Package: alabaster.base 1.7.6

Aaron Lun

alabaster.base: Save Bioconductor Objects to File

Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Authors:Aaron Lun [aut, cre]

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alabaster.base/json (API)
NEWS

# Install 'alabaster.base' in R:
install.packages('alabaster.base', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/artifactdb/alabaster.base/issues

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:alabaster.base-1.7.4(bioc 3.21)alabaster.base-1.6.1(bioc 3.20)

datarepresentationdataimportzlibcpp

8.40 score 3 stars 14 packages 58 scripts 4.0k downloads 103 exports 13 dependencies

Last updated 16 days agofrom:0535541441. Checks:1 OK, 10 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 04 2025
R-4.5-win-x86_64NOTEFeb 04 2025
R-4.5-mac-x86_64NOTEFeb 04 2025
R-4.5-mac-aarch64NOTEFeb 04 2025
R-4.5-linux-x86_64NOTEFeb 04 2025
R-4.4-win-x86_64NOTEFeb 04 2025
R-4.4-mac-x86_64NOTEFeb 04 2025
R-4.4-mac-aarch64NOTEFeb 04 2025
R-4.3-win-x86_64NOTEFeb 04 2025
R-4.3-mac-x86_64NOTEFeb 04 2025
R-4.3-mac-aarch64NOTEFeb 04 2025

Exports:.addMissingStringPlaceholderAttribute.altLoadObject.altStageObject.chooseMissingStringPlaceholder.createRedirection.loadObject.loadObjectInternal.processMcols.processMetadata.quickReadCsv.quickWriteCsv.restoreMetadata.saveBaseListFormat.saveDataFrameFormat.searchForMethods.stageObject.writeMetadataabsolutizePathacquireFileacquireMetadataaddMissingPlaceholderAttributeForHdf5addObjectToDedupSessionaltLoadObjectaltLoadObjectFunctionaltReadObjectaltReadObjectFunctionaltSaveObjectaltSaveObjectFunctionaltStageObjectaltStageObjectFunctionanyMissingas.Rfc3339checkObjectInDedupSessioncheckValidDirectorychooseMissingPlaceholderForHdf5cloneDirectorycreateDedupSessioncreateRedirectioncustomloadObjectHelperformatSaveEnvironmentgetSaveEnvironmenth5_casth5_create_vectorh5_guess_vector_chunksh5_object_existsh5_read_attributeh5_read_vectorh5_write_attributeh5_write_vectoris.missingis.Rfc3339listDirectorylistLocalObjectslistObjectsloadAtomicVectorloadBaseFactorloadBaseListloadDataFrameloadDataFrameFactorloadDirectoryloadObjectloadSaveEnvironmentmissingPlaceholderNamemoveObjectprocessMcolsprocessMetadataquickLoadObjectquickReadCsvquickStageObjectquickWriteCsvreadAtomicVectorreadBaseFactorreadBaseListreadDataFramereadDataFrameFactorreadLocalObjectreadMetadatareadObjectreadObjectFilereadObjectFunctionRegistryregisterReadObjectFunctionregisterSaveEnvironmentregisterValidateObjectDerivedFromregisterValidateObjectDimensionsFunctionregisterValidateObjectFunctionregisterValidateObjectHeightFunctionregisterValidateObjectSatisfiesInterfaceremoveObjectrestoreMetadatasaveBaseListFormatsaveDataFrameFormatsaveLocalObjectsaveMetadatasaveObjectsaveObjectFileschemaLocationssearchForMethodsstageObjecttransformVectorForHdf5useSaveEnvironmentvalidateDirectoryvalidateObjectwriteMetadata

Dependencies:alabaster.schemasassortheadBiocGenericscurlgenericsjsonlitejsonvalidateRcpprhdf5rhdf5filtersRhdf5libS4VectorsV8

Saving objects to artifacts and back again

Rendered fromuserguide.Rmdusingknitr::rmarkdownon Feb 04 2025.

