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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('octad_1.15.0.tar.gz','quit-with-status'=TRUE)"
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── Installing octad ────────────────────────────────────────────────────────────
✔ Package installed successfully
── octad session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpWo4Hi7/filef8dc540b6fc9a/octad
→ BiocVersion: 3.24
→ Package: octad
→ PackageVersion: 1.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/octad.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpWo4Hi7/filef8dc540b6fc9a/octad
→ installDir: /tmp/RtmpWo4Hi7/filef8dc54ce7481c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on octad ──────────────────────────────────────────────────
* 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 4.2.0 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: Transcription,
Sequencing, Proteomics, Epigenetics, Transcriptomics, Coverage, Normalization,
Pathways, Preprocessing, Bayesian, Clustering, Regression, DNAMethylation,
RNASeq, ChIPSeq, SingleCell, CellBiology, BiomedicalInformatics,
FunctionalGenomics, SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialExpression, DifferentialMethylation, DifferentialSplicing,
BatchEffect, MultipleComparison, QualityControl, TimeCourse, ThirdPartyClient,
DataImport, GUI
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (42%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of octad...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/octadDrugEnrichment.R (line 127, column 39)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/octadDrugEnrichment.R (line 71, column 18)
    • R/octadDrugEnrichment.R (line 127, column 24)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressMessages() in R/computeCellLine.R (line 71, column 31)
  • suppressMessages() in R/diffExp.R (line 85, column 31)
  • suppressMessages() in R/diffExp.R (line 224, column 29)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • runsRGES() (R/runsRGES_ultimate.R): 248 lines
    • ...
    • computeCellLine() (R/computeCellLine.R): 100 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/octad.Rd
* Checking package 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; 247 lines (18%) are > 80 characters long.
  First few lines:
    • R/computeCellLine.R#L11 computeCellLine <- function(case_id = ca ...
    • ...
    • vignettes/octad.Rmd#L149 Here is the output of sessionInfo on the ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 231 lines (17%) are
not.
  First few lines:
    • R/computeRefTissue.R#L80 error = function(c) "f ...
    • ...
    • vignettes/octad.Rmd#L54 ...
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 | ⚠ 1 WARNINGS | ℹ 13 NOTES
ℹ See the octad.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.