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Changelog

Source: NEWS.md

extractox 1.2.0

CRAN release: 2025-07-15

Major Changes & Enhancements

  • Automated Server Compatibility: Functions connecting to EPA servers (e.g., extr_comptox, extr_iris, extr_pprtv) now automatically handle connection issues that can occur on systems with modern libcurl and OpenSSL. The functions detect problematic configurations and use the condathis package to perform requests with a compatible version of curl in an isolated environment. This ensures reliability without requiring manual user intervention.

Minor Enhancements

  • extr_chem_info now accepts the argument domain to specify the PubChem domain (substance or compound).
  • extr_tox now accepts a delay parameter to control the delay between requests, helping to avoid rate-limiting errors.
  • Request Throttling**: Added a delay parameter to PubChem functions to allow for a pause between requests, helping to avoid rate-limiting errors.
  • Verbose Option: A verbose option has been added to several functions for more detailed output during execution.

Bug Fixes

  • Testing: Corrected various tests, including a fix for an incorrect row count expectation in the PubChem test.

  • Fixed extr_chem_info duplicated name in outout columns (#47).

  • Function Cleanup: Refined the extr_comptox function, removing unnecessary requirements and cleaning up the code.

extractox 1.0.0

CRAN release: 2025-01-07

Bug Fixes

  • Fixed extr_iris extracting the correct number of chemicals without repetition (#15).
  • Fixed extr_comtox working when a single download_items different from DTXCID is selected (#17).
  • Fixed extr_casrn_from_cid failure when no results are found.

New Features

  • Added extr_ice_assay_names to retrieve ICE assay names (#16).
  • Added extr_monograph to check if a substance is listed in WHO IARC monograph and return its details (#19).
  • Added extr_pprtv to extract information from the EPA Provisional Peer-Reviewed Toxicity Values database (#20). Introduced save_to_cache and load_from_cache functions to avoid re-downloading the file each time. See force argument.

Other Breaking Changes

  • Removed cancer_types argument from extr_iris. Database returns a dataframe with different columns based on request arguments.
  • Removed stop_at_warning argument from extr_casrn_from_cid. Now warns and returns a dataframe with NA if no IDs are found.
  • extr_tox now returns a longer list of dataframes, including the outputs of extr_monograph and extr_pprtv.

Enhancements and Fixes

  • Added verbose argument to all extr_ functions (#18).
  • Unified behavior across all extr_ functions when chemicals are not found (#30-#35):
    • For all functions except extr_comptox, a query column reports the IDs searched. In extr_comptox, this info is in the main_sheet element. For extr_ice, query values contain all IDs found.
    • Results now contain rows with NA values for all columns (except query).
    • extr_pprtv and extr_monograph use save_and_match to output results with NA for missing IDs.
  • Improved and extended all unit tests.
  • extr_comptox now outputs a list of dataframes with clean names.
  • Fixed extr_ctd column names: pub_med_ids or pub_med_i_ds are now pubmed_ids.
  • Introduced extr_pubchem_section_ internal function to fetch FEMA and GHS info, avoiding repeated code.
  • Introduced check_na_warn internal function to generate warnings for missing IDs.
  • Created with_extr_sandbox to handle cache for CRAN examples.

extractox 0.1.0

CRAN release: 2024-12-03

  • Initial CRAN submission.