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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('sccomp_2.5.0.tar.gz','quit-with-status'=TRUE)"
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── Installing sccomp ───────────────────────────────────────────────────────────
✔ Package installed successfully
── sccomp session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp7ZbrUR/file129dce5fead11/sccomp
→ BiocVersion: 3.24
→ Package: sccomp
→ PackageVersion: 2.5.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/sccomp.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp7ZbrUR/file129dce5fead11/sccomp
→ installDir: /tmp/Rtmp7ZbrUR/file129dce2ebd4c2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on sccomp ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.3.0 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,
Microbiome, CellBiology, Immunology
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (4%).
* 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:
    • introduction.Rmd
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/model_fitting.R (line 283, column 30)
* Checking for library/require of sccomp...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/sccomp_replicate.R (line 604, column 12)
    • ...
    • R/validation.R (line 288, column 3)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • model_fitting.R (line 79, column 14)
    • ...
    • validation.R (line 155, column 32)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/utilities.R (line 1169, column 34)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/model_fitting.R (line 2, column 11)
    • ...
    • R/validation.R (line 300, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/sccomp_replicate.R (line 222, column 9)
    • ...
    • R/validation.R (line 129, column 7)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/sccomp_replicate.R (line 292, column 32)
! WARNING: .Deprecated / .Defunct usage (found 8 times)
  • deprecate_warn() in R/sccomp_estimate.R (line 557, column 16)
  • ...
  • deprecate_warn() in R/sccomp_remove_unwanted_variation.R (line 52, column
  14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/model_fitting.R (line 394, column 15)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/model_fitting.R (line 240, column 8)
  • ...
  • suppressMessages() in R/utilities.R (line 591, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 30
functions greater than 50 lines.
  The longest 5 functions are:
    • sccomp_remove_outliers.sccomp_tbl() (R/sccomp_remove_outliers.R): 381
    lines
    • ...
    • sccomp_glm_data_frame_counts() (R/sccomp_estimate.R): 254 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • sccomp_calculate_residuals.Rd
  • sccomp_theme.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 67% of man
pages use at least one of these tags.
  Found in files:
    • clear_stan_model_cache.Rd
    • ...
    • simulate_data.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • clear_stan_model_cache.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 878 lines (11%) are > 80 characters long.
  First few lines:
    • R/clear_stan_model_cache.R#L4 #' This function removes the Stan model ...
    • ...
    • vignettes/introduction.Rmd#L517 first cell type. We can see that it has
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • R/nanny.R#L4 .subset <- function(.data, .column) { ...
    • R/nanny.R#L15 select( !!.column, all_of(get_specif ...
    • R/nanny.R#L61 { (.)[lengths((.)) != 0] } %>% ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3105 lines (39%) are
not.
  First few lines:
    • R/clear_stan_model_cache.R#L47 ...
    • ...
    • vignettes/introduction.Rmd#L482 ) ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 23 NOTES
ℹ See the sccomp.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.