Back to Workflows build report for BioC 3.7

BUILD VIG report for cytofWorkflow on malbec2

This page was generated on 2018-02-28 12:45:06 -0500 (Wed, 28 Feb 2018).

Package 4/6HostnameOS / ArchINSTALLBUILDBUILD VIG
cytofWorkflow 1.0.4
Malgorzata Nowicka
Snapshot Date: 2018-02-28 12:11:02 -0500 (Wed, 28 Feb 2018)
URL: https://git.bioconductor.org/packages/cytofWorkflow
Branch: master
Last Commit: d21814b
Last Changed Date: 2017-11-27 16:12:51 -0500 (Mon, 27 Nov 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]YES, package does not exist in internal repository.

Summary

Package: cytofWorkflow
Version: 1.0.4
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildvig/cytofWorkflow/cytofWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildvig/cytofWorkflow/cytofWorkflow.Rmd", ".buildvig/cytofWorkflow/cytofWorkflow.R")'
StartedAt: 2018-02-28 12:31:21 -0500 (Wed, 28 Feb 2018)
EndedAt: 2018-02-28 12:41:16 -0500 (Wed, 28 Feb 2018)
EllapsedTime: 595.0 seconds
RetCode: 0
Status:  OK 

Command output

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


> rmarkdown::render(".buildvig/cytofWorkflow/cytofWorkflow.Rmd", output_format="BiocStyle:::html_fragment")


processing file: cytofWorkflow.Rmd

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label: setup_knitr (with options) 
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label: libraries (with options) 
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label: load-metadata
trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_metadata.xlsx'
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label: download-fcs
trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_fcs_files.zip'
Content type 'application/zip' length 21513634 bytes (20.5 MB)
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label: load-fcs (with options) 
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label: load-panel
trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_panel.xlsx'
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label: sample-ids

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label: plot-merker-expression-distribution (with options) 
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 $ fig.cap: chr "Per-sample smoothed densities of marker expression (arcsinh-transformed) of 10 lineage markers and 14 functiona"| __truncated__


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label: plot-number-of-cells (with options) 
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label: plot-mds (with options) 
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 $ fig.cap: chr "MDS plot for the unstimulated (Ref) and stimulated with BCR/FcR-XL (BCRXL) samples obtained for each of the 8 h"| __truncated__


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label: plot-dendogram (with options) 
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 $ fig.cap: chr "Heatmap of the median (arcsinh-transformed) marker expression of 10 lineage markers and 14 functional markers a"| __truncated__


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label: nrs (with options) 
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 $ fig.cap   : chr "Non-redundancy scores for each of the 10 lineage markers and all samples in the PBMC dataset. The full points r"| __truncated__


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label: flowsom-som
Building SOM

Mapping data to SOM


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label: flowsom-meta-clustering (with options) 
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end fraction
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label: color-clusters

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label: plot-clustering-heatmap1 (with options) 
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label: plot-clustering-distribution1 (with options) 
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 $ fig.height: num 8
 $ fig.cap   : chr "Distributions of marker intensities (arcsinh-transformed) of the 10 lineage markers in the 20 cell populations "| __truncated__

Picking joint bandwidth of 0.127
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Picking joint bandwidth of 0.164
Picking joint bandwidth of 0.142
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Picking joint bandwidth of 0.0553
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Picking joint bandwidth of 0.107
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label: plot-clustering-heatmap1-complex (with options) 
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 $ fig.cap: chr "Heatmap of the median marker intensities of the 10 lineage markers and one signaling marker (pS6) across the 20"| __truncated__


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label: tsne-duplicates-subsampling

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label: tsne-run

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label: tsne-plot-one-expr-CD4 (with options) 
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label: tsne-plot-one-clustering1 (with options) 
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label: tsne-plot-facet-sample (with options) 
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 $ fig.cap: chr "t-SNE plot as in the Figure \\@ref(fig:tsne-plot-one-clustering1), but stratified by sample."


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label: tsne-plot-facet-condition (with options) 
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label: som-codes-size

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label: plot-som-codes1-pca (with options) 
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label: plot-som-codes1-heatmap-complex (with options) 
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label: cluster-merging1
trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_cluster_merging1.xlsx'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 39596 bytes (38 KB)
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label: tsne-plot-one-clustering1m (with options) 
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label: plot-clustering-heatmap1m-merging (with options) 
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label: plot-clustering-heatmap1m (with options) 
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label: consensus-plot (with options) 
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label: cluster-merging2
trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_cluster_merging2.xlsx'
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label: plot-clustering-heatmap2m (with options) 
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label: flowsom-meta-clustering3

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label: tsne-plot-one-clustering3 (with options) 
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label: diff-freqs-plot-props-barplot (with options) 
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label: diff-differential-abundance-wrapper

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label: diff-expr2-plot-median-expr (with options) 
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label: diff-expr2-plot-heatmap-with-significant-markers (with options) 
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label: diff-expr1-plot-median-expr (with options) 
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label: unnamed-chunk-2 (with options) 
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label: unnamed-chunk-3 (with options) 
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label: sessionInfo

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output file: cytofWorkflow.knit.md

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


processing file: .buildvig/cytofWorkflow/cytofWorkflow.Rmd

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  |...............................................................  |  97%Error in eval(x, envir = envir) : object 'on.bioc' not found

  |                                                                       
  |................................................................ |  98%Error in eval(x, envir = envir) : object 'on.bioc' not found

  |                                                                       
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output file: .buildvig/cytofWorkflow/cytofWorkflow.R

[1] ".buildvig/cytofWorkflow/cytofWorkflow.R"
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>