Options and environment variables used by isoformic

isoformic has one package option, isoformic.frozen_mirrors, and is otherwise configured through base R options, the environment variables that locate the user cache and the settings of the packages it builds on. This page lists every setting the package reads or is affected by, what it changes and where it is used. Settings are read at call time, so they can be changed with options() / Sys.setenv() in a session, scoped with withr::with_options() / withr::with_envvar(), or placed in .Rprofile / .Renviron.

Package options

isoformic.frozen_mirrors: Character vector of base URLs tried first by fetch_frozen_data() (and every function that loads a frozen dataset, such as add_appris() or polya_sites(polya_atlas = "polyasite")) before the frozen-data GitHub release and the Zenodo record returned by frozen_mirrors(). Each URL is joined with the file name of the dataset, for example options(isoformic.frozen_mirrors = "https://zenodo.org/records/<id>/files/") pins an analysis to one Zenodo deposit, and "file:///data/isoformic-frozen/" serves the files from a local or institutional mirror. The MD5 recorded in frozen_datasets() is verified whatever the mirror. Default: unset (no extra mirror).

Base R options

timeout: Timeout in seconds of utils::download.file() and url() connections. download_reference(), download_reference_url(), download_hprc_annotation(), download_fantom_cat_tables(), fetch_frozen_data() and the builders in build_frozen_data raise it, for the duration of the download only, to at least the timeout_limit of the call (3600 seconds by default, large reference files are several gigabytes) and never lower it. Set a larger value for slow connections.
download.file.method, download.file.extra: Define what the method = "auto" default of the download functions resolves to and the extra command line flags of the "wget" and "curl" methods. Pass method explicitly to override them for one call.
rlang_interactive: Overrides interactive() for rlang::is_interactive(). In a non-interactive session the download progress is silenced (quiet = TRUE in utils::download.file()) and missing optional packages (fgsea, condathis, readxl, SummarizedExperiment) raise an error instead of an installation prompt.
cli.num_colors, cli.unicode, cli.default_handler, cli.width, cli.progress_show_after: Rendering of every message, warning and error, which the package emits through the cli package. cli.unicode = FALSE and cli.num_colors = 1 produce plain ASCII output for logs; see ?cli::cli-config.

Environment variables

R_USER_CACHE_DIR, XDG_CACHE_HOME: Root of the user cache. get_isoformic_cache() resolves tools::R_user_dir("isoformic", "cache"), which honours R_USER_CACHE_DIR first, then XDG_CACHE_HOME (~/.cache by default on Linux). On macOS the package sets XDG_CACHE_HOME to ~/.cache for the lookup when it is unset, so the cache lives in ~/.cache/R/isoformic/ instead of ~/Library/Caches/org.R-project.R/R/isoformic/ and never contains a space. The cache holds downloaded references (download_reference()), the frozen datasets (frozen/), their sources (sources/<name>/) and the Zenodo bundle (zenodo_deposit/). Point it to a shared or scratch disk on HPC systems.
LOCALAPPDATA: On Windows, the root that tools::R_user_dir() uses when R_USER_CACHE_DIR is unset.
HOME, USERPROFILE: Define the ~ that the defaults above and fs::path_home() expand to.
http_proxy, https_proxy, ftp_proxy, no_proxy: Proxy settings honoured by utils::download.file() and url() (libcurl and internal methods) and therefore by every download in the package, including the connectivity check curl::has_internet().
CURL_CA_BUNDLE, SSL_CERT_FILE: Certificate bundle used by the libcurl download method, needed behind TLS-intercepting proxies.

Settings of other packages

DuckDB: Every Parquet read and write (read_parquet(), write_parquet(), read_tabular()) and the heavy joins run in a short-lived in-memory DuckDB connection with the DuckDB defaults: all CPU cores (threads), 80% of the RAM as memory_limit and a .tmp directory under the working directory when a query spills to disk. The package does not expose these; they are DuckDB session settings and the connections are not shared with user code.
condathis.micromamba_path, CONDATHIS_MICROMAMBA_PATH, CONDA_PREFIX, XDG_DATA_HOME: Read by the condathis package, which salmon_index() and salmon_quant() use to run salmon in a micromamba environment: where the micromamba binary is found and where environments are created. See ?condathis::condathis.
BIOCONDUCTOR_*, R_LIBS*: Only relevant for installing the optional packages (fgsea, SummarizedExperiment); the package itself does not read them.

Development and test settings

These are not read by the package code but control its test suite and checks (see justfile):

TESTTHAT_CPUS: Number of parallel testthat workers used by just test.
NOT_CRAN: Set to "true" by devtools::test(); tests that need optional packages use testthat::skip_if_not_installed() rather than network access, so no test downloads data.
_R_CHECK_SYSTEM_CLOCK_: Set to "0" by just check to skip the clock check of R CMD check --as-cran.
HOME, R_USER_CACHE_DIR, XDG_CACHE_HOME, R_USER_DATA_DIR, XDG_DATA_HOME, LOCALAPPDATA, APPDATA: The test setup redirects all of them to temporary directories so that tests never touch the user cache.

Examples

# Pin the frozen datasets to one Zenodo deposit for a reproducible run
withr::with_options(
  list(isoformic.frozen_mirrors = "https://zenodo.org/records/1234567/files/"),
  frozen_mirrors()
)
#> [1] "https://zenodo.org/records/1234567/files/"                          
#> [2] "https://github.com/luciorq/isoformic/releases/download/frozen-data/"

# Where the cache is, and how to move it
get_isoformic_cache()
#> /home/runner/.cache/R/isoformic
withr::with_envvar(
  list(R_USER_CACHE_DIR = tempdir()),
  get_isoformic_cache("frozen")
)
#> /tmp/RtmpV2WK1u/R/isoformic/frozen