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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('EGAD_1.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing EGAD ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── EGAD session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvxFQkr/file8698720842ed3/EGAD
→ BiocVersion: 3.24
→ Package: EGAD
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/EGAD.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvxFQkr/file8698720842ed3/EGAD
→ installDir: /tmp/RtmpvxFQkr/file869872af40d4d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EGAD ───────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.5 to 4.6.0
* 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...
* 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', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (31%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • rmarkdown
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/EGAD.Rmd
! WARNING: Evaluate more vignette chunks.
ℹ 23 out of 42 code chunks = 54% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • EGAD.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/EGAD.Rmd
* Checking package installation calls in R code...
* Checking for library/require of EGAD...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/auc_multifunc.R (line 28, column 13)
    • ...
    • R/plot_roc_overlay.R (line 43, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • auc_multifunc.R (line 28, column 20)
    • ...
    • plot_roc_overlay.R (line 47, column 80)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/build_coexp_expressionSet.R (line 40, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/filter_network_cols.R (line 37, column 11)
    • ...
    • R/plot_roc_overlay.R (line 44, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
  The longest 5 functions are:
    • neighbor_voting() (R/neighbor_voting.R): 166 lines
    • get_expression_matrix_from_GEO() (R/get_expression_matrix_from_GEO.R): 67
    lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/example_annotations.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/genes.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • build_coexp_GEOID.Rd
  • ...
  • plot_value_compare.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 238 lines (8%) are > 80 characters long.
  First few lines:
    • R/assortativity.R#L5 #' As in most literature, 'similarity' i ...
    • ...
    • vignettes/EGAD.Rmd#L790 We thank Megan Crow for helpful suggesti ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/neighbor_voting.R#L162 nans <- which(test.genes.labels == ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 12 lines (0%) are not.
  First few lines:
    • R/get_expression_data_gemma.R#L26 ...
    • ...
    • R/plot_distribution.R#L40 xlim <- range(auc_hist$breaks) ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the EGAD.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.