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Version 0.2

AcidBase 0.2.0 (2020-10-06)

Major changes:

  • Renamed package from acidbase to AcidBase.

AcidBase 0.2.1 (2020-10-06)

New functions:

  • Added forceDetach, previously used internally inside basejump.
  • Updated documentation to inherit from AcidRoxygen instead of acidroxygen.

AcidBase 0.2.2 (2020-10-07)

New functions:

  • Migrated headtail atomic, matrix, and data.frame methods here from basejump. The methods that work on S4 objects, such as DataFrame, Matrix, GRanges, and SummarizedExperiment are still defined in basejump.
  • showSlotInfo: Migrated from basejump, so we can use in AcidGenomes.

AcidBase 0.2.3 (2020-10-07)

  • Fixed reference to AcidPlots package, renamed from previous “acidplots”.

AcidBase 0.2.4 (2020-11-24)

New functions:

  • sem: Added support for standard error of the mean calculation.

AcidBase 0.2.5 (2020-12-10)

New functions:

  • Added download, which acts as a hardened wrapper for utils::download.file. Annoying, download.file returns status codes but does not intentionally error on any unsuccessful downloads. Our wrapper ensures that R always errors on any file download issue. It also sets a longer timeout internally, to avoid any potential issues with the timeout option being defined in Rprofile.

Bug fixes

  • compress and decompress were found to potentially generate integer overflow warnings on very large files, due to R using 32-bit integers. This issue has been resolving by ensuring the internal nbytes counter is set as numeric instead. See related Stack Overflow post for details on integer overflows in R.
  • sem: Requires AsIs class support, to work inside dplyr summarize calls.
  • Now need to import BiocGenerics, for proper import of AsIs S4 class, which is an oldClass of the S3 class.

AcidBase 0.2.6 (2020-12-15)

Minor changes:

  • download: Function now recursively creates destination file parent directory if necessary.
  • pasteURL: Now defaulting to no protocol (e.g. “https”) by default. This makes pasting of an existing URL with subdirectories easier.