bioconductor-specific check results

Run BiocCheck::BiocCheck(
─ BiocCheckVersion: 1.32.1
─ BiocVersion: 3.15
─ Package: djvdj
─ PackageVersion: 0.0.0.9000
─ sourceDir: /tmp/Rtmp10744r/file1f522fb2e76a/djvdj
─ installDir: /tmp/Rtmp10744r/file1f52e5c49e7
─ BiocCheckDir: /__w/djvdj/djvdj/check/djvdj.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/usr/local/lib/R/bin/R' -q --vanilla --no-echo -f /__w/_temp/Library/BiocCheck/script/checkBadDeps.R --args "/tmp/Rtmp10744r/file1f522fb2e76a/djvdj" "/tmp/Rtmp10744r/file1f52e5c49e7/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
    * ERROR: Package dependencies must be on CRAN or Bioconductor.
      Remove 'Remotes:' from DESCRIPTION
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
    * ERROR: Invalid package Version, see
      http://www.bioconductor.org/developers/how-to/version-numbering/
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
    * ERROR: No biocViews terms found.
Search 'biocViews' at https://contributions.bioconductor.org/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import graphics, grid, utils in DESCRIPTION as well as
      NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking package installation calls in R code...
* Checking for library/require of djvdj...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://packagemanager.rstudio.com/cran/__linux__/focal/latest

* Checking parsed R code in R directory, examples, vignettes...
    Found @ in man/calc_diversity.Rd
    Found @ in man/calc_frequency.Rd
    Found @ in man/calc_similarity.Rd
    Found @ in man/define_clonotypes.Rd
    Found @ in man/filter_vdj.Rd
    Found @ in man/import_vdj.Rd
    Found @ in man/mutate_meta.Rd
    Found @ in man/mutate_vdj.Rd
    Found @ in man/summarize_vdj.Rd
    Found @ in vignettes/abundance.Rmd
    Found @ in vignettes/import_vdj.Rmd
    Found @ in vignettes/mutate.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    * NOTE: Avoid '<<-' if possible (found 1 times)
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.There are 26
      functions > 50 lines.
* Checking man page documentation...
Warning in nzchar(fpath) && !is.na(fpath) :
  'length(x) = 3 > 1' in coercion to 'logical(1)'
Warning in nzchar(fpath) && !is.na(fpath) :
  'length(x) = 3 > 1' in coercion to 'logical(1)'
    * WARNING: Add non-empty \value sections to the following man
      pages: man/plot_mds.Rd, man/plot_motifs.Rd,
      man/plot_similarity.Rd
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 177 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 3270 lines
      (28%) are not.
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
rnabioco / djvdj

bioconductor-specific check results #108
