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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('primirTSS_1.31.0.tar.gz','quit-with-status'=TRUE)"
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── Installing primirTSS ────────────────────────────────────────────────────────
✔ Package installed successfully
── primirTSS session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkNQUXL/file102b3e26d6c1c0/primirTSS
→ BiocVersion: 3.24
→ Package: primirTSS
→ PackageVersion: 1.31.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/primirTSS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpkNQUXL/file102b3e26d6c1c0/primirTSS
→ installDir: /tmp/RtmpkNQUXL/file102b3e380a84ca
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on primirTSS ──────────────────────────────────────────────
* 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 3.5.0 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:
GeneExpression, ChipOnChip, SingleCell, GenePrediction, GeneSetEnrichment
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (43%).
* 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:
    • primirTSS.Rmd
* Checking package installation calls in R code...
* Checking for library/require of primirTSS...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plot_miRNA_track.R (line 87, column 11)
    • R/plot_miRNA_track.R (line 99, column 13)
    • R/transform_cor.R (line 53, column 6)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/transform_cor.R (line 72, column 10)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/eponine_score.R (line 75, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/transform_cor.R (line 54, column 3)
* 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:
    • plot_primiRNA_track() (R/plot_miRNA_track.R): 116 lines
    • ...
    • tss_filter() (R/tss_filter.R): 71 lines
* Checking man page documentation...
Warning: replacing previous import ‘BiocGenerics::setequal’ by ‘dplyr::setequal’ when loading ‘primirTSS’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • run_primirTSSapp.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 43% of man
pages use at least one of these tags.
  Found in files:
    • find_tss.Rd
    • plot_primiRNA.Rd
    • run_primirTSSapp.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • find_tss.Rd
    • plot_primiRNA.Rd
    • run_primirTSSapp.Rd
* 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; 45 lines (2%) are > 80 characters long.
  First few lines:
    • R/candidate_tss.R#L3 #' @rawNamespace import(dplyr, except=c( ...
    • ...
    • vignettes/primirTSS.Rmd#L393 Here is the output of sessionInfo() on t ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 603 lines (32%) are
not.
  First few lines:
    • R/candidate_tss.R#L11 mir_eponine_score <- tibble::tibble(mi ...
    • ...
    • vignettes/primirTSS.Rmd#L315 allmirgene_byforce = TRUE) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 16 NOTES
ℹ See the primirTSS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.