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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Pigengene_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Pigengene ────────────────────────────────────────────────────────
✔ Package installed successfully
── Pigengene session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGcJqEW/fileffca049432d58/Pigengene
→ BiocVersion: 3.24
→ Package: Pigengene
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Pigengene.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpGcJqEW/fileffca049432d58/Pigengene
→ installDir: /tmp/RtmpGcJqEW/fileffca04e3c9849
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Pigengene ──────────────────────────────────────────────
* 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 4.0.3 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:
GenePrediction, Bayesian
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...
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • Pigengene_inference.Rnw
* Checking package installation calls in R code...
* Checking for library/require of Pigengene...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/dcor.matrix.R (line 13, column 20)
    • ...
    • require() in R/hu.mouse.R (line 10, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/module.heatmap.R (line 51, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • add.noise.R (line 37, column 43)
    • ...
    • welch.pvalue.R (line 15, column 16)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/apply.filter.R (line 13, column 9)
    • ...
    • print() in R/wgcna.one.step.R (line 33, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/make.bn.input.R (line 58, column 11)
    • ...
    • R/module.heatmap.R (line 72, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/add.noise.R (line 25, column 17)
    • ...
    • R/wgcna.one.step.R (line 31, column 17)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/determine.modules.R (line 45, column 5)
    • ...
    • system() in R/which.cluster.R (line 19, column 23)
! WARNING: Remove set.seed usage (found 4 times)
  • set.seed() in R/add.noise.R (line 12, column 5)
  • ...
  • set.seed() in R/noise.analysis.R (line 14, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/compute.pigengene.R (line 110, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 24
functions greater than 50 lines.
  The longest 5 functions are:
    • make.decision.tree() (R/make.decision.tree.R): 223 lines
    • ...
    • bn.calculation() (R/bn.calculation.R): 182 lines
* Checking man page documentation...

ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • draw.bn.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; 464 lines (6%) are > 80 characters long.
  First few lines:
    • R/add.noise.R#L5 ## Adds Gaussian noise to the testD ...
    • ...
    • vignettes/Pigengene_inference.Rnw#L279 hematological malignancies is
    presented ...
ℹ NOTE: Consider 4 spaces instead of tabs; 22 lines (0%) contain tabs.
  First few lines:
    • R/apply.filter.R#L21 ## QC ...
    • ...
    • vignettes/Pigengene_inference.Rnw#L253 verbose=1, toCompact=FALS ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1226 lines (17%) are
not.
  First few lines:
    • R/bn.calculation.R#L124 algorithm. ...
    • ...
    • vignettes/Pigengene_inference.Rnw#L270 Org=NULL, OrgDb=or ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the Pigengene.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.