Last update: 2025-02-01
Started: 2022-09-19

Readme and manuals

Help Manual

Help pageTopics
Make an absolute file pathabsolutizePath
Acquire file or metadataacquireFile acquireFile,character-method acquireMetadata acquireMetadata,character-method
Alter the reading function.altLoadObject .loadObject altLoadObject altLoadObjectFunction altReadObject altReadObjectFunction
Alter the saving generic.altStageObject .stageObject altSaveObject altSaveObjectFunction altStageObject altStageObjectFunction
Find missing valuesanyMissing is.missing
Choose a missing value placeholder.addMissingStringPlaceholderAttribute .chooseMissingStringPlaceholder addMissingPlaceholderAttributeForHdf5 chooseMissingPlaceholderForHdf5 missingPlaceholderName
Clone an existing directorycloneDirectory
Deduplicate objects when savingaddObjectToDedupSession checkObjectInDedupSession createDedupSession
Create a redirection file.createRedirection createRedirection
Track the environment used for saving objectsformatSaveEnvironment getSaveEnvironment loadSaveEnvironment registerSaveEnvironment useSaveEnvironment
HDF5 utilitiesh5_cast h5_create_vector h5_guess_vector_chunks h5_object_exists h5_read_attribute h5_read_vector h5_write_attribute h5_write_vector hdf5
List objects in a directorylistDirectory listLocalObjects listObjects
Load all non-child objects in a directoryloadDirectory
Move a non-child object in the staging directorymoveObject
Convenience helpers for handling local directoriesquickLoadObject quickStageObject readLocalObject saveLocalObject
Quickly read and write a CSV file.quickReadCsv .quickWriteCsv quickReadCsv quickWriteCsv
Read an atomic vector from diskloadAtomicVector readAtomicVector
Read a factor from diskloadBaseFactor readBaseFactor
Read a base list from diskloadBaseList readBaseList
Read a DataFrame from diskloadDataFrame readDataFrame
Read a DataFrame factor from diskloadDataFrameFactor readDataFrameFactor
Read R-level metadata.restoreMetadata readMetadata restoreMetadata
Read an object from disk.loadObjectInternal customloadObjectHelper loadObject readObject readObjectFunctionRegistry registerReadObjectFunction schemaLocations
Utilities to read and save the object filereadObjectFile saveObjectFile
Remove a non-child object from the staging directoryremoveObject
Representing Internet date/timesas.character.Rfc3339 as.POSIXct.Rfc3339 as.POSIXlt.Rfc3339 as.Rfc3339 as.Rfc3339.character as.Rfc3339.default as.Rfc3339.POSIXt c.Rfc3339 is.Rfc3339 Rfc3339 saveObject,Rfc3339-method [.Rfc3339 [<-.Rfc3339 [[.Rfc3339 [[<-.Rfc3339
Save atomic vectors to disksaveAtomicVector saveObject,character-method saveObject,Date-method saveObject,double-method saveObject,integer-method saveObject,logical-method saveObject,numeric-method saveObject,numeric_version-method saveObject,POSIXct-method saveObject,POSIXlt-method stageObject,character-method stageObject,Date-method stageObject,double-method stageObject,integer-method stageObject,logical-method stageObject,numeric-method stageObject,POSIXct-method stageObject,POSIXlt-method
Save a factor to disksaveBaseFactor saveObject,factor-method stageObject,factor-method
Save a base list to disk.saveBaseListFormat saveBaseList saveBaseListFormat saveObject,List-method saveObject,list-method stageObject,List-method stageObject,list-method
Choose the format for certain objects.saveDataFrameFormat saveDataFrameFormat saveFormats
Save R-level metadata to disk.processMcols .processMetadata processMcols processMetadata saveMetadata
Save objects to disk.searchForMethods saveObject searchForMethods stageObject stageObject,ANY-method
Save a DataFrame to disksaveObject,data.frame-method saveObject,DataFrame-method stageObject,DataFrame-method
Stage a DataFrameFactor objectsaveObject,DataFrameFactor-method stageObject,DataFrameFactor-method
Transform a vector to save in a HDF5 filetransformVectorForHdf5
Validate a directory of objectscheckValidDirectory validateDirectory
Validate an object's on-disk representationregisterValidateObjectDerivedFrom registerValidateObjectDimensionsFunction registerValidateObjectFunction registerValidateObjectHeightFunction registerValidateObjectSatisfiesInterface validateObject
Saving the metadata.writeMetadata writeMetadata