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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('methylMnM_1.51.0.tar.gz','quit-with-status'=TRUE)"
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── Installing methylMnM ────────────────────────────────────────────────────────
✔ Package installed successfully
── methylMnM session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpwPIO1X/filed65c05ef636f8/methylMnM
→ BiocVersion: 3.24
→ Package: methylMnM
→ PackageVersion: 1.51.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/methylMnM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpwPIO1X/filed65c05ef636f8/methylMnM
→ installDir: /tmp/RtmpwPIO1X/filed65c03af57f5d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on methylMnM ──────────────────────────────────────────────
* 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 2.12.1 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Proteomics, Epigenetics, Transcriptomics, Coverage, Normalization, Pathways,
Bayesian, Clustering, Regression, GeneExpression, RNASeq, ChIPSeq, SingleCell,
CellBiology, BiomedicalInformatics, FunctionalGenomics, SystemsBiology,
ImmunoOncology, AlternativeSplicing, DifferentialExpression,
DifferentialMethylation, DifferentialSplicing, GeneSetEnrichment, BatchEffect,
MultipleComparison, QualityControl, TimeCourse
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 (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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • methylMnM.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • methylMnM.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/methylMnM.Rnw
* Checking package installation calls in R code...
* Checking for library/require of methylMnM...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/MnM.test.R (line 5, column 6)
    • library() in R/MnM.test.R (line 6, column 6)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • CNVnormal.R (line 13, column 16)
    • ...
    • removeblacklist.R (line 11, column 16)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/CNVnormal.R (line 20, column 26)
    • ...
    • print() in R/removeblacklist.R (line 13, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/countcpgbin.R (line 49, column 29)
    • ...
    • R/MnM.test.R (line 302, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/countcpgbin.R (line 4, column 12)
    • ...
    • R/MnM.test.R (line 134, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/countcpgbin.R (line 13, column 35)
    • ...
    • R/MnM.test.R (line 37, column 20)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 18 times:
    • F in R/MnM.selectDMR.R (line 11, column 86)
    • ...
    • T in R/pmultinom.R (line 4, column 42)
* 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • MnM.test() (R/MnM.test.R): 311 lines
    • ...
    • MnM.qvalue() (R/MnM.qvalue.R): 88 lines
* Checking man page documentation...
* 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; 145 lines (6%) are > 80 characters long.
  First few lines:
    • R/calcFactornew.R#L2 function(obs, ref, m, k, logratioTrim=.3 ...
    • ...
    • vignettes/methylMnM.Rnw#L548 identifcation of DMRs. We can use p-valu ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • man/MnM-package.Rd#L11 Nevertheless, functionalities like the ...
    • man/MnM-package.Rd#L12 MeDIP-MRE (methylMnM) test which combin ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 924 lines (36%) are
not.
  First few lines:
    • R/calcFactornew.R#L3 if( all(obs==ref) ) ...
    • ...
    • vignettes/methylMnM.Rnw#L485 The input file is the file which have b ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the methylMnM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.