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Version 0.12

pipette 0.12.0 (2023-08-25)

Major changes:

  • Migrated a number of dependency packages from Suggests to Imports (see DESCRIPTION and IMPORTS files) to avoid issues with missing dependencies in some commonly used Acid Genomics software. Here we are now requiring BiocFileCache, data.table, digest, httr2, jsonlite, readr, rtracklayer, and yaml as standard packages in pipette, so that they get automatically installed. This change only applies when managing dependencies using R directly and doesn’t affect bioconda recipes.
  • Hardened some internal assert checks using isAnExistingURL instead of simply isAURL. This new function available in the goalie package actively checks to see if the URL exists and is active. Note that for FTP directories, such as with the transmit function, the isAnExistingURL check only works if there is a trailing slash.

Minor changes:

  • Disabled examples using the Ensembl REST API server ("rest.ensembl.org"), as this has recently been flaky and can cause build checks to time out.
  • Miscellaneous unit test fixes, now using isAnExistingURL to check.

pipette 0.12.1 (2023-09-12)

Minor changes:

  • as.DataFrame: Fixed support for nesting of DFrame objects.
  • droplevels2: Ensure that original class and object metadata are preserved.

pipette 0.12.2 (2023-09-13)

Minor changes:

  • getURLDirList: Need to move isAnExistingURL assert check down, to not break Ensembl FTP server checks in AcidGenomes makeGRangesFromEnsembl.

pipette 0.12.3 (2023-09-14)

Major changes:

  • After inspecting the package with packageDependencies from AcidDevTools, decided to revert the changes introduced in 0.12.0 back to making more heavy dependencies optional. We are now no longer requiring BiocFileCache, data.table, digest, httr2, readr, and rtracklayer to be installed. This helps speed up attachment of the package, where it is most commonly used to simply import and export CSV files as the primary utility.
  • These package changes will not affect the bioconda recipe, as all optional dependencies are bundled with the recipe.

pipette 0.12.4 (2023-09-15)

  • getURLDirList: Tighten up assert checks to intentionally error if input does not contain an FTP server URL.