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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RFLOMICS_1.5.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RFLOMICS ─────────────────────────────────────────────────────────
✔ Package installed successfully
── RFLOMICS session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkCZYGA/file11a6c7307f481b/RFLOMICS
→ BiocVersion: 3.24
→ Package: RFLOMICS
→ PackageVersion: 1.5.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RFLOMICS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpkCZYGA/file11a6c7307f481b/RFLOMICS
→ installDir: /tmp/RtmpkCZYGA/file11a6c7106456ac
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RFLOMICS ───────────────────────────────────────────────
* 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 4.4.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage, ExperimentalDesign, GeneExpression, RNASeq, ImmunoOncology
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* 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:
    • RFLOMICS-command-line.Rmd
    • RFLOMICS-input-data.Rmd
    • RFLOMICS.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/RFLOMICS-input-data.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RFLOMICS...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/module_04_diff_analysis.R (line 594, column 22)
    • ...
    • R/utils_02_set_stat_model.R (line 717, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • server.R (line 161, column 38)
    • ...
    • utils_04_diff_analysis.R (line 386, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/module_06_annot_enrichment.R (line 1677, column 26)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/RFLOMICS-Methods_03_data_explor.R (line 648, column 18)
    • ...
    • R/utils_04_diff_analysis.R (line 142, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/RFLOMICS-Methods_03_data_explor.R (line 794, column 29)
    • R/RFLOMICS-Methods_03_data_explor.R (line 932, column 29)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/utils_00_common.R (line 228, column 13)
    • R/utils_00_common.R (line 231, column 13)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/RFLOMICS-Methods_00_Common.R (line 234, column 7)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/utils_00_common.R (line 88, column 23)
  • <<- in R/utils_00_common.R (line 92, column 25)
  • <<- in R/utils_07_integration.R (line 303, column 52)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 69
functions greater than 50 lines.
  The longest 5 functions are:
    • QCNormalizationTab() (R/module_03_data_explor.R): 781 lines
    • ...
    • .modLoadData() (R/module_01_load_data.R): 402 lines
* Checking man page documentation...

Registered S3 method overwritten by 'ggnetwork':
  method         from  
  fortify.igraph ggtree
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getAnalysis.Rd
  • rflomicsMAE2MAE.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • inst/NEWS.md
    • RFLOMICS/NEWS.md
* 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; 816 lines (4%) are > 80 characters long.
  First few lines:
    • R/coverPage.R#L12 h1(tags$span("An int ...
    • ...
    • vignettes/RFLOMICS.Rmd#L495 All methods from the MultiAssayExperimen ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • R/utils_01_load_data.R#L285 #' A DataFrame or data.frame of assay n ...
    • R/utils_01_load_data.R#L286 #' and colname samples ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 6048 lines (28%) are
not.
  First few lines:
    • R/coverPage.R#L8 fluidPage( ...
    • ...
    • vignettes/RFLOMICS.Rmd#L483 factorInfo = factorInfo ...
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 | ⚠ 0 WARNINGS | ℹ 20 NOTES
ℹ See the RFLOMICS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.