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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('qusage_2.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing qusage ───────────────────────────────────────────────────────────
✔ Package installed successfully
── qusage session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZnggd1/file1064ff1ad679b7/qusage
→ BiocVersion: 3.24
→ Package: qusage
→ PackageVersion: 2.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/qusage.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZnggd1/file1064ff1ad679b7/qusage
→ installDir: /tmp/RtmpZnggd1/file1064ff5d9376b8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on qusage ─────────────────────────────────────────────────
* 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 2.10 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/RtmpZnggd1/file1064ff1ad679b7/qusage/man/eset.full.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZnggd1/file1064ff1ad679b7/qusage/man/fluVaccine.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZnggd1/file1064ff1ad679b7/qusage/man/GeneSets.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZnggd1/file1064ff1ad679b7/qusage/man/read.gmt.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZnggd1/file1064ff1ad679b7/qusage/vignettes/qusage.Rnw'
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Transcription, Sequencing, Metabolomics, Proteomics,
Epigenetics, Cheminformatics, Transcriptomics, DifferentialExpression,
Normalization, Pathways, KEGG, Preprocessing, Bayesian, Clustering, Regression,
ExonArray, OneChannel, TwoChannel, MicroRNAArray, mRNAMicroarray,
ProprietaryPlatforms, CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, AlternativeSplicing, DifferentialSplicing, BatchEffect,
MultipleComparison, QualityControl, TimeCourse, DataImport
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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:
    • qusage.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • qusage.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/qusage.Rnw (chunk no. 23, line 174, column 57)
    • ...
    • vignettes/qusage.Rnw (chunk no. 24, line 186, column 57)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/qusage.Rnw
* Checking package installation calls in R code...
* Checking for library/require of qusage...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/CombinePDF.R (line 138, column 25)
    • ...
    • R/qusage.R (line 951, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • CombinePDF.R (line 96, column 12)
    • ...
    • qusage.R (line 951, column 20)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/QgenFunctions.R (line 30, column 7)
    • ...
    • cat() in R/qusage.R (line 836, column 29)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CombinePDF.R (line 14, column 17)
    • ...
    • R/qusage.R (line 952, column 28)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/QgenFunctions.R (line 230, column 13)
    • R/qusage.R (line 397, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 46 times:
    • T in R/CombinePDF.R (line 52, column 58)
    • ...
    • F in R/qusage.R (line 908, column 12)
* 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 15
functions greater than 50 lines.
  The longest 5 functions are:
    • plotGeneSetDistributions() (R/QSarray_plotFns.R): 241 lines
    • ...
    • makeComparison() (R/qusage.R): 115 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/GeneSets.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/newQSarray.Rd
    • ...
    • man/plotGeneSetDistributions.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calcBayesCI.Rd
    • ...
    • read.gmt.Rd
* 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; 747 lines (16%) are > 80 characters long.
  First few lines:
    • R/CombinePDF.R#L1 ######################################## ...
    • ...
    • vignettes/qusage.Rnw#L780 \item \textbf{\texttt{QSlist}} - If the ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • man/QSarray-class.Rd#L59 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2045 lines (44%) are
not.
  First few lines:
    • R/CombinePDF.R#L15 path.index=1, ...
    • ...
    • vignettes/qusage.Rnw#L683 colorScheme=col ...
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 | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the qusage.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.