Consider submission to BioConductor

[tuner]

Although devtools::install_github() works, BioConductor would provide stable, archived versions, enforce some code quality, and boost the package's credibility in the bioinformatics community.

Other similar packages available on BioConductor

These are based on htmlwidgets:

• MapScape
• interacCircos

Things to Fix

BiocCheck

> BiocCheck::BiocCheck()
─ BiocCheckVersion: 1.40.0
─ BiocVersion: 3.19
─ Package: jellyfisher
─ PackageVersion: 0.0.0.9000
─ sourceDir: /Users/klavikka/hautaniemi/jellyfisher
─ installDir: /var/folders/s8/c2vgvk853c9162b_xr5zssw151hbdz/T//RtmpW4RvVJ/file74a359dddd61
─ BiocCheckDir: /Users/klavikka/hautaniemi/jellyfisher.BiocCheck
─ platform: unix
─ isTarBall: FALSE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking version number validity...
    * ERROR: Invalid package Version, see https://contributions.bioconductor.org/versionnum.html
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.1.0 to 4.4.0.
* Checking package size...
    Skipped... only checked on source tarball
* 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...
    * NOTE: The Description field in the DESCRIPTION is made up of less than 3 sentences. Provide a more detailed
      description of the package.
* 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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    * WARNING: No Bioconductor dependencies detected. Note that some infrastructure packages may not have
      Bioconductor dependencies.  For more information, reach out to the Bioconductor community and/or consider a
      CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking package installation calls in R code...
* Checking for library/require of jellyfisher...
    * WARNING: Avoid the use of 'library' or 'require' in R code
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There are 2 functions greater than 50 lines.
* Checking man page documentation...
    * WARNING: Empty or missing \value sections found in man page(s).
    * ERROR: At least 80% of man pages documenting exported objects must have runnable examples.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements.
* Checking unit tests...
    * 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...
    * NOTE: Consider shorter lines; 58 lines (13%) are > 80 characters long.
    * NOTE: Consider multiples of 4 spaces for line indents; 104 lines (23%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
* Checking for bioc-devel mailing list subscription...
    * 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 results ──
4 ERRORS | 3 WARNINGS | 10 NOTES

See the jellyfisher.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.