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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ensembldb_2.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ensembldb ────────────────────────────────────────────────────────
✔ Package installed successfully
── ensembldb session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5pPSL8/file1ad4ce6016555a/ensembldb
→ BiocVersion: 3.24
→ Package: ensembldb
→ PackageVersion: 2.37.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/ensembldb.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp5pPSL8/file1ad4ce6016555a/ensembldb
→ installDir: /tmp/Rtmp5pPSL8/file1ad4ce3f79f0c4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ensembldb ──────────────────────────────────────────────
* 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...
! WARNING: Use biocViews from one category only (one of Software,
ExperimentData, AnnotationData, Workflow)
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (78%).
* 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:
    • ensembldb.Rmd
    • MySQL-backend.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ensembldb...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/dbhelpers.R (line 160, column 18)
    • R/functions-create-EnsDb.R (line 252, column 9)
    • R/functions-Filter.R (line 263, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dbhelpers.R (line 71, column 15)
    • ...
    • transcriptToX.R (line 725, column 21)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/functions-create-EnsDb.R (line 1111, column 5)
    • ...
    • cat() in R/functions-create-EnsDb.R (line 1449, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/seqname-utils.R (line 8, column 20)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/functions-Filter.R (line 199, column 14)
    • ...
    • R/transcriptToX.R (line 130, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/functions-Filter.R (line 83, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Deprecated.R (line 129, column 20)
    • functions-create-EnsDb.R (line 269, column 20)
    • Methods.R (line 107, column 17)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/functions-create-EnsDb.R (line 53, column 5)
! WARNING: .Deprecated / .Defunct usage (found 11 times)
  • .Deprecated() in R/Deprecated.R (line 22, column 5)
  • ...
  • .Deprecated() in R/Deprecated.R (line 176, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 5 times)
  • <<- in R/dbhelpers.R (line 137, column 25)
  • ...
  • <<- in R/transcriptToX.R (line 489, column 18)
! WARNING: Avoid 'Sys.setenv' (found 1 times)
  • Sys.setenv() in R/functions-create-EnsDb.R (line 51, column 9)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 25 times)
  • suppressWarnings() in R/dbhelpers.R (line 444, column 13)
  • ...
  • suppressWarnings() in R/proteinToX.R (line 712, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 41
functions greater than 50 lines.
  The longest 5 functions are:
    • ensDbFromGRanges() (R/functions-create-EnsDb.R): 300 lines
    • ...
    • _anonymous_.1419() (R/Methods.R): 139 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/Deprecated.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • Deprecated.Rd
  • listEnsDbs.Rd
  • runEnsDbApp.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 19% of man
pages use at least one of these tags.
  Found in files:
    • EnsDb-sequences.Rd
    • ...
    • useMySQL-EnsDb-method.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • EnsDb-sequences.Rd
    • ...
    • useMySQL-EnsDb-method.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; 196 lines (2%) are > 80 characters long.
  First few lines:
    • R/Classes.R#L228 #' rect(xleft=start(current), xright ...
    • ...
    • vignettes/proteins.Rmd#L289 `protein_id` *ENSP00000445047* are mappe ...
ℹ NOTE: Consider 4 spaces instead of tabs; 33 lines (0%) contain tabs.
  First few lines:
    • R/transcriptToX.R#L571 ids <- names(x) ...
    • ...
    • vignettes/proteins.Rmd#L268 return.type = "AAStringSet") ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1463 lines (12%) are
not.
  First few lines:
    • R/Classes.R#L9 slots = c(ensdb = "DBIConnectio ...
    • ...
    • vignettes/proteins.Rmd#L220 columns = c("TXBIOTYPE", "UNIPROT ...
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 | ⚠ 5 WARNINGS | ℹ 20 NOTES
ℹ See the ensembldb.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.