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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MAST_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MAST ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── MAST session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmptYWv6H/filed045a1f4e0e9/MAST
→ BiocVersion: 3.24
→ Package: MAST
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MAST.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmptYWv6H/filed045a1f4e0e9/MAST
→ installDir: /tmp/RtmptYWv6H/filed045a194320eb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MAST ───────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.5 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:
ImmunoOncology, 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (20%).
* 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: Potential intermediate files found:
  • vignettes/mast-intro.pdf
  • vignettes/mast-intro.tex
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • MAITAnalysis.Rmd
    • MAST-interoperability.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/MAITAnalysis.Rmd
    • vignettes/MAST-interoperability.Rmd
    • vignettes/MAST-Intro.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MAST...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/ZlmFit-bootstrap.R (line 17, column 31)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/bayesglm.R (line 1034, column 26)
    • ...
    • R/zeroinf.R (line 190, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bayesglm.R (line 239, column 19)
    • ...
    • ZlmFit-bootstrap.R (line 60, column 29)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/RNASeqAssay-methods.R (line 66, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/convertMASTClassic.R (line 15, column 37)
    • ...
    • R/ZlmFit-bootstrap.R (line 62, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/Hypothesis.R (line 51, column 40)
    • R/Hypothesis.R (line 51, column 91)
    • R/SingleCellAssay-methods.R (line 404, column 38)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/ZlmFit.R (line 226, column 13)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Hypothesis.R (line 39, column 17)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/zlmHooks.R (line 194, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/gseaAfterBoot.Rd
ℹ Found @ in man/Hypothesis.Rd
ℹ Found @ in vignettes/MAITAnalysis.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/filterEval.R (line 12, column 41)
  • suppressMessages() in R/lrtest.R (line 162, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
  The longest 5 functions are:
    • ridge.fit() (R/lmWrapper-ridge.R): 261 lines
    • ...
    • .bayesglm.fit() (R/bayesglm.R): 165 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/defaultAssay.Rd
    • man/MAST-defunct.Rd
    • man/meld_list_left.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • primerAverage.Rd
  • read.fluidigm.Rd
  • SceToSingleCellAssay.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 1% of man
pages use at least one of these tags.
  Found in files:
    • defaultPrior.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • defaultPrior.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • inst/NEWS
    • MAST/NEWS.md
* 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; 986 lines (13%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L21 setClass('FluidigmAssay', contains='Sing ...
    • ...
    • vignettes/MAST-Intro.Rmd#L301 if it is not.  The `FromMatrix` and `S ...
ℹ NOTE: Consider 4 spaces instead of tabs; 65 lines (1%) contain tabs.
  First few lines:
    • R/convertMASTClassic.R#L16 if(is.null(object)){stop("object mus ...
    • ...
    • R/thresholdSCRNA.R#L161 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 413 lines (5%) are
not.
  First few lines:
    • R/AllClasses.R#L16 slots=list(cmap='character', fm ...
    • ...
    • vignettes/MAST-Intro.Rmd#L301 if it is not.  The `FromMatrix` and `S ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 25 NOTES
ℹ See the MAST.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.