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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('markeR_1.3.0.tar.gz','quit-with-status'=TRUE)"
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── Installing markeR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── markeR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp6U6BWw/filecf463718aced2/markeR
→ BiocVersion: 3.24
→ Package: markeR
→ PackageVersion: 1.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/markeR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp6U6BWw/filecf463718aced2/markeR
→ installDir: /tmp/Rtmp6U6BWw/filecf4637603c3ee
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on markeR ─────────────────────────────────────────────────
* 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 4.5.0 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 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 (19%).
* 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:
    • markeR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of markeR...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/CohenD_IndividualGenes.R (line 220, column 5)
    • ...
    • print() in R/Score_VariableAssociation.R (line 548, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/CalculateScores_logmedian.R (line 48, column 17)
    • ...
    • R/VariableAssociation.R (line 46, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/calculateDE.R (line 112, column 10)
    • ...
    • R/Volcano_Cohen.R (line 69, column 12)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressMessages() in R/FPR_Simulation.R (line 132, column 18)
  • ...
  • suppressMessages() in R/FPR_Simulation.R (line 229, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 34
functions greater than 50 lines.
  The longest 5 functions are:
    • geneset_similarity() (R/geneset_similarity.R): 375 lines
    • ...
    • FPR_Simulation() (R/FPR_Simulation.R): 290 lines
* Checking man page documentation...
* 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; 628 lines (7%) are > 80 characters long.
  First few lines:
    • R/calculateDE.R#L98 colnames_vector <- ifelse(new_coln ...
    • ...
    • vignettes/markeR.Rmd#L523 [tutorial-signaturesimilarity]: https:// ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2647 lines (28%) are
not.
  First few lines:
    • R/calculateDE.R#L92 data <- as.data.frame(data) # Ensure d ...
    • ...
    • vignettes/markeR.Rmd#L502 ...
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 11 NOTES
ℹ See the markeR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.