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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('EnrichmentBrowser_2.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing EnrichmentBrowser ────────────────────────────────────────────────
✔ Package installed successfully
── EnrichmentBrowser session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/Rtmpv5mGxk/file878ae234029e8/EnrichmentBrowser
→ BiocVersion: 3.24
→ Package: EnrichmentBrowser
→ PackageVersion: 2.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/EnrichmentBrowser.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpv5mGxk/file878ae234029e8/EnrichmentBrowser
→ installDir: /tmp/Rtmpv5mGxk/file878ae2fced6e1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EnrichmentBrowser ──────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
RIPSeq, Coverage
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (79%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • EnrichmentBrowser.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/EnrichmentBrowser.Rmd
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install() in R/utils.R (line 44, column 40)
* Checking for library/require of EnrichmentBrowser...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/utils.R (line 47, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/deAna.R (line 144, column 30)
    • ...
    • R/sbea.R (line 780, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • compileGRN.R (line 145, column 43)
    • ...
    • sbea.R (line 869, column 30)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/downloadKEGGPathways.R (line 72, column 9)
    • ...
    • print() in R/plots.R (line 81, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ggeaGraph.R (line 206, column 37)
    • ...
    • R/SAMGS.R (line 323, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/compileGRN.R (line 87, column 14)
    • ...
    • R/utils.R (line 209, column 35)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/pathview2.R (line 67, column 17)
    • ...
    • R/SAMGS.R (line 112, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 7 times:
    • T in R/pathview2.R (line 74, column 52)
    • ...
    • F in R/pathview2.R (line 229, column 104)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • getGenesets.R (line 881, column 37)
    • pathview2.R (line 75, column 24)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/downloadKEGGPathways.R (line 79, column 9)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/GSEA.1.0.R (line 217, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 20 times)
  • suppressMessages() in R/deAna.R (line 213, column 5)
  • ...
  • suppressMessages() in R/probe2gene.R (line 223, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 34
functions greater than 50 lines.
  The longest 5 functions are:
    • GSEA() (R/GSEA.1.0.R): 438 lines
    • ...
    • eaBrowse() (R/html.R): 136 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/export.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • downloadPathways.Rd
  • isAvailable.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 15% of man
pages use at least one of these tags.
  Found in files:
    • downloadPathways.Rd
    • getGenesets.Rd
    • isAvailable.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 149 lines (1%) are > 80 characters long.
  First few lines:
    • R/compileGRN.R#L27 #' 'reactome', 'pathbank', and 'wikipath ...
    • ...
    • vignettes/EnrichmentBrowser.Rmd#L909 dimnames = list(c("DE" ...
ℹ NOTE: Consider 4 spaces instead of tabs; 108 lines (1%) contain tabs.
  First few lines:
    • R/deAna.R#L133 } ...
    • ...
    • R/sbea.R#L484 x <- assay(se) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 229 lines (2%) are
not.
  First few lines:
    • R/compileGRN.R#L206 out.file=NULL ...
    • ...
    • vignettes/EnrichmentBrowser.Rmd#L909 dimnames = list(c("DE" ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 22 NOTES
ℹ See the EnrichmentBrowser.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.