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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('PAST_1.29.0.tar.gz','quit-with-status'=TRUE)"
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── Installing PAST ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── PAST session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpl113OX/filefd0d53964c20d/PAST
→ BiocVersion: 3.24
→ Package: PAST
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/PAST.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpl113OX/filefd0d53964c20d/PAST
→ installDir: /tmp/Rtmpl113OX/filefd0d5236aa701
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on PAST ───────────────────────────────────────────────────
* 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 4.0 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...
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 (31%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/past.Rmd
* Checking package installation calls in R code...
* Checking for library/require of PAST...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/assign_SNPs_to_genes.R (line 336, column 27)
    • library() in R/assign_SNPs_to_genes.R (line 336, column 43)
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/plot_rugplots.R (line 44, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/assign_SNPs_to_genes.R (line 229, column 9)
    • ...
    • R/assign_SNPs_to_genes.R (line 442, column 29)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • find_pathway_significance() (R/find_pathway_significance.R): 223 lines
    • ...
    • plot_pathways() (R/plot_rugplots.R): 77 lines
* Checking man page documentation...
Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::findMatches’ by ‘utils::findMatches’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 26 lines (2%) are > 80 characters long.
  First few lines:
    • R/assign_SNPs_to_genes.R#L103 effects_same_sign ...
    • ...
    • R/find_pathway_significance.R#L256 get_running_enrichment_score(g ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 372 lines (28%) are
not.
  First few lines:
    • R/assign_SNPs_to_genes.R#L37 linked_snp_count = ...
    • ...
    • vignettes/past.Rmd#L215 tempdir()) ...
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 | ⚠ 1 WARNINGS | ℹ 11 NOTES
ℹ See the PAST.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.