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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ChAMP_2.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ChAMP ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ChAMP session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpoVc6ek/file650d319b4340b/ChAMP
→ BiocVersion: 3.24
→ Package: ChAMP
→ PackageVersion: 2.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ChAMP.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpoVc6ek/file650d319b4340b/ChAMP
→ installDir: /tmp/RtmpoVc6ek/file650d330447731
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ChAMP ──────────────────────────────────────────────────
* 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 3.3 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...
! WARNING: Invalid BiocViews term(s):
  • 'CopyNumber'
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
ChipOnChip, Epigenetics, Coverage, DifferentialMethylation, Preprocessing,
QualityControl, GeneExpression, WholeGenome, MultiChannel, OneChannel,
ImmunoOncology, DifferentialExpression, MultipleComparison, TimeCourse,
DataImport, GUI
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2020-11-2
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (37%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ChAMP.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ChAMP.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ChAMP...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/champ.BMIQ.R (line 38, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Block.GUI.R (line 39, column 13)
    • ...
    • R/DMR.GUI.R (line 58, column 47)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Block.GUI.R (line 21, column 49)
    • ...
    • QC.GUI.R (line 99, column 49)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/champ.BMIQ.R (line 69, column 1)
    • ...
    • print() in R/DoPBC.R (line 33, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Block.GUI.R (line 209, column 35)
    • ...
    • R/QC.GUI.R (line 104, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/champ.import.R (line 18, column 15)
    • ...
    • R/champ.process.R (line 269, column 68)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/champ.import.R (line 57, column 15)
    • R/champ.import.R (line 59, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 31 times:
    • T in R/champ.CNA.R (line 131, column 56)
    • ...
    • F in R/QC.GUI.R (line 114, column 29)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Block.GUI.R (line 34, column 24)
    • ...
    • DMR.GUI.R (line 17, column 24)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/champ.BMIQ.R (line 70, column 1)
  • set.seed() in R/champ.BMIQ.R (line 123, column 1)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/champ.import.R (line 30, column 10)
  • ...
  • suppressWarnings() in R/champ.SVD.R (line 68, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 27
functions greater than 50 lines.
  The longest 5 functions are:
    • DMP.GUI() (R/DMP.GUI.R): 412 lines
    • ...
    • DMR.GUI() (R/DMR.GUI.R): 339 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/champ.QC.Rd
    • man/champ.SVD.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
Warning: replacing previous import ‘plyr::mutate’ by ‘plotly::mutate’ when loading ‘ChAMP’
Warning: replacing previous import ‘plyr::rename’ by ‘plotly::rename’ when loading ‘ChAMP’
Warning: replacing previous import ‘plyr::arrange’ by ‘plotly::arrange’ when loading ‘ChAMP’
Warning: replacing previous import ‘plyr::summarise’ by ‘plotly::summarise’ when loading ‘ChAMP’


Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • Block.GUI.Rd
    • ...
    • QC.GUI.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 100% of
man pages use at least one of these tags.
  Found in files:
    • Block.GUI.Rd
    • ...
    • QC.GUI.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • Block.GUI.Rd
    • ...
    • QC.GUI.Rd
* Checking package NEWS...
* 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; 1136 lines (17%) are > 80 characters long.
  First few lines:
    • R/Block.GUI.R#L1 if(getRversion() >= "3.1.0") utils::glob ...
    • ...
    • vignettes/ChAMP.Rmd#L725 > Houseman EA, Accomando WP, Koestler DC ...
ℹ NOTE: Consider 4 spaces instead of tabs; 216 lines (3%) contain tabs.
  First few lines:
    • R/Block.GUI.R#L121 sidebarLayout( ...
    • ...
    • man/CpG.GUI.Rd#L16 \item{CpG}{A list of CpG you want to do ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1111 lines (16%) are
not.
  First few lines:
    • R/Block.GUI.R#L4 beta=myNorm, ...
    • ...
    • man/QC.GUI.Rd#L19 \item{pheno}{This is a categorical ...
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 | ⚠ 6 WARNINGS | ℹ 23 NOTES
ℹ See the ChAMP.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.