BiodbBiocPersistentCache
                        A persistent cache implementation that uses
                        BiocCache package.
BiodbConfig             A class for storing configuration values.
BiodbConn               The mother abstract class of all database
                        connectors.
BiodbConnBase           Base class of 'BiodbConn' for encapsulating all
                        needed information for database access.
BiodbCsvEntry           Entry class for content in CSV format.
BiodbCustomPersistentCache
                        A biodb custom persistent cache implementation.
BiodbDbInfo             A class for describing the characteristics of a
                        database.
BiodbDbsInfo            A class for describing the available databases.
BiodbEntry              The mother abstract class of all database entry
                        classes.
BiodbEntryField         A class for describing an entry field.
BiodbEntryFields        A class for handling description of all entry
                        fields.
BiodbFactory            A class for constructing biodb objects.
BiodbHtmlEntry          Entry class for content in HTML format.
BiodbJsonEntry          Entry class for content in JSON format.
BiodbListEntry          Entry class for content in list format.
BiodbMain               The central class of the biodb package.
BiodbPersistentCache    The abstract class for handling file caching.
BiodbRequest            Class Request.
BiodbRequestScheduler   Class for handling requests.
BiodbRequestSchedulerRule
                        Scheduler rule class.
BiodbSdfEntry           Entry class for content in SDF format.
BiodbSqlBinaryOp        This class represents an SQL binary operator.
BiodbSqlExpr            The SQL Expression abstact class.
BiodbSqlField           This class represents an SQL field.
BiodbSqlList            This class represents an SQL list.
BiodbSqlLogicalOp       This class represents an SQL logical operator.
BiodbSqlQuery           This class handles an SQL Query.
BiodbSqlValue           This class represents an SQL value.
BiodbTestMsgAck         A class for acknowledging messages during
                        tests.
BiodbTxtEntry           Entry class for content in text format.
BiodbUrl                Class URL.
BiodbXmlEntry           Entry class for content in XML format.
CompCsvFileConn         Compound CSV File connector class.
CompCsvFileEntry        Compound CSV File entry class.
CompSqliteConn          Class for handling a Compound database in
                        SQLite format.
CompSqliteEntry         Compound SQLite entry class.
CsvFileConn             CSV File connector class.
ExtConnClass            Extension connector clas
ExtCpp                  Extension C++ code class
ExtDefinitions          Extension defintions file class
ExtDescriptionFile      Extension DESCRIPTION file
ExtEntryClass           Extension entry class
ExtFileGenerator        Extension file generator abstract class
ExtGenerator            Extension generator abstract class
ExtGitignore            Extension Gitignore file class
ExtLicense              Extension license
ExtMakefile             Extension Makefile
ExtPackage              Extension package class
ExtPackageFile          Extension package file class.
ExtRbuildignore         Extension Rbuildignore file class
ExtReadme               Extension README file class
ExtTests                Extension tests class
ExtTravisFile           Extension Travis YAML file generator class
ExtVignette             Extension vignette class
FileTemplate            File template class.
MassCsvFileConn         Mass CSV File connector class.
MassCsvFileEntry        Mass CSV File entry class.
MassSqliteConn          Class for handling a Mass spectrometry database
                        in SQLite format.
MassSqliteEntry         Mass spectra SQLite entry class.
Progress                Progress class.
Range                   Range class.
RequestResult           Class RequestResult.
SqliteConn              SQLite connector class.
TestRefEntries          A class for accessing the test reference
                        entries.
abstractClass           Declares a class as abstract.
abstractMethod          Declares a method as abstract
biodb-package           biodb: biodb, a library and a development
                        framework for connecting to chemical and
                        biological databases
checkDeprecatedCacheFolders
                        Check deprecated default cache folders.
closeMatchPpm           Close match PPM
connNameToClassPrefix   Convert connector name into class prefix.
createBiodbTestInstance
                        Creating a BiodbMain instance for tests.
df2str                  Convert a data.frame into a string.
doesRCurlRequestUrlExist
                        Test if a URL is valid according to RCurl
error                   Throw an error and log it too.
error0                  Throw an error and log it too.
genNewExtPkg            Generate a new extension package for biodb.
getBaseUrlContent       Get URL content using base::url().
getBaseUrlRequestResult
                        Get URL request result using base::url().
getConnClassName        Get connector class name.
getConnTypes            Get connector types.
getDefaultCacheDir      Get default cache folder.
getEntryClassName       Get entry class name.
getEntryTypes           Get entry types.
getLicenses             Get the available licenses for extension
                        packages.
getLogger               Get the main package logger.
getPkgName              Get the package name from a package folder
                        path.
getRCurlContent         Get URL content using RCurl::getURL().
getRCurlRequestResult   Get URL request result using RCurcl::getURL().
getReposName            Extract the repository name from a package
                        folder.
getTestOutputDir        Get the test output directory.
getUrlContent           Get a URL content.
getUrlRequestResult     Send a request and get results.
listTestRefEntries      List test reference entries.
loadFileContents        Loads the contents of files in memory.
logDebug                Log debug message.
logDebug0               Log debug message.
logInfo                 Log information message.
logInfo0                Log information message.
logTrace                Log trace message.
logTrace0               Log trace message.
lst2str                 Convert a list into a string.
makeRCurlOptions        Build an RCurl::CURLOptions object.
newInst                 Create a new BiodbMain instance.
prepareFileContents     Prepares file contents for saving.
runGenericTests         Run generic tests.
saveContentsToFiles     Saves contents to files.
testContext             Set a test context.
testThat                Run a test.
upgradeExtPkg           Upgrading an existing extension package for
                        biodb.
warn                    Throw a warning and log it too.
warn0                   Throw a warning and log it too.
