##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MOMA_1.25.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing MOMA ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── MOMA session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpx9wyZs/filede33338568e95/MOMA
→ BiocVersion: 3.24
→ Package: MOMA
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MOMA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpx9wyZs/filede33338568e95/MOMA
→ installDir: /tmp/Rtmpx9wyZs/filede333156231a8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MOMA ───────────────────────────────────────────────────
* 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 4.0 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...
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...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (13%).
* 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:
    • moma.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MOMA...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cluster.r (line 170, column 7)
    • ...
    • R/moma.r (line 164, column 44)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/genomic.saturation.r (line 112, column 21)
    • R/make.interactions.r (line 123, column 10)
    • R/rank.r (line 279, column 16)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 12 times)
  • <<- in R/moma.r (line 114, column 36)
  • ...
  • <<- in R/moma.r (line 339, column 37)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/moma.r (line 591, column 11)
  • suppressMessages() in R/moma.r (line 591, column 41)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 19
functions greater than 50 lines.
  The longest 5 functions are:
    • oncoprintPlot() (R/make.saturation.plots.r): 266 lines
    • ...
    • saveData() (R/moma.r): 127 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • makeSaturationPlots.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • makeSaturationPlots.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • makeSaturationPlots.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; 375 lines (11%) are > 80 characters long.
  First few lines:
    • R/cluster.r#L3 #' This function generate an cluster str ...
    • ...
    • vignettes/moma.Rmd#L241 in the designated output folder. If no n ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
  First few lines:
    • R/make.saturation.plots.r#L127 if (!is.null(fusions.mat)) { ...
    • ...
    • R/make.saturation.plots.r#L771 i = 1 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1092 lines (32%) are
not.
  First few lines:
    • R/cluster.r#L16 ...
    • ...
    • vignettes/moma.Rmd#L234 ...
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 | ⚠ 0 WARNINGS | ℹ 18 NOTES
ℹ See the MOMA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.