Package: MAGeCKFlute

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MAGeCKFlute

StartedAt: 2020-01-15 23:43:48 -0500 (Wed, 15 Jan 2020)

EndedAt: 2020-01-15 23:58:33 -0500 (Wed, 15 Jan 2020)

EllapsedTime: 884.3 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MAGeCKFlute
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* checking for file ‘MAGeCKFlute/DESCRIPTION’ ... OK
* preparing ‘MAGeCKFlute’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MAGeCKFlute.Rmd’ using rmarkdown

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Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
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MAGeCKFlute is an open source software package. Users are required to formally
cite the original MAGeCKFlute paper in publications.
2020-01-15 23:45:06 # Read gene summary file ...
2020-01-15 23:45:06 # Read sgRNA summary file ...
trying URL 'https://ndownloader.figshare.com/files/20234073'
Content type 'text/csv' length 199874652 bytes (190.6 MB)
==================================================
downloaded 190.6 MB

Quitting from lines 135-137 (MAGeCKFlute.Rmd) 
Error: processing vignette 'MAGeCKFlute.Rmd' failed with diagnostics:
missing values in 'row.names' are not allowed
--- failed re-building ‘MAGeCKFlute.Rmd’

--- re-building ‘MAGeCKFlute_enrichment.Rmd’ using rmarkdown
2020-01-15 23:48:03 # Read gene summary file ...
2020-01-15 23:48:03 # Running Pathway+GOBP enrichment analysis
	500 genes are mapped ...
	500 genes are mapped ...
2020-01-15 23:50:52 # Running Pathway+GOBP enrichment analysis
	500 genes are mapped ...
	500 genes are mapped ...
2020-01-15 23:51:23 # Running Pathway+GOBP enrichment analysis
	10243 genes are mapped ...
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
	10243 genes are mapped ...
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
wrong orderBy parameter; set to default `orderBy = "x"`
2020-01-15 23:53:39 # Running KEGG+REACTOME enrichment analysis
	445 genes are mapped ...
2020-01-15 23:53:45 # Running KEGG enrichment analysis
	243 genes are mapped ...
2020-01-15 23:53:47 # Running GOBP+GOMF enrichment analysis
	496 genes are mapped ...
2020-01-15 23:54:54 # Running CORUM+CPX enrichment analysis
	337 genes are mapped ...
2020-01-15 23:54:59 # Running GOBP+KEGG enrichment analysis
	485 genes are mapped ...
2020-01-15 23:55:47 # Running GOBP enrichment analysis
	433 genes are mapped ...
2020-01-15 23:56:15 # Running GOMF+GOBP enrichment analysis
	496 genes are mapped ...
2020-01-15 23:57:20 # Running GOMF+GOBP enrichment analysis
	496 genes are mapped ...
Error reading bibliography ./library.bib (line 106, column 10):
unexpected ","
expecting white space
Error running filter /usr/local/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'MAGeCKFlute_enrichment.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘MAGeCKFlute_enrichment.Rmd’

SUMMARY: processing the following files failed:
  ‘MAGeCKFlute.Rmd’ ‘MAGeCKFlute_enrichment.Rmd’

Error: Vignette re-building failed.
Execution halted