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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('MLInterfaces_1.92.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MLInterfaces ─────────────────────────────────────────────────────
✔ Package installed successfully
── MLInterfaces session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsYj11w/file837c42f330bad/MLInterfaces
→ BiocVersion: 3.23
→ Package: MLInterfaces
→ PackageVersion: 1.92.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MLInterfaces.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpsYj11w/file837c42f330bad/MLInterfaces
→ installDir: /tmp/RtmpsYj11w/file837c43b7bdfdc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MLInterfaces ───────────────────────────────────────────
* 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 3.5 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 that Package field matches directory/tarball name...
* Checking for Version: field...
* 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 (19%).
* 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:
    • xvalComputerClusters.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • MLprac2_2.Rmd
    • xvalComputerClusters.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/MLint_devel.Rmd
    • vignettes/xvalComputerClusters.Rnw
* Checking package installation calls in R code...
* Checking for library/require of MLInterfaces...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/MLearn.R (line 216, column 22)
    • ...
    • R/plspinHcube.R (line 265, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • varImp.R (line 43, column 24)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/localBridge.R (line 20, column 5)
    • ...
    • print() in R/RAB.R (line 89, column 2)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 116, column 33)
    • ...
    • R/varImp.R (line 80, column 20)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/MLearn.R (line 14, column 51)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/MLearn.R (line 217, column 35)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • localBridge.R (line 239, column 18)
    • ...
    • varImp.R (line 30, column 39)
! WARNING: Remove set.seed usage (found 3 times)
  • set.seed() in R/mlw.R (line 123, column 6)
  • set.seed() in R/mlw.R (line 155, column 14)
  • set.seed() in R/mlw.R (line 174, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/projectLearnerToGrid.Rd
ℹ Found @ in vignettes/MLint_devel.Rmd
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 9
functions greater than 50 lines.
  The longest 5 functions are:
    • mlearnWidget() (R/mlw.R): 166 lines
    • ...
    • _anonymous_.155() (R/MLearn.R): 108 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/confuMat-methods.Rd
    • man/performance-analytics.Rd
    • man/planarPlot-methods.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • MLIntInternals.Rd
  • predict.classifierOutput.Rd
  • xvalLoop.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:
    • predict.classifierOutput.Rd
    • xvalLoop.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • predict.classifierOutput.Rd
    • xvalLoop.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; 359 lines (6%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L96 partitionFunc = fun ...
    • ...
    • vignettes/xvalComputerClusters.Rnw#L302 An emphasis is the division of
    labor bet ...
ℹ NOTE: Consider 4 spaces instead of tabs; 94 lines (1%) contain tabs.
  First few lines:
    • R/AllClasses.R#L5 ## packageName="character", ...
    • ...
    • man/raboostCont-class.Rd#L35 % or \code{\linkS4class{CLASSNAME}} for ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1445 lines (23%) are
not.
  First few lines:
    • R/AllClasses.R#L20 representation(packageName="cha ...
    • ...
    • vignettes/xvalComputerClusters.Rnw#L214 \label{fig:clusterResults} ...
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 504 Gateway
Timeout.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 20 NOTES
ℹ See the MLInterfaces.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.