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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('geNetClassifier_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing geNetClassifier ──────────────────────────────────────────────────
✔ Package installed successfully
── geNetClassifier session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpg2WpQR/filea3bee30a534b9/geNetClassifier
→ BiocVersion: 3.24
→ Package: geNetClassifier
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/geNetClassifier.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpg2WpQR/filea3bee30a534b9/geNetClassifier
→ installDir: /tmp/Rtmpg2WpQR/filea3bee1ecc5526
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on geNetClassifier ────────────────────────────────────────
* 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 2.10.1 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpg2WpQR/filea3bee30a534b9/geNetClassifier/man/getSubNetwork-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpg2WpQR/filea3bee30a534b9/geNetClassifier/man/numGenes-methods.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Network, Clustering, NetworkInference, GraphAndNetwork
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (43%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • geNetClassifier-vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • geNetClassifier-vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/geNetClassifier-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of geNetClassifier...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/class.GeNetClassifierReturn.R (line 88, column 45)
    • ...
    • R/functions.public.R (line 1523, column 82)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • class.GeneralizationError.R (line 73, column 69)
    • ...
    • functions.public.R (line 1523, column 138)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • functions.private.R (line 303, column 63)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/class.GeneralizationError.R (line 60, column 9)
    • ...
    • print() in R/functions.public.R (line 868, column 45)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/functions.public.R (line 168, column 12)
    • R/functions.public.R (line 285, column 23)
    • R/functions.public.R (line 1544, column 30)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/function.main.R (line 78, column 45)
    • ...
    • R/functions.public.R (line 1632, column 35)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/function.main.R (line 102, column 43)
    • ...
    • R/function.main.R (line 772, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • class.GenesNetwork.R (line 105, column 43)
    • ...
    • functions.public.R (line 1305, column 50)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/calculateGenesRanking.Rd
ℹ Found @ in man/gClasses-methods.Rd
ℹ Found @ in man/GeneralizationError-class.Rd
ℹ Found @ in man/genesDetails-methods.Rd
ℹ Found @ in man/GenesNetwork-class.Rd
ℹ Found @ in man/GenesRanking-class.Rd
ℹ Found @ in man/GeNetClassifierReturn-class.Rd
ℹ Found @ in man/getEdges-methods.Rd
ℹ Found @ in man/getNodes-methods.Rd
ℹ Found @ in man/getNumEdges-methods.Rd
ℹ Found @ in man/getNumNodes-methods.Rd
ℹ Found @ in man/getRanking-methods.Rd
ℹ Found @ in man/getSubNetwork-methods.Rd
ℹ Found @ in man/getTopRanking-methods.Rd
ℹ Found @ in man/leukemiasClassifier.Rd
ℹ Found @ in man/network2txt.Rd
ℹ Found @ in man/numGenes-methods.Rd
ℹ Found @ in man/numSignificantGenes-methods.Rd
ℹ Found @ in man/overview-methods.Rd
ℹ Found @ in man/plot.GenesRanking.Rd
ℹ Found @ in man/plotDiscriminantPower.Rd
ℹ Found @ in man/plotExpressionProfiles.Rd
ℹ Found @ in man/plotNetwork.Rd
ℹ Found @ in vignettes/geNetClassifier-vignette.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 18
functions greater than 50 lines.
  The longest 5 functions are:
    • geNetClassifier() (R/function.main.R): 881 lines
    • ...
    • calculateGenesRanking() (R/functions.public.R): 143 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/queryGeNetClassifier.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/gClasses-methods.Rd
    • ...
    • man/setProperties-methods.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • setProperties-methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
  Found in files:
    • calculateGenesRanking.Rd
    • GenesRanking-class.Rd
    • geNetClassifier.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • calculateGenesRanking.Rd
    • GenesRanking-class.Rd
    • geNetClassifier.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; 1471 lines (18%) are > 80 characters long.
  First few lines:
    • R/class.GeneralizationError.R#L2 # test <- new("GeneralizationError", ...
    • ...
    • vignettes/geNetClassifier-vignette.Rnw#L947 \bibitem{fdr} Benjamini Y,
    Hochberg Y (1 ...
ℹ NOTE: Consider 4 spaces instead of tabs; 33 lines (0%) contain tabs.
  First few lines:
    • man/GeneralizationError-class.Rd#L39 \examples{ ...
    • ...
    • man/plotNetwork.Rd#L78 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 420 lines (5%) are
not.
  First few lines:
    • R/class.GeneralizationError.R#L3 ...
    • ...
    • vignettes/geNetClassifier-vignette.Rnw#L781 type="boxplot", g ...
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 22 NOTES
ℹ See the geNetClassifier.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.