##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('EnMCB_1.25.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing EnMCB ────────────────────────────────────────────────────────────
✔ Package installed successfully
── EnMCB session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUuqaC7/file8758424752dae/EnMCB
→ BiocVersion: 3.24
→ Package: EnMCB
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/EnMCB.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUuqaC7/file8758424752dae/EnMCB
→ installDir: /tmp/RtmpUuqaC7/file875842f1cd717
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EnMCB ──────────────────────────────────────────────────
* 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 4.0 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2023-3-13
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (8%).
* 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 EnMCB...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/DiffMCB.R (line 135, column 32)
    • R/utils.R (line 820, column 32)
    • R/utils.R (line 838, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • CompareMCB.R (line 54, column 13)
    • ...
    • utils.R (line 885, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/IdentifyMCB_parallel.R (line 52, column 3)
    • ...
    • print in R/utils.R (line 112, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CompareMCB.R (line 40, column 7)
    • ...
    • R/utils.R (line 1105, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/IdentifyMCB_parallel.R (line 50, column 10)
    • ...
    • R/metricMCB.R (line 102, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/ensemble_model.R (line 51, column 25)
    • ...
    • R/utils.R (line 494, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 10 times:
    • T in R/IdentifyMCB_parallel.R (line 47, column 15)
    • ...
    • F in R/utils.R (line 856, column 79)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ensemble_prediction.R (line 51, column 41)
    • ...
    • utils.R (line 492, column 46)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • metricMCB() (R/metricMCB.R): 368 lines
    • ...
    • IdentifyMCB() (R/IdentifyMCB.R): 136 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/as.data.frame.ridgemat.Rd
    • man/as.ridgemat.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • as.ridgemat.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; 332 lines (11%) are > 80 characters long.
  First few lines:
    • R/CompareMCB.R#L3 #' @description This function is used to ...
    • ...
    • vignettes/vignette.Rmd#L134 This function will return the single vec ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1295 lines (43%) are
not.
  First few lines:
    • R/CompareMCB.R#L33 MCBs, ...
    • ...
    • vignettes/vignette.Rmd#L109 ...
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 15 NOTES
ℹ See the EnMCB.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.