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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GLAD_2.77.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GLAD ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── GLAD session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAh6Zfe/filea71794a9fe44f/GLAD
→ BiocVersion: 3.24
→ Package: GLAD
→ PackageVersion: 2.77.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GLAD.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpAh6Zfe/filea71794a9fe44f/GLAD
→ installDir: /tmp/RtmpAh6Zfe/filea71797def3081
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GLAD ───────────────────────────────────────────────────
* 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 2.10 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...
* 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • GLAD.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GLAD.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/GLAD.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GLAD...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/affectationGNL.R (line 75, column 19)
    • R/affectationGNL.R (line 76, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • arrayPlot.R (line 45, column 21)
    • ...
    • titi.R (line 80, column 36)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/affectationGNL.R (line 13, column 16)
    • ...
    • print() in R/plotProfile.R (line 48, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/HaarSeg.R (line 40, column 12)
    • ...
    • R/HaarSeg.R (line 328, column 25)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/arrayPlot.R (line 26, column 10)
    • ...
    • R/CheckData.R (line 42, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/as.profileCGH.R (line 32, column 20)
    • ...
    • R/titi.R (line 76, column 12)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 9 times:
    • T in R/HaarSeg.R (line 127, column 9)
    • ...
    • T in R/HaarSeg.R (line 315, column 12)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • findCluster.R (line 82, column 21)
* 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 27
functions greater than 50 lines.
  The longest 5 functions are:
    • chrBreakpoints.profileCGH() (R/chrBreakpoints.R): 379 lines
    • ...
    • affectationGNL.profileCGH() (R/affectationGNL.R): 192 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/cytoband.Rd
    • man/snijders.Rd
    • man/veltman.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ChrNumeric.Rd
    • man/ColorBar.Rd
    • man/kernel.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • arrayPersp.Rd
    • GLAD-internal.Rd
    • kernel.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • arrayPersp.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • arrayPersp.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; 449 lines (9%) are > 80 characters long.
  First few lines:
    • R/affectationGNL.R#L11 affectationGNL.profileCGH <- function(pr ...
    • ...
    • vignettes/GLAD.Rnw#L320 plotProfile(res, unit=3, Bkp=TRUE, label ...
ℹ NOTE: Consider 4 spaces instead of tabs; 29 lines (1%) contain tabs.
  First few lines:
    • R/arrayPlot.R#L196 mediancenter=FALSE, ...
    • ...
    • R/titi.R#L54 d <- as.dist(as.matrix(d*d)*coeff) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1500 lines (30%) are
not.
  First few lines:
    • R/affectationGNL.R#L7 UseMethod("affectationGNL") ...
    • ...
    • vignettes/GLAD.Rnw#L207 MinBkpWeight=0.35, ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 6 WARNINGS | ℹ 20 NOTES
ℹ See the GLAD.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.