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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('divergence_1.29.0.tar.gz','quit-with-status'=TRUE)"
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── Installing divergence ───────────────────────────────────────────────────────
✔ Package installed successfully
── divergence session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCtn1kg/file836fd690b1f32/divergence
→ BiocVersion: 3.24
→ Package: divergence
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/divergence.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpCtn1kg/file836fd690b1f32/divergence
→ installDir: /tmp/RtmpCtn1kg/file836fd24b8884a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on divergence ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.6 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: Sequencing,
Coverage
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 (100%).
* 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:
    • divergence.Rmd
* Checking package installation calls in R code...
* Checking for library/require of divergence...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/init.R (line 2, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/chisq.R (line 21, column 24)
    • ...
    • R/util.R (line 7, column 60)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • divergence.R (line 128, column 28)
    • ...
    • setDivergence.R (line 158, column 48)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/divergence.R (line 155, column 28)
    • print() in R/divergence.R (line 212, column 30)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/chisq.R (line 6, column 10)
    • ...
    • R/util.R (line 113, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/divergence.R (line 209, column 15)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • computeFeatureSetDigitization() (R/setDivergence.R): 90 lines
    • ...
    • getRangeList() (R/divergence.R): 61 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; 191 lines (11%) are > 80 characters long.
  First few lines:
    • R/data.R#L3 #' A data matrix containing a subset of ...
    • ...
    • vignettes/divergence.Rmd#L373 The above workflows provide a concise su
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 116 lines (6%) contain tabs.
  First few lines:
    • R/chisq.R#L17 stop("Not all given classes are av ...
    • ...
    • R/util.R#L81 # user has set parallel = TRUE but is ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 436 lines (24%) are
not.
  First few lines:
    • R/chisq.R#L10 list(statistic=NA, p.value=NA) ...
    • ...
    • vignettes/divergence.Rmd#L364 classes = c("Positive", "Negative") ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 18 NOTES
ℹ See the divergence.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.