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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CPSM_1.5.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CPSM ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── CPSM session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpgOvyom/file7a8be36bcd8ec/CPSM
→ BiocVersion: 3.24
→ Package: CPSM
→ PackageVersion: 1.5.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CPSM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpgOvyom/file7a8be36bcd8ec/CPSM
→ installDir: /tmp/RtmpgOvyom/file7a8be39d3c85c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CPSM ───────────────────────────────────────────────────
* 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 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 (6%).
* 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:
    • CPSM.Rmd
* Checking package installation calls in R code...
* Checking for library/require of CPSM...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Univariate_sig_features_f.R (line 180, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Lasso_PI_scores_f.R (line 118, column 55)
    • ...
    • predict_survival_risk_group_f.R (line 202, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/predict_survival_risk_group_f.R (line 134, column 5)
    • cat() in R/predict_survival_risk_group_f.R (line 203, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/MTLR_pred_model_f.R (line 1146, column 25)
    • ...
    • R/MTLR_pred_model_f.R (line 1177, column 24)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/data_process_f.R (line 37, column 13)
    • ...
    • R/Univariate_sig_features_f.R (line 103, column 13)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/Nomogram_generate_f.R (line 205, column 8)
  • suppressMessages() in R/Nomogram_generate_f.R (line 205, column 25)
  • suppressMessages() in R/Univariate_sig_features_f.R (line 151, column 4)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • MTLR_pred_model_f() (R/MTLR_pred_model_f.R): 1132 lines
    • ...
    • Nomogram_generate_f() (R/Nomogram_generate_f.R): 156 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; 233 lines (5%) are > 80 characters long.
  First few lines:
    • R/km_overlay_plot_f.R#L4 #' This function generates an overlayed ...
    • ...
    • vignettes/CPSM.Rmd#L1030 After running the function, the output i ...
ℹ NOTE: Consider 4 spaces instead of tabs; 116 lines (3%) contain tabs.
  First few lines:
    • R/km_overlay_plot_f.R#L91 font_size = 12, # ...
    • ...
    • vignettes/CPSM.Rmd#L960 annotation_col = "black" ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1006 lines (24%) are
not.
  First few lines:
    • R/data_process_f.R#L34 # Check if any input variable is empty ...
    • ...
    • vignettes/CPSM.Rmd#L1016 col_grid = gray(c(0.85, 0.95)) ...
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 14 NOTES
ℹ See the CPSM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.