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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('sampleClassifier_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing sampleClassifier ─────────────────────────────────────────────────
✔ Package installed successfully
── sampleClassifier session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/RtmpB3xIWS/file1282c54ec6911f/sampleClassifier
→ BiocVersion: 3.24
→ Package: sampleClassifier
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/sampleClassifier.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpB3xIWS/file1282c54ec6911f/sampleClassifier
→ installDir: /tmp/RtmpB3xIWS/file1282c5268d0d3c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on sampleClassifier ───────────────────────────────────────
* 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 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/RtmpB3xIWS/file1282c54ec6911f/sampleClassifier/man/classifyProfile.svm.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: ChipOnChip,
Pathways, GO
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 (43%).
* 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:
    • sampleClassifier.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • sampleClassifier.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • sampleClassifier.Rnw
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/internal.R (line 12, column 7)
* Checking for library/require of sampleClassifier...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/internal.R (line 10, column 7)
    • require() in R/internal.R (line 13, column 13)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/classifyProfile.R (line 53, column 1)
    • R/classifyProfile.rnaseq.R (line 35, column 1)
    • R/internal.R (line 120, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • get.heatmap.R (line 9, column 10)
    • ...
    • internal.R (line 150, column 44)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/classifyProfile.R (line 17, column 1)
    • ...
    • cat() in R/classifyProfile.svm.R (line 45, column 1)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/sampleClassifier-internal.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
  Found in files:
    • sampleClassifier-package.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • sampleClassifier-package.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; 163 lines (15%) are > 80 characters long.
  First few lines:
    • R/classifyProfile.R#L4 ### ref_matrix: the expression matrix us ...
    • ...
    • vignettes/sampleClassifier.Rnw#L318 the query and the reference. For each
    qu ...
ℹ NOTE: Consider 4 spaces instead of tabs; 33 lines (3%) contain tabs.
  First few lines:
    • R/internal.R#L23 return(annot.df) ...
    • ...
    • vignettes/sampleClassifier.Rnw#L245 The sample 'GSM44673' (tissue:
    spleen) w ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 42 lines (4%) are not.
  First few lines:
    • R/classifyProfile.R#L54 function (x) write.csv2(predicted[[x]], ...
    • ...
    • vignettes/sampleClassifier.Rnw#L18 Charit\'e - Universit\"at ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the sampleClassifier.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.