Error(s) in re-building vignettes:
--- re-building 'case_study.Rmd' using rmarkdown
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

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

    getClasses, getMethods

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

    attach, detach, load, save

R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

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

    cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
    warnings


Attaching package: 'igraph'

The following object is masked from 'package:R.oo':

    hierarchy

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

    decompose, spectrum

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    union

Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    normalize, path, union

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

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: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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    I, expand.grid, unname


Attaching package: 'IRanges'

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    trim

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    windows



clusterProfiler v4.3.4  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141

Attaching package: 'clusterProfiler'

The following object is masked from 'package:AnnotationDbi':

    select

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    slice

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    rename

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    simplify

The following object is masked from 'package:stats':

    filter

trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 11004 bytes (10 KB)
==================================================
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)
==================================================
downloaded 57 KB

Picking joint bandwidth of 0.0412
Picking joint bandwidth of 0.0496
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Warning in utils::download.file(url, quiet = TRUE, method = method, ...) :
  URL 'https://rest.kegg.jp/link/hsa/pathway': status was 'Failure when receiving data from the peer'
Quitting from lines 240-254 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
Failed to download KEGG data. Wrong 'species' or the network is unreachable. The 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'
--- failed re-building 'case_study.Rmd'

--- re-building 'using_cRegulome.Rmd' using rmarkdown
Picking joint bandwidth of 0.0445
--- finished re-building 'using_cRegulome.Rmd'

SUMMARY: processing the following file failed:
  'case_study.Rmd'

Error: Vignette re-building failed.
Execution halted