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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('wateRmelon_2.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing wateRmelon ───────────────────────────────────────────────────────
✔ Package installed successfully
── wateRmelon session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpLALt6d/file15338d65c4210c/wateRmelon
→ BiocVersion: 3.24
→ Package: wateRmelon
→ PackageVersion: 2.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/wateRmelon.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpLALt6d/file15338d65c4210c/wateRmelon
→ installDir: /tmp/RtmpLALt6d/file15338d59b5d633
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on wateRmelon ─────────────────────────────────────────────
* 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 3.5.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLALt6d/file15338d65c4210c/wateRmelon/man/outlyx-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpLALt6d/file15338d65c4210c/wateRmelon/man/pwod-methods.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Sequencing, MethylationArray, Metabolomics, Proteomics, Epigenetics,
Cheminformatics, Transcriptomics, Normalization, Bayesian, Clustering,
Regression, CpGIsland, ExonArray, GeneExpression, RNASeq, OneChannel,
MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, CellBiology,
BiomedicalInformatics, FunctionalGenomics, SystemsBiology, ImmunoOncology,
AlternativeSplicing, DifferentialExpression, DifferentialSplicing,
GeneSetEnrichment, BatchEffect, MultipleComparison, 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...
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: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (70%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • wateRmelon.Rmd
* Checking package installation calls in R code...
* Checking for library/require of wateRmelon...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/BMIQ_1.1.R (line 120, column 5)
    • ...
    • require() in R/readEPIC.R (line 49, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/adjustedDasen.R (line 137, column 19)
    • ...
    • R/y_minfi.R (line 666, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • adjustedDasen.R (line 101, column 29)
    • ...
    • swan2.R (line 53, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/adaptRefQuantiles.R (line 34, column 29)
    • ...
    • cat() in R/robustQuantileNorm_Illumina450K.R (line 29, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/adjustedDasen.R (line 77, column 11)
    • ...
    • R/uSexQN.R (line 20, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/dmrse_row.R (line 4, column 15)
    • ...
    • R/readEPIC.R (line 743, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/readEPIC.R (line 718, column 21)
    • ...
    • R/readEPIC.R (line 743, column 23)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 75 times:
    • T in R/adjustedDasen.R (line 168, column 59)
    • ...
    • T in R/y_minfi.R (line 364, column 22)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/metrics.Rd
ℹ Found @ in man/seabi.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/readAny.R (line 71, column 14)
  • <<- in R/readEPIC.R (line 82, column 23)
  • <<- in R/readEPIC.R (line 96, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 28
functions greater than 50 lines.
  The longest 5 functions are:
    • BMIQ() (R/BMIQ_1.1.R): 209 lines
    • ...
    • getMethylationBeadMappers2() (R/readEPIC.R): 142 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/adaptRefQuantiles.Rd
  • ...
  • man/wm_internal.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/adaptRefQuantiles.Rd
    • ...
    • man/wm_internal.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’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • adaptRefQuantiles.Rd
    • ...
    • wm_internal.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • adjustedFunnorm.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • adjustedFunnorm.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; 437 lines (6%) are > 80 characters long.
  First few lines:
    • R/adaptRefQuantiles.R#L34 if(verbose) cat("\t\t adaptRefQuantile ...
    • ...
    • vignettes/wateRmelon.Rmd#L169 Although we cannot predict what type of ...
ℹ NOTE: Consider 4 spaces instead of tabs; 658 lines (9%) contain tabs.
  First few lines:
    • R/adaptRefQuantiles.R#L28 #print(paste("Length sizeNew2: ", sizeN ...
    • ...
    • R/y_minfi.R#L782 returnAll=returnAll, meanPlot=mea ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2116 lines (29%) are
not.
  First few lines:
    • R/adjustedFunnorm.R#L88 mu.norm = spri ...
    • ...
    • wateRmelon/NAMESPACE#L7 "write.csv", "write.table") ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 24 NOTES
ℹ See the wateRmelon.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.