##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ExperimentHub_3.2.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing ExperimentHub ────────────────────────────────────────────────────
✔ Package installed successfully
── ExperimentHub session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmpzQZaEc/file77e7311648fd9/ExperimentHub
→ BiocVersion: 3.23
→ Package: ExperimentHub
→ PackageVersion: 3.2.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ExperimentHub.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpzQZaEc/file77e7311648fd9/ExperimentHub
→ installDir: /tmp/RtmpzQZaEc/file77e734a47f106
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ExperimentHub ──────────────────────────────────────────
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* 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 (50%).
* 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:
    • ExperimentHub.Rmd
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install() in R/ExperimentHub-class.R (line 105, column 26)
* Checking for library/require of ExperimentHub...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/ExperimentHub-class.R (line 110, column 13)
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ExperimentHub-class.R (line 20, column 20)
    • R/ExperimentHub-class.R (line 25, column 19)
    • R/ExperimentHub-class.R (line 134, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ExperimentHub-class.R (line 22, column 22)
    • R/utilities.R (line 53, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/ExperimentHub-class.R (line 38, column 20)
  • suppressMessages() in R/utilities.R (line 51, column 5)
* Checking function lengths...
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 67% of man
pages use at least one of these tags.
  Found in files:
    • getExperimentHubOption.Rd
    • listResources.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getExperimentHubOption.Rd
    • listResources.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 24 lines (3%) are > 80 characters long.
  First few lines:
    • R/ExperimentHub-class.R#L19 if ((cache == R_user_dir("Experiment ...
    • ...
    • vignettes/ExperimentHub.Rmd#L262 ExperimentHub location, to continue usin
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 12 lines (2%) contain tabs.
  First few lines:
    • vignettes/ExperimentHub.Rmd#L287 olddir <- path.expand(rappdirs::user ...
    • ...
    • vignettes/ExperimentHub.Rmd#L298 if(all(moveres)) unlink(olddir, recu ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 44 lines (6%) are not.
  First few lines:
    • R/ExperimentHub-class.R#L14 cache=getExperimentHubOptio ...
    • ...
    • vignettes/ExperimentHub.Rmd#L339 resources will have to be re-downloade
    ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 13 NOTES
ℹ See the ExperimentHub.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.