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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('oposSOM_2.31.0.tar.gz','quit-with-status'=TRUE)"
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── Installing oposSOM ──────────────────────────────────────────────────────────
✔ Package installed successfully
── oposSOM session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpSIdzyp/filefae237e880b66/oposSOM
→ BiocVersion: 3.24
→ Package: oposSOM
→ PackageVersion: 2.31.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/oposSOM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpSIdzyp/filefae237e880b66/oposSOM
→ installDir: /tmp/RtmpSIdzyp/filefae231f50bb2b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on oposSOM ────────────────────────────────────────────────
* 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 4.0.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpSIdzyp/filefae237e880b66/oposSOM/man/opossom.genesets.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
Clustering, DimensionReduction, FeatureExtraction, MultidimensionalScaling
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (19%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • Vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of oposSOM...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cancer_hallmarks.r (line 59, column 19)
    • ...
    • R/workspace_check.r (line 180, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • affymetrix_quality_check.r (line 21, column 18)
    • ...
    • topology_profiles.r (line 91, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/diffExpression_statistics.r (line 4, column 67)
    • ...
    • cat() in R/workspace_check.r (line 208, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/affymetrix_quality_check.r (line 3, column 21)
    • ...
    • R/workspace_check.r (line 180, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 11 times:
    • F in R/geneset_profiles_and_maps.r (line 22, column 45)
    • ...
    • F in R/workspace_check.r (line 198, column 8)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • workspace_check.r (line 190, column 16)
    • workspace_check.r (line 194, column 16)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/som.training.r (line 11, column 10)
  • <<- in R/som.training.r (line 19, column 9)
  • <<- in R/som.training.r (line 20, column 9)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 18 times)
  • suppressMessages() in R/biomart_available.r (line 3, column 17)
  • ...
  • suppressWarnings() in R/supporting_maps.r (line 140, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 58
functions greater than 50 lines.
  The longest 5 functions are:
    • pipeline.summarySheetsGroups() (R/summary_sheets_groups.r): 599 lines
    • ...
    • pipeline.htmlSummary() (R/html_summary.r): 338 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/opossom.genesets.Rd
    • man/opossom.run.Rd
    • man/opossom.tissues.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; 1266 lines (11%) are > 80 characters long.
  First few lines:
    • R/affymetrix_quality_check.r#L3 spike.in.controls = c("AFFX-LysX-3_at"
    ...
    • ...
    • vignettes/Vignette.Rnw#L331 \textbf{\textit{database.id.type}} provi ...
ℹ NOTE: Consider 4 spaces instead of tabs; 185 lines (2%) contain tabs.
  First few lines:
    • R/affymetrix_quality_check.r#L13 barplot( env$indata[i,], col=env$g ...
    • ...
    • vignettes/Vignette.Rnw#L313 \label{fig:Size recommendation} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 5295 lines (46%) are
not.
  First few lines:
    • R/affymetrix_quality_check.r#L3 spike.in.controls = c("AFFX-LysX-3_at"
    ...
    • ...
    • vignettes/Vignette.Rnw#L298 c("accumbens","cerebral co ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the oposSOM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.