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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BgeeCall_1.29.0.tar.gz','quit-with-status'=TRUE)"
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── Installing BgeeCall ─────────────────────────────────────────────────────────
✔ Package installed successfully
── BgeeCall session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkFQ77K/file5ad4e3dcdedfc/BgeeCall
→ BiocVersion: 3.24
→ Package: BgeeCall
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BgeeCall.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpkFQ77K/file5ad4e3dcdedfc/BgeeCall
→ installDir: /tmp/RtmpkFQ77K/file5ad4e48165661
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BgeeCall ───────────────────────────────────────────────
* 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 3.6 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...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2021-05
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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...
! WARNING: Evaluate more vignette chunks.
ℹ 24 out of 44 code chunks = 54% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • bgeecall-manual.Rmd
* Checking package installation calls in R code...
* Checking for library/require of BgeeCall...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/generateIntergenicRegions.R (line 223, column 13)
    • ...
    • R/generateIntergenicRegions.R (line 261, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bgeePipelineFunctions.R (line 456, column 15)
    • ...
    • utils.R (line 781, column 66)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/generateIntergenicRegions.R (line 192, column 1)
    • ...
    • print() in R/retrieveAnnotationTranscriptome.R (line 408, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bgeePipelineFunctions.R (line 402, column 31)
    • ...
    • R/utils.R (line 348, column 31)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/bgeePipelineFunctions.R (line 388, column 17)
    • ...
    • R/utils.R (line 573, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/BgeeMetadata.R (line 63, column 25)
    • ...
    • R/utils.R (line 243, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 13 times:
    • T in R/generateIntergenicRegions.R (line 23, column 76)
    • ...
    • T in R/mergingLibraries.R (line 212, column 41)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/kallisto.R (line 280, column 11)
    • ...
    • system() in R/retrievelibraries.R (line 68, column 13)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/generateIntergenicRegions.R (line 764, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/bgeecall-manual.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressMessages() in R/presenceAbsence.R (line 151, column 28)
  • ...
  • suppressMessages() in R/transcriptToGene.R (line 265, column 35)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 24
functions greater than 50 lines.
  The longest 5 functions are:
    • find_reference_intergenic_regions() (R/generateIntergenicRegions.R): 316
    lines
    • ...
    • plot_distributions() (R/bgeePipelineFunctions.R): 101 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/generate_initial_intergenic_regions.Rd
    • man/generate_reference_intergenic_regions.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • create_kallisto_index.Rd
    • ...
    • run_kallisto.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • create_kallisto_index.Rd
    • ...
    • run_kallisto.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • create_kallisto_index.Rd
    • ...
    • run_kallisto.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; 892 lines (12%) are > 80 characters long.
  First few lines:
    • R/AbundanceMetadata.R#L19 #' calls. If value of the slot cutoff_ty ...
    • ...
    • vignettes/bgeecall-manual.Rmd#L638
    unlink(file.path(getWorkingPath(user_Bge ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/generateIntergenicRegions.R#L41 ## sequence in 2. It will potentially c
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 799 lines (11%) are
not.
  First few lines:
    • R/bgeePipelineFunctions.R#L361 ...
    • ...
    • vignettes/bgeecall-manual.Rmd#L470 This can sometimes (not always) be fix
    ...
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 | ⚠ 4 WARNINGS | ℹ 21 NOTES
ℹ See the BgeeCall.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.