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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ViSEAGO_1.27.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ViSEAGO ──────────────────────────────────────────────────────────
✔ Package installed successfully
── ViSEAGO session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKqKpEE/file152b9c3cf07621/ViSEAGO
→ BiocVersion: 3.24
→ Package: ViSEAGO
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ViSEAGO.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpKqKpEE/file152b9c3cf07621/ViSEAGO
→ installDir: /tmp/RtmpKqKpEE/file152b9c4025ffa7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ViSEAGO ────────────────────────────────────────────────
* 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...
ℹ NOTE: Update R version dependency from 3.6 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
FunctionalGenomics, ExperimentalDesign
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
ℹ NOTE: License 'GPL-3 bioconductor.org' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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: Package installation calls found in vignette(s)
  Found in files:
    • vignettes/ViSEAGO.Rmd (chunk no. 2, line 49, column 14)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/fgsea_alternative.Rmd
    • vignettes/SS_choice.Rmd
    • vignettes/ViSEAGO.Rmd
! WARNING: Vignette set global option 'eval=FALSE'
  Found in files:
    • vignettes/fgsea_alternative.Rmd
    • ...
    • vignettes/ViSEAGO.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ViSEAGO...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/annotate.R (line 306, column 13)
    • require() in R/create_topGOdata.R (line 138, column 9)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • GOcount.R (line 96, column 22)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotate.R (line 158, column 18)
    • ...
    • R/Upset.R (line 95, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/annotate.R (line 296, column 21)
    • R/GOclusters_heatmap.R (line 126, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • T in R/MDSplot.R (line 134, column 49)
    • ...
    • T in R/merge_enrich_terms.R (line 1064, column 109)
* 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 31
functions greater than 50 lines.
  The longest 5 functions are:
    • definition() (R/GOterms_heatmap.R): 1016 lines
    • ...
    • definition() (R/compare_clusters.R): 311 lines
* Checking man page documentation...

Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’
Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • annotate-methods.Rd
    • ...
    • Uniprot2GO.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 55% of man
pages use at least one of these tags.
  Found in files:
    • annotate-methods.Rd
    • ...
    • Uniprot2GO.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • annotate-methods.Rd
    • ...
    • Uniprot2GO.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; 513 lines (6%) are > 80 characters long.
  First few lines:
    • R/annotate.R#L14 #' @param object a required \code{\link{ ...
    • ...
    • vignettes/ViSEAGO.Rmd#L466 Moreover, we can explore the effect of t ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 102 lines (1%) are
not.
  First few lines:
    • R/annotate.R#L354 values=TRUE, ...
    • ...
    • vignettes/ViSEAGO.Rmd#L467 ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the ViSEAGO.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.