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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ISAnalytics_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ISAnalytics ──────────────────────────────────────────────────────
✔ Package installed successfully
── ISAnalytics session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpK2vyTZ/filec4edd7e47a99c/ISAnalytics
→ BiocVersion: 3.24
→ Package: ISAnalytics
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ISAnalytics.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpK2vyTZ/filec4edd7e47a99c/ISAnalytics
→ installDir: /tmp/RtmpK2vyTZ/filec4edd5186a3d6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ISAnalytics ────────────────────────────────────────────
* 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 4.5 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...
* 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: Vignette(s) found with missing chunk labels
  Found in files:
    • workflow_start.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ISAnalytics...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/internal-functions.R (line 704, column 39)
    • ...
    • print() in R/internal-functions.R (line 4232, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/internal-functions.R (line 3741, column 18)
    • R/internal-functions.R (line 3747, column 18)
    • R/internal-functions.R (line 3940, column 14)
! WARNING: .Deprecated / .Defunct usage (found 11 times)
  • deprecate_warn() in R/aggregate-functions.R (line 56, column 20)
  • ...
  • deprecate_stop() in R/utility-functions.R (line 1125, column 16)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/aggregate-functions.R (line 113, column 34)
  • ...
  • suppressWarnings() in R/internal-functions.R (line 1467, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 89
functions greater than 50 lines.
  The longest 5 functions are:
    • top_cis_overtime_heatmap() (R/plotting-functions.R): 415 lines
    • ...
    • import_Vispa2_stats() (R/import-functions.R): 211 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • circos_genomic_density.Rd
  • ...
  • unzip_file_system.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • circos_genomic_density.Rd
    • NGSdataExplorer.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • NGSdataExplorer.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 30 lines (0%) are > 80 characters long.
  First few lines:
    • R/analysis-functions.R#L193 details = "The function will be ...
    • ...
    • vignettes/workflow_start.Rmd#L1395 ```{r vignetteBiblio, results =
    "asis", ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 60 lines (0%) are not.
  First few lines:
    • R/import-functions.R#L1246 is.na(.x), ...
    • ...
    • vignettes/workflow_start.Rmd#L500 * Set it to a folder (if it doesn't ex
    ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the ISAnalytics.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.