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Version 0.6

goalie 0.6.0 (2022-03-11)

Major changes:

  • assert: Engine will use AcidCLI::abort if installed, to return richer error messages in the console. Also improved named message handling, similar to stopifnot conventions.
  • Updated minimum R version dependency to 4.1, matching Bioconductor 3.14.

Minor changes:

  • Improved some cause attributes to use better CLI formatting.
  • Migrated some check functions from pointillism / AcidSingleCell packages: hasClusters, hasMultipleSamples, and isBiocParallelParam.
  • Migrated isDark check here from AcidPlots package.
  • Updated pkgdown website to use bootstrap 5 template.

goalie 0.6.1 (2022-04-29)

Minor changes:

  • Updated R dependency to 4.2.

goalie 0.6.2 (2022-05-09)

Minor changes:

  • validateClasses: Reworked internal code to use isAny, to allowing “or” checking for multiple acceptable class types. Currently needed to update validity checks against sessionInfo (utils package) vs. session_info (sessioninfo package) in our S4 classes that extend SummarizedExperiment.

goalie 0.6.3 (2022-05-13)

Minor changes:

  • Reworked package to support new lintr and testthat releases.
  • Now using Map internally instead of mapply, as recommended by lintr.

goalie 0.6.4 (2022-05-31)

Minor changes:

  • isGitRepo: Return with classed cause in the event that Git is not installed.

goalie 0.6.5 (2022-10-18)

Minor changes:

  • Using isSubset in place of %in% where possible.
  • isInstalled: Now calling .packages internally instead of checking rownames on installed.packages return.
  • hasDuplicates, hasNoDuplicates: Hardened internal calls to anyDuplicated to check whether values return non-zero or not.
  • isCleanSystemLibrary: NAMESPACE fix for installed.packages call.

goalie 0.6.6 (2022-10-18)

New functions:

  • isVSCode: Check if R session is running inside of Visual Studio Code.

goalie 0.6.7 (2022-12-14)

New functions:

  • isIntegerish: New check function that will also return true for vector-like classes, including factor and S4 Rle.

Minor changes:

  • hasRownames: Should now return TRUE for data.frame with integer row names out of order. This is useful for matrix export method defined in pipette package.
  • Added support for S4 Rle class handling in isSubset, areDisjointSets, areIntersectingSets, areSetEqual.
  • Removed unused skip_on_docker test function.

goalie 0.6.8 (2023-01-12)

New functions:

  • requireNamespaces: Migrated this useful base function from AcidBase package here to goalie instead, as this is often used inside of assert checks.

Minor changes:

  • hasNoDuplicates: Improve support for Rle handling. Note that S4Vectors currently doesn’t define a duplicated method for Rle, so we have to work around this at the moment.

goalie 0.6.9 (2023-04-26)

New functions:

  • quietly: Useful expression wrapper that suppresses all warnings, messages, and console output. Now used internally in requireNamespaces to suppress unwanted warnings from some Bioconductor packages, such as AnnotationHub, which now masks utils in the 3.17 release.

Minor changes:

  • validateClasses: Improved assert check for input of empty list.

goalie 0.6.10 (2023-05-31)

Minor changes:

  • compressExtPattern: Updated to ensure that maching is case insensitive.
  • Relaxed suggested package dependencies.

goalie 0.6.11 (2023-07-13)

New functions:

  • isTempFile / isATempFile / allAreTempFiles: Check functions to determine if a file exists on disk as a temporary file, defined by tempfile. Checks directory path internally against tempdir return. This function will be used in pipette update for compressed file cleanup during import calls.

Minor changes:

  • Now requiring R 4.3 / Bioconductor 3.17.

goalie 0.6.12 (2023-07-24)

New functions:

  • isTximport: New check function to perform validity checks on tximport list return, which isn’t currently classed.

Minor changes:

  • Updated lintr checks to be compatible with new release.

goalie 0.6.13 (2023-07-27)

Minor changes:

  • isURL now returns FALSE for non-encoded URLs (e.g. containing spaces, other invalid characters). This helps protect against unwanted input into httr2 engine for REST API calls. Refer to utils::URLencode for encoding checks.

goalie 0.6.14 (2023-08-10)

New functions:

  • hasCPU: Does the current machine have a sufficient number of CPU cores?
  • hasRAM: Does the current machine have sufficient memory (in GB)?

goalie 0.6.15 (2023-08-24)

New functions:

  • Added isExistingURL variants of isURL, which check if the connection is active and that the URL actually exists, rather than whether it is merely formatted correctly. Also added isAnExistingURL and allAreExistingURLs variants, similar to the simpler isURL checks. The internal logic of this check was ported from the previous hasInternet function, but speed up to use a try call with a faster timeout.

Major changes:

  • hasInternet has been reworked to simply wrap isAnExistingURL with a call to check if the Bioconductor website is up.

goalie 0.6.16 (2023-09-15)

Minor changes:

  • isAnExistingURL: Reworked internal code to use RCurl::url.exists instead of a direct connection check, as this is more reliable for returning FALSE for some offline servers, such as the Ensembl FTP server, which has stability issues.
  • Now using requireNamespaces instead of requireNamespace consistently internally in the package.

goalie 0.6.17 (2023-09-15)

Minor changes:

  • isAnExistingURL: Reworked engine back to use base R via curlGetHeaders function. Returns FALSE for status codes >= 400 for both HTTP(S) and FTP. No longer need to include RCurl as a suggested package.

goalie 0.6.18 (2023-09-19)

New functions:

  • isDuplicate: Variant of base duplicated that returns TRUE for all observed duplicated values in a vector. Differs from base duplicated, which only starts to return TRUE on the second observed value.
  • allAreIntegerish: Added an additional scalar variant of isIntegerish.

Minor changes:

  • hasDims, hasRows, hasCols: Now support n argument for checking expected dimensions. Note that for hasDims, this needs to be length 2. Integerish values (e.g. 1 instead of 1L) are supported, but direct input of integer is recommended.
  • isExistingURL: Now checks for libcurl support in R session.