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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('daMA_1.85.0.tar.gz','quit-with-status'=TRUE)"
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── Installing daMA ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── daMA session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpW5CeD2/file7d8b04647c87c/daMA
→ BiocVersion: 3.24
→ Package: daMA
→ PackageVersion: 1.85.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/daMA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpW5CeD2/file7d8b04647c87c/daMA
→ installDir: /tmp/RtmpW5CeD2/file7d8b03d5d156e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on daMA ───────────────────────────────────────────────────
* 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...
* 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...
No vignettes found.
ℹ NOTE: Consider adding these automatically suggested biocViews:
ExperimentalDesign, KEGG
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: 'Date:' field format is not 'YYYY-MM-DD': 1. October 2003
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...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
✖ ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of daMA...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/analyseMA.R (line 19, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/designMA.R (line 220, column 59)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • analyseMA.R (line 52, column 19)
    • ...
    • designMA.R (line 232, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/analyseMA.R (line 41, column 9)
* 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 2
functions greater than 50 lines.
  The longest 5 functions are:
    • designMA() (R/designMA.R): 69 lines
    • core() (R/analyseMA.R): 62 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/cinfo.Rd
    • ...
    • man/cmatB.AB.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/core.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • analyseMA.Rd
    • ...
    • designs.basic.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • analyseMA.Rd
    • designMA.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • analyseMA.Rd
    • designMA.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; 123 lines (15%) are > 80 characters long.
  First few lines:
    • R/analyseMA.R#L9 # cmat : P x (K+2) contrasts matrix ( ...
    • ...
    • man/id.3x2.Rd#L4 \title{A vector of length 30012 containi ...
ℹ NOTE: Consider 4 spaces instead of tabs; 242 lines (30%) contain tabs.
  First few lines:
    • R/analyseMA.R#L6 # data : G x N data matrix (rows: ge ...
    • ...
    • man/designMA.Rd#L82 # experiment using 18 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 69 lines (9%) are not.
  First few lines:
    • R/analyseMA.R#L84 # compute variance estimate ...
    • ...
    • man/id.3x2.Rd#L12 num [1:30012] 12 24 108 120 204 216 300 ...
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 | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the daMA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.