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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('tidybulk_2.3.0.tar.gz','quit-with-status'=TRUE)"
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── Installing tidybulk ─────────────────────────────────────────────────────────
✔ Package installed successfully
── tidybulk session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk
→ BiocVersion: 3.24
→ Package: tidybulk
→ PackageVersion: 2.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/tidybulk.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk
→ installDir: /tmp/Rtmp4Cyopf/file14c0a254a75327
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on tidybulk ───────────────────────────────────────────────
* 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 4.4.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: ATACSeq,
Microarray, BatchEffect, KEGG
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 (14%).
* 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:
    • comparison_coding.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/utilities.R (line 1392, column 9)
    • install() in R/utilities.R (line 1394, column 20)
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/fill_missing_abundance-methods.Rd:34: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/keep_abundant.Rd:60: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/test_gene_rank-methods.Rd:61: unknown macro '\lifecycle'
* Checking for library/require of tidybulk...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/glmmSeq.R (line 18, column 34)
    • ...
    • R/validation.R (line 397, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cibersort.R (line 72, column 70)
    • ...
    • validation.R (line 393, column 243)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/glmmSeq.R (line 841, column 7)
    • ...
    • print() in R/glmmSeq.R (line 878, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/adjust_abundance.R (line 110, column 22)
    • ...
    • R/zzz.R (line 25, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/deconvolve_cellularity.R (line 192, column 12)
    • R/glmmSeq.R (line 505, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/cluster_elements.R (line 95, column 12)
    • ...
    • R/test_differential_abundance.R (line 857, column 10)
! WARNING: .Deprecated / .Defunct usage (found 34 times)
  • deprecate_warn() in R/adjust_abundance.R (line 140, column 16)
  • ...
  • deprecate_warn() in R/validation.R (line 206, column 28)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 22 times)
  • suppressWarnings() in R/aggregate_duplicates.R (line 282, column 7)
  • ...
  • suppressMessages() in R/tidySummarizedExperiment.R (line 272, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 44
functions greater than 50 lines.
  The longest 5 functions are:
    • my_bibliography() (R/bibliography.R): 410 lines
    • ...
    • .adjust_abundance_se() (R/adjust_abundance.R): 190 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/fill_missing_abundance-methods.Rd:34: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/keep_abundant.Rd:60: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/test_gene_rank-methods.Rd:61: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/fill_missing_abundance-methods.Rd:34: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/keep_abundant.Rd:60: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/test_gene_rank-methods.Rd:61: unknown macro '\lifecycle'
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • log10_reverse_trans.Rd
  • resolve_complete_confounders_of_non_interest.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/fill_missing_abundance-methods.Rd:34: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/keep_abundant.Rd:60: unknown macro '\lifecycle'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/Rtmp4Cyopf/file14c0a2cf3acc6/tidybulk/man/test_gene_rank-methods.Rd:61: unknown macro '\lifecycle'
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 16% of man
pages use at least one of these tags.
  Found in files:
    • cluster_elements-methods.Rd
    • ...
    • test_gene_rank-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • cluster_elements-methods.Rd
    • ...
    • test_gene_rank-methods.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; 1044 lines (8%) are > 80 characters long.
  First few lines:
    • R/adjust_abundance.R#L5 #' @description adjust_abundance() takes ...
    • ...
    • vignettes/introduction.Rmd#L1169 `tidybulk` allows you to get the bibliog
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 935 lines (7%) contain tabs.
  First few lines:
    • R/adjust_abundance.R#L37 #' sva::ComBat(data, batch = my_batch, ...
    • ...
    • vignettes/introduction.Rmd#L1152 airway |> ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3893 lines (29%) are
not.
  First few lines:
    • R/adjust_abundance.R#L131 ...
    • ...
    • vignettes/introduction.Rmd#L1162 ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 22 NOTES
ℹ See the tidybulk.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.