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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('conumee_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing conumee ──────────────────────────────────────────────────────────
✔ Package installed successfully
── conumee session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1k2vso/file794b2199df67a/conumee
→ BiocVersion: 3.24
→ Package: conumee
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/conumee.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1k2vso/file794b2199df67a/conumee
→ installDir: /tmp/Rtmp1k2vso/file794b226af8a55
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on conumee ────────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Epigenetics,
Regression, MultiChannel, TwoChannel, ImmunoOncology, DifferentialMethylation,
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 (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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • conumee.Rmd
* Checking package installation calls in R code...
* Checking for library/require of conumee...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/annotation.R (line 45, column 28)
    • ...
    • R/process.R (line 272, column 32)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • annotation.R (line 59, column 58)
    • annotation.R (line 62, column 56)
    • annotation.R (line 232, column 43)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/process.R (line 321, column 14)
    • R/process.R (line 327, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/annotation.R (line 45, column 78)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • annotation.R (line 113, column 34)
    • annotation.R (line 131, column 33)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/classes.R (line 37, column 44)
  • suppressWarnings() in R/classes.R (line 39, column 14)
* 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:
    • CNV.create_anno() (R/annotation.R): 143 lines
    • ...
    • _anonymous_.374() (R/output.R): 57 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/detail_regions.Rd
    • ...
    • man/tcgaBRCA.sentrix2name.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • CNV.process.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; 196 lines (11%) are > 80 characters long.
  First few lines:
    • R/annotation.R#L16 #' @param bin_minprobes numeric. Minimum ...
    • ...
    • vignettes/conumee.Rmd#L181 ```{r, echo = TRUE, collapse = TRUE, res ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 80 lines (5%) are not.
  First few lines:
    • R/annotation.R#L39 if (is.element(an, names(a2))) { ...
    • ...
    • R/process.R#L356 } ...
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 | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the conumee.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.