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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('txdbmaker_1.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing txdbmaker ────────────────────────────────────────────────────────
✔ Package installed successfully
── txdbmaker session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpM6Nvx6/file1cbcb612107730/txdbmaker
→ BiocVersion: 3.24
→ Package: txdbmaker
→ PackageVersion: 1.9.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/txdbmaker.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpM6Nvx6/file1cbcb612107730/txdbmaker
→ installDir: /tmp/RtmpM6Nvx6/file1cbcb6180c9bd5
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on txdbmaker ──────────────────────────────────────────────
* 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...
* 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: GO
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 (62%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of txdbmaker...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • findCompatibleMarts.R (line 200, column 52)
    • makeTxDbFromBiomart.R (line 299, column 18)
    • makeTxDbFromBiomart.R (line 328, column 42)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/findCompatibleMarts.R (line 188, column 5)
    • ...
    • cat() in R/utils.R (line 38, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/makeFeatureDbFromUCSC.R (line 218, column 19)
    • R/makeFeatureDbFromUCSC.R (line 231, column 19)
    • R/makeTxDbFromUCSC.R (line 741, column 19)
! WARNING: .Deprecated / .Defunct usage (found 6 times)
  • .Deprecated() in R/makeFeatureDbFromUCSC.R (line 130, column 3)
  • ...
  • .Deprecated() in R/makeFeatureDbFromUCSC.R (line 189, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/Ensembl-utils.R (line 36, column 21)
  • ...
  • suppressWarnings() in R/makeTxDbFromGRanges.R (line 635, column 13)
* 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:
    • makeTxDbFromGRanges() (R/makeTxDbFromGRanges.R): 215 lines
    • ...
    • makeFeatureDbFromUCSC() (R/makeFeatureDbFromUCSC.R): 93 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 22% of man
pages use at least one of these tags.
  Found in files:
    • makeTxDbFromBiomart.Rd
    • makeTxDbPackage.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; 3 lines (0%) are > 80 characters long.
  First few lines:
    • R/makeTxDbFromGRanges.R#L1358 ## ftp://plantgenie.org/Data/ConGenI ...
    • man/makeTxDbFromBiomart.Rd#L159 mart <- useEnsembl(biomart="ENSEMBL_MART
    ...
    • man/txdbmaker-package.Rd#L30 \url{https://bioconductor.org/packages ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1237 lines (15%) are
not.
  First few lines:
    • R/Ensembl-utils.R#L122 "\" dataset at ", mysql_url ...
    • ...
    • man/txdbmaker-package.Rd#L30 \url{https://bioconductor.org/packages ...
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 12 NOTES
ℹ See the txdbmaker.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.