##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GA4GHshiny_1.35.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing GA4GHshiny ───────────────────────────────────────────────────────
✔ Package installed successfully
── GA4GHshiny session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpnXxSqM/filea0636667bc13f/GA4GHshiny
→ BiocVersion: 3.24
→ Package: GA4GHshiny
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GA4GHshiny.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpnXxSqM/filea0636667bc13f/GA4GHshiny
→ installDir: /tmp/RtmpnXxSqM/filea0636272cb01b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GA4GHshiny ─────────────────────────────────────────────
* 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: Network
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 (44%).
* 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 1 out of 2 code chunks = 50% unevaluated
ℹ 
* Checking package installation calls in R code...
* Checking for library/require of GA4GHshiny...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/app.R (line 24, column 14)
    • require() in R/app.R (line 26, column 14)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllUtilities.R (line 107, column 37)
    • R/AllUtilities.R (line 112, column 29)
    • R/AllUtilities.R (line 117, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/app.R (line 25, column 18)
    • R/app.R (line 27, column 18)
    • R/server.R (line 153, column 25)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
  The longest 5 functions are:
    • server() (R/server.R): 208 lines
    • _anonymous_.2() (R/server.R): 206 lines
    • ui() (R/ui.R): 58 lines
* Checking man page documentation...
No methods found in package ‘BiocGenerics’ for request: ‘lengths’ when loading ‘GA4GHclient’
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-app.R
test-initializeReferences.R test-initializeVariantSet.R
test-searchVariantsByGeneSymbol.R test-tidyVariants.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 35 lines (5%) are > 80 characters long.
  First few lines:
    • R/AllUtilities.R#L71 # This function returns a list of availa ...
    • ...
    • vignettes/GA4GHshiny.Rmd#L61 Create an `app.R` file inside ShinyServe ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 10 NOTES
ℹ See the GA4GHshiny.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.