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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('OrganismDbi_1.55.1.tar.gz','quit-with-status'=TRUE)"
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── Installing OrganismDbi ──────────────────────────────────────────────────────
✔ Package installed successfully
── OrganismDbi session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpfZXi9C/file19fef73fd7dbee/OrganismDbi
→ BiocVersion: 3.24
→ Package: OrganismDbi
→ PackageVersion: 1.55.1
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/OrganismDbi.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpfZXi9C/file19fef73fd7dbee/OrganismDbi
→ installDir: /tmp/RtmpfZXi9C/file19fef755adbd7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on OrganismDbi ────────────────────────────────────────────
* 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 2.14.0 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,
Alignment, GenomeAssembly
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (67%).
* 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/OrganismDbi.Rmd
* Checking package installation calls in R code...
* Checking for library/require of OrganismDbi...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/createOrganismPackage.R (line 267, column 13)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/createOrganismPackage.R (line 204, column 13)
    • R/methods-select.R (line 173, column 19)
    • R/methods-select.R (line 214, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllClasses.R (line 67, column 47)
    • ...
    • methods-select.R (line 117, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllClasses.R (line 185, column 5)
    • ...
    • cat() in R/AllClasses.R (line 253, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/methods-select.R (line 474, column 19)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • AllClasses.R (line 107, column 20)
    • methods-transcripts.R (line 54, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/methods-select.R (line 234, column 5)
  • suppressMessages() in R/methods-select.R (line 251, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • makeOrganismPackage() (R/createOrganismPackage.R): 96 lines
    • ...
    • .select() (R/methods-select.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/OrganismDb.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • makeOrganismDbFromTxDb.Rd
    • makeOrganismDbFromUCSC.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 29% of man
pages use at least one of these tags.
  Found in files:
    • makeOrganismDbFromTxDb.Rd
    • makeOrganismDbFromUCSC.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • makeOrganismDbFromTxDb.Rd
    • makeOrganismDbFromUCSC.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; 67 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L115 ## TODO: add to this so that we populate ...
    • ...
    • vignettes/OrganismDbi.Rmd#L36 ```{r figure, fig.cap = "Relationships b
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 18 lines (0%) contain tabs.
  First few lines:
    • R/seqinfo.R#L30 seqinfo(txdb) ...
    • ...
    • man/OrganismDb.Rd#L117 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 718 lines (20%) are
not.
  First few lines:
    • R/AllClasses.R#L46 representation(keys="matrix ...
    • ...
    • vignettes/OrganismDbi.Rmd#L177 license = "Artistic-2.0" ...
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 email is ok.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the OrganismDbi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.