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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('TOAST_1.27.0.tar.gz','quit-with-status'=TRUE)"
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── Installing TOAST ────────────────────────────────────────────────────────────
✔ Package installed successfully
── TOAST session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1gaM0v/file14dcc214e99842/TOAST
→ BiocVersion: 3.24
→ Package: TOAST
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/TOAST.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1gaM0v/file14dcc214e99842/TOAST
→ installDir: /tmp/Rtmp1gaM0v/file14dcc253de2617
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TOAST ──────────────────────────────────────────────────
* 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 3.6 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: Transcription,
Sequencing, Metabolomics, Proteomics, Cheminformatics, Transcriptomics,
Normalization, Preprocessing, Bayesian, Clustering, Regression, ExonArray,
RNASeq, OneChannel, TwoChannel, MicroRNAArray, mRNAMicroarray,
ProprietaryPlatforms, CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, ImmunoOncology, AlternativeSplicing, DifferentialSplicing,
GeneSetEnrichment, 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (23%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • TOAST.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/TOAST.Rmd (chunk no. 41, line 737, column 62)
* Checking package installation calls in R code...
* Checking for library/require of TOAST...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/myRefFreeCellMixInitialize.R (line 19, column 6)
    • R/sisal.R (line 176, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cedar.R (line 84, column 15)
    • ...
    • vca.R (line 46, column 16)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/cedar.R (line 118, column 11)
    • cat() in R/cedar.R (line 132, column 11)
    • print() in R/myRefFreeCellMix.R (line 25, column 16)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cedar.R (line 80, column 10)
    • ...
    • R/vca.R (line 55, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/cedar.R (line 218, column 13)
    • ...
    • R/MDeconv.R (line 44, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 6 times:
    • T in R/cedar.R (line 337, column 77)
    • ...
    • F in R/cedar.R (line 689, column 96)
* 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 21
functions greater than 50 lines.
  The longest 5 functions are:
    • cedar() (R/cedar.R): 247 lines
    • ...
    • DEKTissue() (R/DEKTissue.R): 111 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/cedar.Rd
  • man/plotCorr.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/CBS_PBMC_array.Rd
    • man/RA_100samples.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • myprojectMix.Rd
  • myRefFreeCellMix.Rd
  • myRefFreeCellMixInitialize.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; 158 lines (3%) are > 80 characters long.
  First few lines:
    • R/cedar.R#L25 # If assign cell type ...
    • ...
    • vignettes/TOAST.Rmd#L976 ### Testing the differences of two cell ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1563 lines (30%) are
not.
  First few lines:
    • R/cedar.R#L2 prop, # cell type pr ...
    • ...
    • vignettes/TOAST.Rmd#L996 contrast_matrix = NULL) ...
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 | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the TOAST.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.