##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SPONGE_1.35.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing SPONGE ───────────────────────────────────────────────────────────
✔ Package installed successfully
── SPONGE session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpd5sLsf/file14612e386c7f4c/SPONGE
→ BiocVersion: 3.24
→ Package: SPONGE
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SPONGE.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpd5sLsf/file14612e386c7f4c/SPONGE
→ installDir: /tmp/Rtmpd5sLsf/file14612e3f52c88e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SPONGE ─────────────────────────────────────────────────
* 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 3.6 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...
! WARNING: Invalid BiocViews term(s):
  • 'RandomForest'
  • 'MachineLearning'
* Checking for recommended biocViews...
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...
* Checking License: for restrictive use...
* 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 (11%).
* 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:
    • SPONGE.Rmd
    • spongEffects.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/spongEffects.Rmd (chunk no. 10, line 92, column 164)
    • ...
    • vignettes/spongEffects.Rmd (chunk no. 24, line 259, column 50)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/SPONGE.Rmd
    • vignettes/spongEffects.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SPONGE...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/fn_network_centralities.R (line 103, column 31)
    • R/fn_spongeffects_utility.R (line 1092, column 20)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • fn_check_and_convert_expr_data.R (line 15, column 37)
    • ...
    • fn_spongeffects_utility.R (line 1707, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/fn_spongeffects_utility.R (line 358, column 13)
    • ...
    • print() in R/fn_subsampling.R (line 80, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/fn_simulation.R (line 114, column 50)
    • ...
    • R/fn_spongeffects_utility.R (line 1797, column 56)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/fn_significance.R (line 127, column 18)
    • R/fn_significance.R (line 254, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 27 times:
    • T in R/fn_spongeffects_utility.R (line 76, column 45)
    • ...
    • F in R/fn_spongeffects_utility.R (line 1634, column 68)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/fn_spongeffects_utility.R (line 229, column 5)
  • set.seed() in R/fn_spongeffects_utility.R (line 437, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/fn_gene_miRNA_regression_models.R (line 9, column 7)
  • <<- in R/fn_sponge.R (line 362, column 11)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/fn_sponge.R (line 378, column 9)
* 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:
    • sponge_gene_miRNA_interaction_filter()
    (R/fn_gene_miRNA_regression_models.R): 263 lines
    • ...
    • plot_accuracy_sensitivity_specificity() (R/fn_spongeffects_utility.R):
    178 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/fn_RF_classifier.Rd
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • build_classifier_central_genes.Rd
    • ...
    • sponge_plot_network_centralities.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • check_and_convert_expression_data.Rd
    • sponge_plot_network_centralities.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • check_and_convert_expression_data.Rd
    • sponge_plot_network_centralities.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; 395 lines (8%) are > 80 characters long.
  First few lines:
    • R/data.R#L73 #' @format a data frame with sample meta ...
    • ...
    • vignettes/spongEffects.Rmd#L267 gene_mir ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 386 lines (8%) are
not.
  First few lines:
    • R/fn_benchmark.R#L28 mir_exp ...
    • ...
    • vignettes/spongEffects.Rmd#L259 show.rownames = F, show.co ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the SPONGE.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.