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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('cghMCR_1.71.0.tar.gz','quit-with-status'=TRUE)"
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── Installing cghMCR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── cghMCR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpItRSz0/file64f3c7cff533d/cghMCR
→ BiocVersion: 3.24
→ Package: cghMCR
→ PackageVersion: 1.71.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/cghMCR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpItRSz0/file64f3c7cff533d/cghMCR
→ installDir: /tmp/RtmpItRSz0/file64f3c396cf113
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on cghMCR ─────────────────────────────────────────────────
* 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...
* 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: Transcription,
Sequencing, Metabolomics, Proteomics, Epigenetics, Cheminformatics,
Transcriptomics, Normalization, Preprocessing, Bayesian, Clustering,
Regression, ExonArray, GeneExpression, RNASeq, OneChannel, TwoChannel,
MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, CellBiology,
BiomedicalInformatics, FunctionalGenomics, SystemsBiology, ImmunoOncology,
AlternativeSplicing, DifferentialExpression, DifferentialSplicing,
GeneSetEnrichment, BatchEffect, MultipleComparison, QualityControl, TimeCourse,
DataImport
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 (67%).
* 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:
    • findMCR.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • findMCR.Rnw
* Checking package installation calls in R code...
* Checking for library/require of cghMCR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/mcrFunctions.R (line 525, column 3)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/mcrFunctions.R (line 772, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cghMCR.R (line 78, column 32)
    • ...
    • mcrFunctions.R (line 784, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/mcrFunctions.R (line 40, column 5)
    • cat() in R/mcrFunctions.R (line 42, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/mcrFunctions.R (line 364, column 8)
    • ...
    • R/mcrFunctions.R (line 633, column 10)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/mcrFunctions.R (line 526, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/mcrFunctions.R (line 32, column 12)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • getMCR() (R/mcrFunctions.R): 58 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/methods.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 38 lines (2%) are > 80 characters long.
  First few lines:
    • R/mcrFunctions.R#L521 ma <- normalizeWithinArrays(background ...
    • ...
    • vignettes/findMCR.Rnw#L176 mcrs <- mergeMCRProbes(mcrs[mcrs[, "chro ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • man/cghMCR-class.Rd#L54 } ...
    • man/SGOL-class.Rd#L24 \describe{ ...
    • man/SGOL-class.Rd#L44 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 546 lines (35%) are
not.
  First few lines:
    • R/cghMCR.R#L8 DNADat ...
    • ...
    • vignettes/findMCR.Rnw#L178 "probes")])) ...
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 | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the cghMCR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.