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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('mosdef_1.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing mosdef ───────────────────────────────────────────────────────────
✔ Package installed successfully
── mosdef session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZLMBOs/filee07af549a9d01/mosdef
→ BiocVersion: 3.24
→ Package: mosdef
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/mosdef.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZLMBOs/filee07af549a9d01/mosdef
→ installDir: /tmp/RtmpZLMBOs/filee07af1fd995a2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mosdef ─────────────────────────────────────────────────
* 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...
* 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 (33%).
* 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 mosdef...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/gene_annotation.R (line 59, column 8)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • expression_summaries.R (line 38, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/run_enrichment.R (line 874, column 7)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/run_enrichment.R (line 170, column 13)
    • R/run_enrichment.R (line 472, column 13)
    • R/run_enrichment.R (line 749, column 13)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/expression_summaries.R (line 37, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressMessages() in R/run_enrichment.R (line 257, column 3)
  • suppressMessages() in R/run_enrichment.R (line 268, column 3)
  • suppressMessages() in R/run_enrichment.R (line 272, column 3)
* 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:
    • run_topGO() (R/run_enrichment.R): 236 lines
    • ...
    • plot_ma() (R/plot_de_summaries.R): 111 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; 268 lines (8%) are > 80 characters long.
  First few lines:
    • R/buttonifier.R#L3 #' A function to turn Gene Symbols into ...
    • ...
    • vignettes/mosdef_userguide.Rmd#L635 This approach can be extended to link
    to ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 903 lines (25%) are
not.
  First few lines:
    • R/buttonifier.R#L53 if (!(col_to_use %in% colnames(df))) { ...
    • ...
    • vignettes/mosdef_userguide.Rmd#L621 ) ...
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 10 NOTES
ℹ See the mosdef.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.