Changelog

Source: NEWS.md

regutools 1.3.2

SIGNIFICANT USER-VISIBLE CHANGES

• The link provided inside connect_database() has been updated in order to connect with the latest version of regulonDB v10.8.

regutools 1.3.1

BUG FIXES

• Fixed URL for the database. Resolves https://github.com/ComunidadBioInfo/regutools/issues/33.

regutools 1.1.3

SIGNIFICANT USER-VISIBLE CHANGES

• The package CITATION file has been updated now that the online paper on regutools is available at https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa575/5861528 with DOI 10.1093/bioinformatics/btaa575 and PMID: 32573705.

DOCUMENTATION UPDATES

• roxygen version update was included and documentation was build under the new roxygen version.

regutools 1.1.1

SIGNIFICANT USER-VISIBLE CHANGES

• The package CITATION file has been updated now that the pre-print on regutools is available at https://www.biorxiv.org/content/10.1101/2020.04.29.068551v1 with DOI https://doi.org/10.1101/2020.04.29.068551.

regutools 0.99.14

SIGNIFICANT USER-VISIBLE CHANGES

• Now connect_database() as a bfc parameter instead of path.

regutools 0.99.13

SIGNIFICANT USER-VISIBLE CHANGES

• Now connect_database() uses BiocFileCache::BiocFileCache() and BiocFileCache::bfcrpath() to download the database from Dropbox when it’s not available from AnnotationHub::query() and caches the file so you don’t have to re-download it multiple times.

regutools 0.99.12

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://comunidadbioinfo.github.io/regutools/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

regutools 0.99.11

BUG FIXES

• Manual adjustment for lines > 80 chr in parameters description.

regutools 0.99.10

BUG FIXES

• Bump Version to run R CMD check

regutools 0.99.9

BUG FIXES

• Add a suggested biocView Transcription.

regutools 0.99.8

BUG FIXES

• Change biocViews from AnnotationData to Software

regutools 0.99.7

BUG FIXES

• Fix a bug in pkgdown that is currently resolved by Rscript -e 'remotes::install_github("r-lib/pkgdown#1276")'. Details at https://github.com/r-lib/pkgdown/pull/1276 and related issues.

regutools 0.99.6

BUG FIXES

• Manual adjust for some lines > 80 characters

regutools 0.99.5

BUG FIXES

• Reindent lines and try line-wrapping for lines > 80 characters

regutools 0.99.4

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

regutools 0.99.3

SIGNIFICANT USER-VISIBLE CHANGES

• DESCRIPTION file now contains an article-like summary in the field regutools package Description.
• DESCRIPTION was updated to show only one maintainer as required by http://bioconductor.org/developers/package-guidelines/#description

BUG FIXES

• Fix a bug in the function get_regulatory_network() related with Cytoscape conection.

regutools 0.99.2

SIGNIFICANT CHANGES

• Removed the regutools.Rproj file (you can still have it, but it’s not version controlled).
• Bump R depends to 4.0 as required by BiocCheck. We’ll see if it breaks.

regutools 0.99.1

BUG FIXES

• Address as many errors, warnings and notes as possible from http://bioconductor.org/spb_reports/regutools_buildreport_20200302121040.html#malbec2_check_anchor. For the Windows error, it’s likely related to mode = "w" versus mode = "wb" for utils::download.file() as in https://github.com/LieberInstitute/spatialLIBD/commit/7ac24dc72cc75e42c9af8382c661517f4a64f08d.

regutools 0.99.0

NEW FEATURES

• Submitted to Bioconductor