Back to Workflows build report for BioC 3.7

BUILD WEB VIG report for cytofWorkflow on malbec2

This page was generated on 2018-05-18 12:48:03 -0400 (Fri, 18 May 2018).

Package 5/21HostnameOS / ArchINSTALLBUILDBUILD WEB VIG
cytofWorkflow 1.2.0
Malgorzata Nowicka
Snapshot Date: 2018-05-18 07:35:08 -0400 (Fri, 18 May 2018)
URL: https://git.bioconductor.org/packages/cytofWorkflow
Branch: RELEASE_3_7
Last Commit: e4bd529
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: cytofWorkflow
Version: 1.2.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/cytofWorkflow/cytofWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/cytofWorkflow/cytofWorkflow.Rmd", ".buildwebvig/cytofWorkflow/cytofWorkflow.R")'
StartedAt: 2018-05-18 08:42:35 -0400 (Fri, 18 May 2018)
EndedAt: 2018-05-18 09:01:13 -0400 (Fri, 18 May 2018)
EllapsedTime: 1117.8 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(".buildwebvig/cytofWorkflow/cytofWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/cytofWorkflow/cytofWorkflow.Rmd", ".buildwebvig/cytofWorkflow/cytofWorkflow.R")'
###
##############################################################################
##############################################################################


> rmarkdown::render(".buildwebvig/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'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 56676 bytes (55 KB)
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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-fcs2 (with options) 
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label: load-panel
trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_panel.xlsx'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 44134 bytes (43 KB)
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label: extract-expression

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label: 01-transformation

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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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 $ fig.height: num 4
 $ fig.cap   : chr "Barplot showing the number of cells measured for each sample in the PBMC dataset. Bars are colored by experimen"| __truncated__


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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.height: num 4
 $ 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) 
List of 1
 $ message: logi FALSE

end fraction
clustered
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label: color-clusters

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label: plot-clustering-heatmap1 (with options) 
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 $ fig.cap: chr "Heatmap of the median marker intensities of the 10 lineage markers across the 20 cell populations obtained with"| __truncated__


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label: plot-clustering-distribution1 (with options) 
List of 2
 $ 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
Picking joint bandwidth of 0.128
Picking joint bandwidth of 0.164
Picking joint bandwidth of 0.142
Picking joint bandwidth of 0.113
Picking joint bandwidth of 0.0553
Picking joint bandwidth of 0.092
Picking joint bandwidth of 0.107
Picking joint bandwidth of 0.111
Picking joint bandwidth of 0.136

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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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 $ fig.cap: chr "t-SNE plot based on the arcsinh-transformed expression of the 10 lineage markers in the cells from the PBMC dat"| __truncated__


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label: tsne-plot-one-clustering1 (with options) 
List of 1
 $ fig.cap: chr "t-SNE plot based on the arcsinh-transformed expression of the 10 lineage markers in the cells from the PBMC dat"| __truncated__


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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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 $ fig.height: num 3
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label: som-codes-size

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label: plot-som-codes1-tsne

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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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 $ fig.height: num 5
 $ fig.cap   : chr "Heatmap as in Figure \\@ref(fig:plot-clustering-heatmap1), where the additional color bar on the left indicates"| __truncated__


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label: plot-clustering-heatmap1m (with options) 
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 $ fig.cap   : chr "Heatmap of the median marker intensities of the 10 lineage markers in the 8 PBMC cell populations obtained by m"| __truncated__


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label: consensus-plot (with options) 
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 $ fig.cap  : chr "The delta area plot generated in the metaclustering step by the ConsensusClusterPlus function. The delta area s"| __truncated__


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label: flowsom-meta-clustering2

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label: tsne-plot-one-clustering2 (with options) 
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 $ fig.cap: chr "t-SNE plot for the PBMC dataset, where cells are colored according to the 12 cell populations obtained with Flo"| __truncated__


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label: plot-clustering-heatmap2 (with options) 
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label: cluster-merging2
trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_cluster_merging2.xlsx'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 34877 bytes (34 KB)
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downloaded 34 KB


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label: tsne-plot-one-clustering2m (with options) 
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label: plot-clustering-heatmap2-merging (with options) 
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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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 $ fig.height: num 8
 $ fig.cap   : chr "t-SNE plots with cells colored according to (A) the expert merging of 12 metaclusters obtained with FlowSOM int"| __truncated__


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label: plot-clustering-heatmap3 (with options) 
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label: diff-FDR-cutoff

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label: diff-freqs-plot-props-barplot (with options) 
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 $ fig.cap: chr "Relative abundance of the 8 PBMC populations in each sample (x-axis), in the PBMC dataset, represented with a b"| __truncated__


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label: diff-freqs-plot-props-boxplot (with options) 
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label: diff-formula-glmer-binomial

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label: diff-differential-abundance-wrapper

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label: diff-freqs-plot-heatmap-with-significant-clusters (with options) 
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label: diff-expr2-median-expression

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label: diff-expr2-plot-median-expr (with options) 
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 $ fig.height: num 8
 $ fig.cap   : chr "Median (arcsinh-transformed) expression of 14 signaling markers (x-axis) across the 8 identified PBMC cell popu"| __truncated__


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label: diff-differential-expression-wrapper

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label: diff-expr2-formula

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label: diff-expr2-plot-heatmap-with-significant-markers (with options) 
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 $ fig.cap   : chr "Normalized expression of signaling markers in the 8 PBMC populations that are significantly differentially expr"| __truncated__


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label: diff-expr1-plot-median-expr (with options) 
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label: diff-expr1-fit-model

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label: diff-expr1-plot-heatmap-with-significant-markers (with options) 
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label: unnamed-chunk-2 (with options) 
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 $ results: chr "asis"
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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(".buildwebvig/cytofWorkflow/cytofWorkflow.Rmd", ".buildwebvig/cytofWorkflow/cytofWorkflow.R")


processing file: .buildwebvig/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: .buildwebvig/cytofWorkflow/cytofWorkflow.R

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