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Version 0.3

AcidBase 0.3.0 (2021-01-06)

Major changes:

  • Reworked internal function organization a bit, handing off some functions back into the goalie package.
  • Now that goalie doesn’t depend on AcidBase, we can import and use the superior assert checks defined in the package.

AcidBase 0.3.1 (2021-01-06)

Minor changes:

  • Now importing new AcidCLI package, to improve CLI messages.

AcidBase 0.3.2 (2021-01-15)

Minor changes:

  • Removed sampleId from metadataBlacklist global.
  • pasteURL now supports “s3” as a protocol value.

AcidBase 0.3.3 (2021-01-21)

Minor changes:

  • pasteURL: Added support for rsync as a protocol. Using this in future update in AcidGenomes package for downloading from UCSC server.

AcidBase 0.3.4 (2021-01-28)

New functions:

  • Added classContains utility function.

AcidBase 0.3.5 (2021-02-04)

Major changes:

  • Migrated geometricMean and sem methods from basejump.
  • Migrated showHeader from basejump.
  • Migrated coerceToList from basejump.
  • Migrated log ratio functions from basejump.
  • Migrated intersection functions from basejump.

Minor changes:

  • Made matchArgsToDoCall function defunct. Doesn’t always evaluate arguments correctly when called inside nested functions or complex S4 stacks.

AcidBase 0.3.6 (2021-02-11)

Minor changes:

  • Now reexporting all functions used in other Acid Genomics packages defined in base/recommended R packages here, including: grDevices, grid, methods, and stats, utils.

AcidBase 0.3.7 (2021-02-12)

Minor changes:

  • Including download.file as a reexport from utils.

AcidBase 0.3.8 (2021-02-17)

Minor changes:

  • Including formula and untar as reexports, which are used in the WormBase package.

AcidBase 0.3.9 (2021-02-21)

Minor changes:

  • Reexporting URLencode from utils, which is used downstream in Cellosaurus package.

AcidBase 0.3.10 (2021-02-23)

Minor changes:

  • Migrated printString back here from goalie package.
  • showHeader now checks for packageVersion inside of metadata as default instead of version.

AcidBase 0.3.11 (2021-02-25)

Minor changes:

  • Deprecating metadataBlacklist in favor of metadataDenylist.

AcidBase 0.3.12 (2021-03-01)

Minor changes:

  • Added install.packages as a reexport, which is used by r-koopa.
  • Also including head and tail as reexports.

AcidBase 0.3.13 (2021-03-02)

Minor changes:

  • Including data and median as reexports.

AcidBase 0.3.14 (2021-06-20)

Minor changes:

  • standardizeCall: Updated handling of dots handoff to match.call in R 4.1.
  • Now importing median and quantile functions from AcidGenerics, which use S4 defined in IRanges, rather than the base version defined in stats.

AcidBase 0.3.15 (2021-08-04)

New functions:

  • simpleClass: Added utility function for simple class checks, primarily intended for unit testing with testthat package.

AcidBase 0.3.16 (2021-08-13)

Minor changes:

  • Reworked package to use AcidCLI for improved error messages, which are now called via abort instead of stop internally.