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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('netboost_2.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing netboost ─────────────────────────────────────────────────────────
✔ Package installed successfully
── netboost session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCT5N75/filef6c5a784e206f/netboost
→ BiocVersion: 3.24
→ Package: netboost
→ PackageVersion: 2.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/netboost.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpCT5N75/filef6c5a784e206f/netboost
→ installDir: /tmp/RtmpCT5N75/filef6c5a71c4c926
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on netboost ───────────────────────────────────────────────
* 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 4.0.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (8%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of netboost...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/netboost.R (line 7, column 32)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • netboost.R (line 339, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/nb_consensus.R (line 390, column 14)
    • ...
    • R/zzz.R (line 95, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/netboost.R (line 102, column 18)
    • ...
    • R/zzz.R (line 96, column 23)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Avoid 'Sys.setenv' (found 1 times)
  • Sys.setenv() in R/netboost.R (line 6, column 1)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • nb_consensus() (R/nb_consensus.R): 693 lines
    • ...
    • nb_summary() (R/netboost.R): 156 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • nb_moduleEigengenes.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • dot-onAttach.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • dot-onAttach.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; 55 lines (2%) are > 80 characters long.
  First few lines:
    • R/nb_consensus.R#L47 #' @param deepSplit Integer passed to \c ...
    • ...
    • vignettes/netboost.Rmd#L124 Netboost now also has a fully non-parame ...
ℹ NOTE: Consider 4 spaces instead of tabs; 42 lines (1%) contain tabs.
  First few lines:
    • R/netboost.R#L53 #' @param robust_PCs Should PCA be calcu ...
    • ...
    • R/netboost.R#L1662 message(paste(space ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 252 lines (7%) are
not.
  First few lines:
    • R/nb_consensus.R#L143 i, nrow(d))) ...
    • ...
    • vignettes/netboost.Rmd#L56 For details on the options please see ` ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the netboost.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.