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Version 0.7

AcidDevTools 0.7.0 (2023-09-28)

New functions:

  • cacheTestFiles: New utility function used in other packages to quickly cache files for testthat build checks.
  • longtest: Variant of test that runs optional tests defined in longtests. This is useful for matching recommended Bioconductor conventions. These tests are run in a temporary directory.
  • nonCamelArgs: Check for documented arguments that are not correctly formatted in strict camel case.
  • nonCamelExports: Check for exported functions that are not correctly formatted in strict camel case.

Minor changes:

  • check: Now returns the amount of time required to run checks.
  • Enforcing strict camel case in function names. As a result, we have renamed pkgdownDeployToAWS to pkgdownDeployToAws.

AcidDevTools 0.7.1 (2023-10-03)

Minor changes:

  • No longer reexporting functions from remotes.

AcidDevTools 0.7.2 (2023-10-06)

Minor changes:

  • view2: Need to set optional = TRUE for as.data.frame coercion.

AcidDevTools 0.7.3 (2023-10-24)

New functions:

  • rebuildBinary: New function for updating problematic binary file in drat repo. Added this after I hit S4 subclass caching issues related to the change in AcidGenomes from HumanToMouse to JaxHumanToMouse. This affected AcidSingleCell and DESeqAnalysis. Function is vectorized, supporting multiple packageName in a single call.

AcidDevTools 0.7.4 (2023-12-13)

New functions:

  • inspectRow: Quickly examine nested values in a data.frame row. Supports any object that can be coerced to a data.frame.

AcidDevTools 0.7.5 (2025-03-21)

  • publish: Change repo argument to inherit ACIDGENOMICS_REPO environment variable, which should be defined in ~/.Renviron.

AcidDevTools 0.7.6 (2025-04-24)

  • Added languageserver and later as suggested packages, which makes bootstrapping a new R developer environment easier.
  • check now disables styler checks by default (styler = FALSE). We are testing out using the air formatter instead.

AcidDevTools 0.7.7 (2025-05-25)

  • install no longer automatically attempts to build data.table from source on macOS to enable parallel threads. The latest version of data.table 1.17.2 now supports this automatically on macOS.

AcidDevTools 0.7.8 (2026-03-02)

  • valid: Removed internal override for pkgType passthrough. This wasn’t returning invalid pre-release software packages without binaries correctly.

AcidDevTools 0.7.9 (2026-06-20)

  • publish: Delegate build, drat insert, S3 sync, and CloudFront invalidation to koopa app r publish. The repo and deploy parameters are removed; koopa reads ACIDGENOMICS_REPO from the environment. Check and pkgdown steps remain in R as before.

AcidDevTools 0.7.10 (2026-06-19)

License changes:

  • Relicensed from AGPL-3 to Apache 2.0.

Minor changes:

  • Modernized tooling: removed per-package .lintr in favour of global ~/.lintr; added air.toml; migrated to roxygen2 8.0 (Config/roxygen2/version).

AcidDevTools 0.7.11 (2026-06-20)

Bug fixes:

AcidDevTools 0.7.12 (2026-07-20)

Bug fixes:

  • install(): Fixed an over-broad USE.NAMES → useNames rename introduced in d28d156 (0.7.11) that clobbered five base-R vapply() calls, causing .requireNamespaces("utils") is not TRUE on every call. Restored USE.NAMES on all five sites. Also removed the redundant .requireNamespaces("utils") guard from install() — base packages must not be passed to this helper.
  • valid(): Filter utils::old.packages() results to packages where a strictly newer binary version is actually available in the configured repos, using the ReposVer column. Previously, checkBuilt = TRUE caused packages built against a prior R patch release (e.g. built for 4.6.0, running 4.6.1) to be flagged even when binary repos carry only the same version — reinstalling produced an infinite loop with no change in the installed binary.