##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Statial_1.15.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing Statial ──────────────────────────────────────────────────────────
✔ Package installed successfully
── Statial session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpD0r1iP/file147c3019036ddf/Statial
→ BiocVersion: 3.24
→ Package: Statial
→ PackageVersion: 1.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Statial.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpD0r1iP/file147c3019036ddf/Statial
→ installDir: /tmp/RtmpD0r1iP/file147c304b329d3d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Statial ────────────────────────────────────────────────
* 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 4.1.0 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (32%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of Statial...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Statial.R (line 42, column 24)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • parentCombinations.R (line 120, column 24)
    • Statial.R (line 640, column 30)
    • Statial.R (line 640, column 56)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/Statial.R (line 386, column 5)
    • print() in R/Statial.R (line 399, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/calcKontextual.R (line 15, column 13)
    • ...
    • R/parentCombinations.R (line 134, column 21)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • parentCombinations.R (line 110, column 24)
    • ...
    • Statial.R (line 536, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/Statial.R (line 695, column 38)
  • ...
  • suppressMessages() in R/Statial.R (line 699, column 15)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • Kontextual() (R/Konditional.R): 266 lines
    • ...
    • relabelKontextual() (R/relabelKonditional.R): 80 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/calcContamination.Rd
    • ...
    • man/prepMatrix.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getParentPhylo.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 166 lines (5%) are > 80 characters long.
  First few lines:
    • R/calcKontextual.R#L53 .Kontext <- function(closePairs, counts, ...
    • ...
    • vignettes/Statial.Rmd#L639 Keren, L., Bosse, M., Marquez, D., Angos ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 972 lines (32%) are
not.
  First few lines:
    • R/calcKontextual.R#L4 ...
    • ...
    • vignettes/Statial.Rmd#L634 theme(axis.text.x = element_text(angle ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 14 NOTES
ℹ See the Statial.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.