Package: biodb
Title: Biodb, a Library and a Development Framework for Connecting to
        Chemical and Biological Databases
Version: 1.21.0
Authors@R: c(person("Pierrick", "Roger", email="pierrick.roger@cea.fr", role=c("aut", "cre"), comment=c(ORCID="0000-0001-8177-4873")),
             person("Alexis", "Delabrière", email="delabriere@imsb.biol.ethz.ch", role="ctb", comment=c(ORCID="0000-0003-3308-4549")))
Description: The biodb package provides access to standard remote
        chemical and biological databases (ChEBI, KEGG, HMDB, ...), as
        well as to in-house local database files (CSV, SQLite), with
        easy retrieval of entries, access to web services, search of
        compounds by mass and/or name, and mass spectra matching for
        LCMS and MSMS. Its architecture as a development framework
        facilitates the development of new database connectors for
        local projects or inside separate published packages.
URL: https://gitlab.com/rbiodb/biodb
BugReports: https://gitlab.com/rbiodb/biodb/-/issues
biocViews: Software, Infrastructure, DataImport, KEGG
Depends: R (>= 4.1.0)
License: AGPL-3
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
        rmarkdown, xml2
Imports: R6, RSQLite, Rcpp, XML, chk, fscache (>= 1.0.2), jsonlite,
        lgr, lifecycle, methods, openssl, plyr, progress, rappdirs,
        sched (>= 1.0.1), sqlq, stats, stringr, tools, withr, yaml
LinkingTo: Rcpp, testthat
NeedsCompilation: yes
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Collate: 'BiodbConfig.R' 'BiodbConnBase.R' 'BiodbConn.R' 'BiodbEntry.R'
        'BiodbCsvEntry.R' 'BiodbDbInfo.R' 'BiodbDbsInfo.R'
        'BiodbEntryField.R' 'BiodbMain.R' 'BiodbEntryFields.R'
        'BiodbFactory.R' 'BiodbXmlEntry.R' 'BiodbHtmlEntry.R'
        'BiodbJsonEntry.R' 'BiodbListEntry.R' 'BiodbTxtEntry.R'
        'BiodbSdfEntry.R' 'BiodbTestMsgAck.R' 'CsvFileConn.R'
        'CompCsvFileConn.R' 'CompCsvFileEntry.R' 'SqliteConn.R'
        'CompSqliteConn.R' 'CompSqliteEntry.R' 'FileTemplate.R'
        'MassCsvFileConn.R' 'MassCsvFileEntry.R' 'MassSqliteConn.R'
        'MassSqliteEntry.R' 'Progress.R' 'Range.R' 'RcppExports.R'
        'TestRefEntries.R' 'catch-routine-registration.R'
        'fcts_biodb.R' 'fcts_deprecated.R' 'fcts_mass.R' 'fcts_misc.R'
        'generic_tests.R' 'package.R' 'spec-dist.R' 'test_framework.R'
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libxml2-dev
        libssl-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:56:00 UTC
RemoteUrl: https://github.com/bioc/biodb
RemoteRef: HEAD
RemoteSha: cd5fba650d92e2d024e29600cd079b47da6b535e
Packaged: 2026-06-23 19:21:40 UTC; root
Author: Pierrick Roger [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8177-4873>),
  Alexis Delabrière [ctb] (ORCID:
    <https://orcid.org/0000-0003-3308-4549>)
Maintainer: Pierrick Roger <pierrick.roger@cea.fr>