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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('oligoClasses_1.75.0.tar.gz','quit-with-status'=TRUE)"
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── Installing oligoClasses ─────────────────────────────────────────────────────
✔ Package installed successfully
── oligoClasses session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpVWrFXF/filef929725419f3b/oligoClasses
→ BiocVersion: 3.24
→ Package: oligoClasses
→ PackageVersion: 1.75.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/oligoClasses.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpVWrFXF/filef929725419f3b/oligoClasses
→ installDir: /tmp/RtmpVWrFXF/filef92972da48653
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on oligoClasses ───────────────────────────────────────────
* 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 2.14 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', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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...
✖ ERROR: No vignette sources in vignettes/ directory.
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/utils-general.R (line 51, column 7)
* Checking for library/require of oligoClasses...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/utils-general.R (line 194, column 40)
    • require() in R/utils-general.R (line 11, column 36)
    • require() in R/utils-general.R (line 54, column 17)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/methods-GenomeAnnotatedDataFrame.R (line 340, column 23)
    • ...
    • R/utils-general.R (line 43, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • initialize-methods.R (line 45, column 54)
    • ...
    • utils-parallel.R (line 75, column 23)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/methods-gSetList.R (line 87, column 30)
    • R/methods-SnpSet.R (line 72, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/methods-GenomeAnnotatedDataFrame.R (line 208, column 30)
    • R/methods-GenomeAnnotatedDataFrame.R (line 274, column 15)
    • R/methods-gSet.R (line 49, column 65)
! WARNING: .Deprecated / .Defunct usage (found 6 times)
  • .Defunct() in R/AllClasses.R (line 118, column 9)
  • ...
  • .Deprecated() in R/utils-parallel.R (line 101, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/utils-general.R (line 11, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • addFeatureAnnotation.crlmm2() (R/methods-GenomeAnnotatedDataFrame.R): 80
    lines
    • ...
    • pdPkgFromBioC() (R/utils-general.R): 51 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/ff_or_matrix-class.Rd
  • man/SnpSet2-class.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/oligoSetExample.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/AssayData-methods.Rd
    • ...
    • man/SummarizedExperiment-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • AlleleSet-methods.Rd
    • ...
    • requireClusterPkgSetDeprecated.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • celfileName.Rd
    • ...
    • requireAnnotation.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • celfileName.Rd
    • ...
    • requireAnnotation.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; 165 lines (4%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L93 setClass("oligoSnpSet", contains="SnpSet ...
    • ...
    • oligoClasses/NAMESPACE#L159 export(setCluster, getCluster, delCluste ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1774 lines (47%) contain tabs.
  First few lines:
    • R/AllClasses.R#L88 representation(##featureData="GenomeAn ...
    • ...
    • oligoClasses/NAMESPACE#L135 clone2) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 562 lines (15%) are
not.
  First few lines:
    • R/AllClasses.R#L5 representation=representation( ...
    • ...
    • oligoClasses/NAMESPACE#L155 getSequenceLengths) ...
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 ───────────────────────────────────────────────────
✖ 5 ERRORS | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the oligoClasses.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.