##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BgeeDB_2.39.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing BgeeDB ───────────────────────────────────────────────────────────
✔ Package installed successfully
── BgeeDB session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpuX1LF9/file5ae812b32f15a/BgeeDB
→ BiocVersion: 3.24
→ Package: BgeeDB
→ PackageVersion: 2.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BgeeDB.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpuX1LF9/file5ae812b32f15a/BgeeDB
→ installDir: /tmp/RtmpuX1LF9/file5ae8149b0a420
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BgeeDB ─────────────────────────────────────────────────
* 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 3.6.0 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: SingleCell,
Transcriptomics, GeneTarget, Pathways, SystemsBiology
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 (28%).
* 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:
    • BgeeDB_Manual.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/BgeeDB_Manual.Rmd
* Checking package installation calls in R code...
* Checking for library/require of BgeeDB...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/listBgeeRelease.R (line 51, column 41)
    • R/topAnat.R (line 148, column 28)
    • R/topAnat.R (line 152, column 36)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Bgee.R (line 66, column 123)
    • ...
    • topAnat.R (line 208, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Bgee.R (line 64, column 9)
    • ...
    • cat() in R/makeTable.R (line 131, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/formatData.R (line 43, column 12)
    • ...
    • R/topAnat.R (line 304, column 30)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/Bgee.R (line 154, column 16)
    • ...
    • R/loadTopAnatData.R (line 328, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Bgee.R (line 67, column 14)
    • ...
    • R/utils.R (line 26, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/Bgee.R (line 105, column 82)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Bgee.R (line 91, column 30)
    • ...
    • loadTopAnatData.R (line 166, column 31)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/getData.R (line 63, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 42 times)
  • <<- in R/Bgee.R (line 65, column 18)
  • ...
  • <<- in R/getCellProcessedData.R (line 36, column 42)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/getSampleProcessedData.R (line 175, column 17)
  • suppressMessages() in R/getSampleProcessedData.R (line 539, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • loadTopAnatData() (R/loadTopAnatData.R): 296 lines
    • ...
    • getAnnotation() (R/getAnnotation.R): 86 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/deleteLocalData.Rd
    • man/deleteOldData.Rd
    • man/getCellProcessedData.Rd

Registered S3 method overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
  Found in files:
    • getCellProcessedData.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getCellProcessedData.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; 886 lines (27%) are > 80 characters long.
  First few lines:
    • R/Bgee.R#L3 #' @description This is used to specify ...
    • ...
    • vignettes/BgeeDB_Manual.Rmd#L294 As the new SQLite approach use more disk
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/loadTopAnatData.R#L342 ## Add BGEE:0 / root to organNames ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1120 lines (34%) are
not.
  First few lines:
    • R/Bgee.R#L36 "Bgee", ...
    • ...
    • vignettes/BgeeDB_Manual.Rmd#L13 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 20 NOTES
ℹ See the BgeeDB.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.