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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('M3Drop_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing M3Drop ───────────────────────────────────────────────────────────
✔ Package installed successfully
── M3Drop session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpk3gBpw/filecaeca216ee7cb/M3Drop
→ BiocVersion: 3.24
→ Package: M3Drop
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/M3Drop.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpk3gBpw/filecaeca216ee7cb/M3Drop
→ installDir: /tmp/Rtmpk3gBpw/filecaeca687f0a5b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on M3Drop ─────────────────────────────────────────────────
* 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 3.4 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: SingleCell,
Clustering
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (7%).
* 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:
    • M3Drop_Vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • M3Drop_Vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/M3Drop_Vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of M3Drop...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/NB_UMI.R (line 54, column 22)
    • ...
    • R/Traditional_DE.R (line 155, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Brennecke_implementation.R (line 80, column 45)
    • ...
    • Traditional_DE.R (line 155, column 33)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/basics.R (line 20, column 17)
    • ...
    • print() in R/NB_UMI.R (line 578, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/basics.R (line 162, column 11)
    • ...
    • R/Traditional_DE.R (line 167, column 56)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/basics.R (line 69, column 22)
    • ...
    • R/Plotting_fxns.R (line 81, column 43)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/basics.R (line 38, column 30)
    • ...
    • R/Traditional_DE.R (line 136, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 22 times:
    • T in R/basics.R (line 19, column 61)
    • ...
    • T in R/Traditional_DE.R (line 146, column 40)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • basics.R (line 89, column 28)
    • basics.R (line 89, column 61)
    • basics.R (line 89, column 97)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressWarnings() in R/Curve_fitting.R (line 24, column 22)
  • ...
  • suppressWarnings() in R/Plotting_fxns.R (line 159, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • obsolete__calc_DE_stats() (R/Simulations_Functions.R): 105 lines
    • ...
    • Consensus_FS() (R/Other_FS_functions.R): 77 lines
* Checking man page documentation...
* 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; 564 lines (12%) are > 80 characters long.
  First few lines:
    • R/basics.R#L17 M3DropConvertData <- function(input, is. ...
    • ...
    • vignettes/M3Drop_Vignette.Rnw#L319 Philip Brennecke, Simon Anders, Jong
    Kyo ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2122 lines (44%) contain tabs.
  First few lines:
    • R/basics.R#L18 remove_undetected_genes <- function(mat ...
    • ...
    • vignettes/M3Drop_Vignette.Rnw#L309 cell_labels = labels) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 295 lines (6%) are
not.
  First few lines:
    • R/basics.R#L98 sum_zero <- prod(dim(expr_mat)) - s ...
    • ...
    • man/PoissonUMIFeatureSelectionDropouts.Rd#L12 \item{fit}{output from
    NBumiFitModel o ...
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 18 NOTES
ℹ See the M3Drop.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.