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--- re-building ‘case_study.Rmd’ using rmarkdown
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

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    attach, detach, gc, load, save

R.utils v2.8.0 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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Attaching package: 'igraph'

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Loading required package: stats4
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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")'.

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clusterProfiler v3.11.1  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

Attaching package: 'clusterProfiler'

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trying URL ‘https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx’
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/zip' length 11004 bytes (10 KB)
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downloaded 10 KB

trying URL ‘https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s003.xls’
Content type 'application/vnd.ms-office' length 58880 bytes (57 KB)
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downloaded 57 KB

Picking joint bandwidth of 0.0412
Quitting from lines 117-121 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘case_study.Rmd’

--- re-building ‘using_cRegulome.Rmd’ using rmarkdown
Quitting from lines 85-87 (using_cRegulome.Rmd) 
Error: processing vignette 'using_cRegulome.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using_cRegulome.Rmd’

SUMMARY: processing the following files failed:
  ‘case_study.Rmd’ ‘using_cRegulome.Rmd’

Error: Vignette re-building failed.
Execution halted