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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('LedPred_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing LedPred ──────────────────────────────────────────────────────────
✔ Package installed successfully
── LedPred session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUGmEY5/filec8242270fa67a/LedPred
→ BiocVersion: 3.24
→ Package: LedPred
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/LedPred.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUGmEY5/filec8242270fa67a/LedPred
→ installDir: /tmp/RtmpUGmEY5/filec82422c25395c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on LedPred ────────────────────────────────────────────────
* 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 3.2.0 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • LedPred.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • LedPred.Rnw
* Checking package installation calls in R code...
* Checking for library/require of LedPred...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/Model.R (line 55, column 7)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/FeatureRanking.R (line 55, column 30)
    • ...
    • R/ModelPerformance.R (line 79, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Data.R (line 60, column 31)
    • ...
    • ParameterTuner.R (line 138, column 26)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/createModel.R (line 25, column 13)
    • ...
    • R/tuneFeatureNb.R (line 37, column 18)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/FeatureRanking.R (line 70, column 7)
  • set.seed() in R/Model.R (line 76, column 7)
* 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 4
functions greater than 50 lines.
  The longest 5 functions are:
    • mcTune() (R/ParameterTuner.R): 163 lines
    • ...
    • FUN() (R/ParameterTuner.R): 62 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/crm.features.Rd
    • man/feature.ranking.Rd
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘LedPred’
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • mapFeaturesToCRMs.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
  Found in files:
    • mapFeaturesToCRMs.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • mapFeaturesToCRMs.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; 258 lines (15%) are > 80 characters long.
  First few lines:
    • R/createModel.R#L3 #' \code{createModel} function creates a ...
    • ...
    • vignettes/LedPred.Rnw#L323 Chang, Chih-Chung and Lin, Chih-Jen : \t ...
ℹ NOTE: Consider 4 spaces instead of tabs; 14 lines (1%) contain tabs.
  First few lines:
    • R/mapFeaturesToCRMs.R#L181 while (!RCurl::url.exists(json.decoded[ ...
    • ...
    • R/scoreData.R#L30 write.table(scores, file=score.file, qu ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 537 lines (32%) are
not.
  First few lines:
    • R/createModel.R#L26 1, valid.times = 10, featur ...
    • ...
    • R/tuneFeatureNb.R#L39 valid.times, ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 16 NOTES
ℹ See the LedPred.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.