'binary/octet-stream' length 5324456 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/proB-8113.bam'
Content type 'binary/octet-stream' length 325151168 bytes (310.1 MB)
==================================================
downloaded 310.1 MB

trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/proB-8113.bam.bai'
Content type 'binary/octet-stream' length 5347848 bytes (5.1 MB)
==================================================
downloaded 5.1 MB


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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/mm10.blacklist.bed.gz'
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==================================================
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Loading required package: SummarizedExperiment
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'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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    type

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output file: work-3-h3k9ac.knit.md

/usr/bin/pandoc +RTS -K512m -RTS work-3-h3k9ac.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output work-3-h3k9ac.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: work-3-h3k9ac.html
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 9 out-of-bound ranges located on sequences
  chr1_GL456212_random, chr1_GL456221_random, chr4_GL456350_random,
  chr4_JH584293_random, and chr4_JH584294_random. Note that ranges
  located on a sequence whose length is unknown (NA) or on a circular
  sequence are not considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
> 
> 
> knitr::purl(".buildwebvig/chipseqDB/work-3-h3k9ac.Rmd", ".buildwebvig/chipseqDB/work-3-h3k9ac.R")


processing file: .buildwebvig/chipseqDB/work-3-h3k9ac.Rmd

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output file: .buildwebvig/chipseqDB/work-3-h3k9ac.R

[1] ".buildwebvig/chipseqDB/work-3-h3k9ac.R"
> 
> 
> rmarkdown::render(".buildwebvig/chipseqDB/work-4-cbp.Rmd", output_format="BiocStyle:::html_fragment")


processing file: work-4-cbp.Rmd

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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145787.bam'
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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145787.bam.bai'
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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145788.bam'
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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145788.bam.bai'
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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145789.bam'
Content type 'binary/octet-stream' length 2082656812 bytes (1986.2 MB)
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downloaded 1986.2 MB

trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145789.bam.bai'
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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145790.bam'
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trying URL 'http://s3.amazonaws.com/chipseqdb-bamfiles/SRR1145790.bam.bai'
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output file: work-4-cbp.knit.md

/usr/bin/pandoc +RTS -K512m -RTS work-4-cbp.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output work-4-cbp.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: work-4-cbp.html
> 
> 
> knitr::purl(".buildwebvig/chipseqDB/work-4-cbp.Rmd", ".buildwebvig/chipseqDB/work-4-cbp.R")


processing file: .buildwebvig/chipseqDB/work-4-cbp.Rmd

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output file: .buildwebvig/chipseqDB/work-4-cbp.R

[1] ".buildwebvig/chipseqDB/work-4-cbp.R"
> 
>