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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('decontam_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing decontam ─────────────────────────────────────────────────────────
✔ Package installed successfully
── decontam session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNWrAeV/file7ea514f175bc4/decontam
→ BiocVersion: 3.24
→ Package: decontam
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/decontam.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNWrAeV/file7ea514f175bc4/decontam
→ installDir: /tmp/RtmpNWrAeV/file7ea5123f7e0b7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on decontam ───────────────────────────────────────────────
* 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 3.4.1 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: Normalization,
FeatureExtraction
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...
* 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...
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/decontam_intro.Rmd
* Checking package installation calls in R code...
* Checking for library/require of decontam...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • plotting.R (line 100, column 42)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/decontam.R (line 433, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/decontam.R (line 208, column 7)
  • ...
  • suppressWarnings() in R/decontam.R (line 220, column 7)
* 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:
    • .is_contaminant() (R/decontam.R): 126 lines
    • plot_frequency() (R/plotting.R): 77 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plot_condition.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • inst/NEWS
    • decontam/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; 157 lines (19%) are > 80 characters long.
  First few lines:
    • R/decontam.R#L3 #' The frequency of each sequence (or OT ...
    • ...
    • vignettes/decontam_intro.Rmd#L160 [Removing contaminants makes the
    charact ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 212 lines (25%) are
not.
  First few lines:
    • R/decontam.R#L86 function(seqtab, ...) ...
    • ...
    • vignettes/decontam_intro.Rmd#L147 xlab("Prevalence (Negative Controls)")
    ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 14 NOTES
ℹ See the decontam.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.