##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('openCyto_2.24.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing openCyto ─────────────────────────────────────────────────────────
✔ Package installed successfully
── openCyto session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpqJTiKW/file862ea1947bd0a/openCyto
→ BiocVersion: 3.23
→ Package: openCyto
→ PackageVersion: 2.24.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/openCyto.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpqJTiKW/file862ea1947bd0a/openCyto
→ installDir: /tmp/RtmpqJTiKW/file862ea7dc9070f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on openCyto ───────────────────────────────────────────────
* 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 3.5.0 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 that Package field matches directory/tarball name...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
ℹ NOTE: License 'AGPL-3.0-only' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* 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 (38%).
* 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:
    • HowToAutoGating.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/HowToWriteCSVTemplate.Rmd (chunk no. 3, line 56, column 38)
    • ...
    • vignettes/HowToWriteCSVTemplate.Rmd (chunk no. 13, line 168, column 63)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/HowToAutoGating.Rmd
    • vignettes/HowToWriteCSVTemplate.Rmd
    • vignettes/openCytoVignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of openCyto...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/wrapper-functions.R (line 19, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/add.R (line 118, column 11)
    • ...
    • R/wrapper-functions.R (line 524, column 6)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllClasses.R (line 438, column 13)
    • ...
    • wrapper-functions.R (line 147, column 24)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/gating-methods.R (line 354, column 7)
    • ...
    • cat() in R/pluginFramework.R (line 48, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/add_pop.R (line 97, column 8)
    • ...
    • R/robust_m_estimator.R (line 21, column 8)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllClasses.R (line 370, column 11)
    • ...
    • R/wrapper-functions.R (line 111, column 25)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 9 times:
    • F in R/add_pop.R (line 101, column 34)
    • ...
    • T in R/toggle.helperGates.R (line 54, column 51)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • add.R (line 95, column 16)
    • ...
    • gatingTemplate-methods.R (line 291, column 29)
! WARNING: .Deprecated / .Defunct usage (found 26 times)
  • .Deprecated() in R/add_pop.R (line 156, column 3)
  • ...
  • .Defunct() in R/wrapper-functions.R (line 402, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 5 times)
  • <<- in R/template_gating.R (line 539, column 31)
  • ...
  • <<- in R/template_gating.R (line 623, column 30)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressMessages() in R/add_pop.R (line 105, column 3)
  • suppressMessages() in R/add_pop.R (line 107, column 3)
  • suppressWarnings() in R/preprocessing-method.R (line 67, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 36
functions greater than 50 lines.
  The longest 5 functions are:
    • generate_gate_template() (R/template_gating.R): 498 lines
    • ...
    • gate_flowclust_1d() (R/gating-functions.R): 226 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/add.Rd
    • ...
    • man/show-gtMethod-method.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • CytoExploreR_exports.Rd
    • ...
    • register_plugins.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 35% of man
pages use at least one of these tags.
  Found in files:
    • gate_flowclust_1d.Rd
    • ...
    • prior_flowclust.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • gate_flowclust_1d.Rd
    • ...
    • prior_flowclust.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; 596 lines (7%) are > 80 characters long.
  First few lines:
    • R/add_pop.R#L12 #' When interacting with the existing ga ...
    • ...
    • vignettes/openCytoVignette.Rmd#L332 and increases the speed as well as
    the r ...
ℹ NOTE: Consider 4 spaces instead of tabs; 65 lines (1%) contain tabs.
  First few lines:
    • R/add.R#L46 ...
    • ...
    • vignettes/openCytoVignette.Rmd#L284 ) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3010 lines (33%) are
not.
  First few lines:
    • R/add_pop.R#L48 , pop = "+" ...
    • ...
    • vignettes/openCytoVignette.Rmd#L316 gating_method = ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 6 WARNINGS | ℹ 20 NOTES
ℹ See the openCyto.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.