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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('glmGamPoi_1.24.0.tar.gz','quit-with-status'=TRUE)"
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── Installing glmGamPoi ────────────────────────────────────────────────────────
✔ Package installed successfully
── glmGamPoi session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpmh2eS2/file15c29958c5218c/glmGamPoi
→ BiocVersion: 3.23
→ Package: glmGamPoi
→ PackageVersion: 1.24.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/glmGamPoi.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmpmh2eS2/file15c29958c5218c/glmGamPoi
→ installDir: /tmp/Rtmpmh2eS2/file15c299741a1f07
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on glmGamPoi ──────────────────────────────────────────────
* 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 4.1.0 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 that Package field matches directory/tarball name...
* 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 (53%).
* 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:
    • glmGamPoi.Rmd
    • pseudobulk.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/pseudobulk.Rmd
* Checking package installation calls in R code...
* Checking for library/require of glmGamPoi...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • quasi_gamma_poisson_shrinkage.R (line 197, column 41)
    • quasi_gamma_poisson_shrinkage.R (line 201, column 59)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/overdispersion.R (line 176, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/glm_gp.R (line 420, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/estimate_size_factors.R (line 36, column 14)
    • ...
    • R/predict.R (line 178, column 25)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/test_pseudobulk.R (line 43, column 3)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
  The longest 5 functions are:
    • test_de_q() (R/test_de.R): 185 lines
    • ...
    • handle_design_parameter() (R/glm_gp.R): 91 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/loc_median_fit.Rd
    • man/solve_lm_for_A.Rd
    • man/vars.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • vars.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; 619 lines (15%) are > 80 characters long.
  First few lines:
    • R/calculate_mu.R#L8 De ...
    • ...
    • vignettes/pseudobulk.Rmd#L89 Originally, `glmGamPoi`'s API encouraged ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1416 lines (34%) are
not.
  First few lines:
    • R/calculate_mu.R#L5 make_offset_hdf5_mat <- is(offset_matr ...
    • ...
    • vignettes/pseudobulk.Rmd#L82 geom_point(aes(color = adj_pval < 0.01 ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the glmGamPoi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.