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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('cola_2.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing cola ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── cola session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp6BI3hs/file77fe83a4616ce/cola
→ BiocVersion: 3.24
→ Package: cola
→ PackageVersion: 2.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/cola.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp6BI3hs/file77fe83a4616ce/cola
→ installDir: /tmp/Rtmp6BI3hs/file77fe872056166
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on cola ───────────────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (9%).
* 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...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/utils.R (line 429, column 41)
    • install.packages() in R/utils.R (line 437, column 33)
    • install() in R/utils.R (line 431, column 46)
* Checking for library/require of cola...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/collect.R (line 121, column 16)
    • ...
    • R/z.register.R (line 349, column 24)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • consensus_partition.R (line 342, column 64)
    • ...
    • z.register.R (line 387, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/cola.R (line 55, column 5)
    • ...
    • cat() in R/use.R (line 16, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/00_classes.R (line 36, column 24)
    • ...
    • R/zzz.R (line 4, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 5 times:
    • F in R/stat.R (line 287, column 9)
    • ...
    • F in R/stat.R (line 449, column 9)
! WARNING: Remove set.seed usage (found 6 times)
  • set.seed() in R/hierarchical_methods.R (line 201, column 25)
  • ...
  • set.seed() in R/signatures.R (line 445, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/dend_utils.R (line 6, column 27)
  • <<- in R/dend_utils.R (line 8, column 27)
  • <<- in R/z.global.R (line 70, column 22)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/consensus_partition.R (line 987, column 9)
  • ...
  • suppressWarnings() in R/z.register.R (line 433, column 33)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 32
functions greater than 50 lines.
  The longest 5 functions are:
    • .consensus_partition() (R/consensus_partition.R): 452 lines
    • ...
    • run_all_consensus_partition_methods() (R/run_all_methods.R): 209 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/cola_rl.Rd
    • ...
    • man/golub_cola.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ATC_approx.Rd
    • ...
    • man/top_rows_overlap-dispatch.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • compare_partitions-ConsensusPartition-method.Rd
  • ...
  • run_all_consensus_partition_methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • collect_plots-ConsensusPartition-method.Rd
    • ...
    • top_rows_heatmap-ConsensusPartitionList-method.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • compare_partitions-ConsensusPartition-method.Rd
    • ...
    • run_all_consensus_partition_methods.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; 1819 lines (10%) are > 80 characters long.
  First few lines:
    • R/00_classes.R#L17 # -`top_rows_overlap,ConsensusPartitionL ...
    • ...
    • man/top_rows_overlap-matrix-method.Rd#L26 It first calculates scores for
    every top ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6950 lines (37%) contain tabs.
  First few lines:
    • R/00_classes.R#L37 slots = list( ...
    • ...
    • man/relabel_class.Rd#L16 \item{full_set}{The full set of labels ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 879 lines (5%) are
not.
  First few lines:
    • R/00_classes.R#L1 ...
    • ...
    • man/top_rows_overlap-matrix-method.Rd#L22 \item{...}{Additional arguments
    passed ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the cola.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.