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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('TCC_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing TCC ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── TCC session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0w4icn/file14ab2c67af6ce0/TCC
→ BiocVersion: 3.24
→ Package: TCC
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/TCC.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp0w4icn/file14ab2c67af6ce0/TCC
→ installDir: /tmp/Rtmp0w4icn/file14ab2c7e6d813e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TCC ────────────────────────────────────────────────────
* 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 3.0 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:
GeneExpression, Transcription, MultiChannel, OneChannel, TwoChannel,
Proteomics, Epigenetics, Transcriptomics, Coverage, Normalization, Pathways,
Bayesian, Clustering, Regression, DNAMethylation, ChIPSeq, SingleCell,
CellBiology, BiomedicalInformatics, FunctionalGenomics, SystemsBiology,
AlternativeSplicing, DifferentialMethylation, DifferentialSplicing,
GeneSetEnrichment, BatchEffect, MultipleComparison, QualityControl, TimeCourse
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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (75%).
* 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:
    • TCC.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • TCC.Rnw
* Checking package installation calls in R code...
* Checking for library/require of TCC...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/TCC.estimateDE.SAMseq.R (line 2, column 1)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ROKU.R (line 12, column 24)
    • ...
    • YAYOI.R (line 110, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/TCC.generic.R (line 69, column 5)
    • ...
    • print() in R/TCC.generic.R (line 105, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/TCC_0.4.R (line 90, column 16)
    • ...
    • R/TCC.public.R (line 95, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/TCC.calcNormFactors.R (line 131, column 17)
    • ...
    • R/TCC.simulation.R (line 142, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/TCC.calcNormFactors.R (line 128, column 18)
    • ...
    • R/YAYOI.R (line 39, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 9 times:
    • F in R/TCC.generic.R (line 38, column 16)
    • ...
    • T in R/TCC.R (line 80, column 29)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • clusterSample.R (line 5, column 24)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 136 times)
  • <<- in R/TCC.calcNormFactors.R (line 98, column 25)
  • ...
  • <<- in R/TCC.R (line 76, column 43)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 95 times)
  • suppressMessages() in R/TCC.calcNormFactors.R (line 6, column 5)
  • ...
  • suppressMessages() in R/YAYOI.R (line 74, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
  The longest 5 functions are:
    • simulateReadCounts() (R/TCC.simulation.R): 182 lines
    • ...
    • .testByDeseq2() (R/TCC.estimateDE.DESeq2.R): 151 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plotFCPseudocolor.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; 139 lines (2%) are > 80 characters long.
  First few lines:
    • R/TCC_0.4.R#L127 retval <- list(norm_f_TbT, Aval, Mva ...
    • ...
    • vignettes/TCC.Rnw#L1953 <<maplot_normed_simulate_data_1000_2, fi ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 692 lines (11%) are
not.
  First few lines:
    • R/clusterSample.R#L2 hclust.method ...
    • ...
    • vignettes/TCC.Rnw#L1955 iteration = 3, FD ...
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 | ⚠ 5 WARNINGS | ℹ 15 NOTES
ℹ See the TCC.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.