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  "Title": "Save Bioconductor Objects to File",
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  "Date": "2026-01-04",
  "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\"), email=\"infinite.monkeys.with.keyboards@gmail.com\")",
  "License": "MIT + file LICENSE",
  "Description": "Save Bioconductor data structures into file artifacts, and\nload them back into memory. This is a more robust and portable\nalternative to serialization of such objects into RDS files.\nEach artifact is associated with metadata for further\ninterpretation; downstream applications can enrich this\nmetadata with context-specific properties.",
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    ".altLoadObject",
    ".altStageObject",
    ".chooseMissingStringPlaceholder",
    ".createRedirection",
    ".loadObject",
    ".loadObjectInternal",
    ".processMcols",
    ".processMetadata",
    ".quickReadCsv",
    ".quickWriteCsv",
    ".restoreMetadata",
    ".saveBaseListFormat",
    ".saveDataFrameFormat",
    ".searchForMethods",
    ".stageObject",
    ".writeMetadata",
    "absolutizePath",
    "acquireFile",
    "acquireMetadata",
    "addMissingPlaceholderAttributeForHdf5",
    "addObjectToDedupSession",
    "altLoadObject",
    "altLoadObjectFunction",
    "altReadObject",
    "altReadObjectFunction",
    "altSaveObject",
    "altSaveObjectFunction",
    "altStageObject",
    "altStageObjectFunction",
    "anyMissing",
    "as.Rfc3339",
    "checkObjectInDedupSession",
    "checkValidDirectory",
    "chooseMissingPlaceholderForHdf5",
    "cloneDirectory",
    "cloneFile",
    "createDedupSession",
    "createRedirection",
    "customloadObjectHelper",
    "formatSaveEnvironment",
    "getSaveEnvironment",
    "h5_cast",
    "h5_create_vector",
    "h5_guess_vector_chunks",
    "h5_object_exists",
    "h5_read_attribute",
    "h5_read_vector",
    "h5_read_vls_array",
    "h5_use_vls",
    "h5_write_attribute",
    "h5_write_vector",
    "h5_write_vls_array",
    "is.missing",
    "is.Rfc3339",
    "listDirectory",
    "listLocalObjects",
    "listObjects",
    "loadAtomicVector",
    "loadBaseFactor",
    "loadBaseList",
    "loadDataFrame",
    "loadDataFrameFactor",
    "loadDirectory",
    "loadObject",
    "loadSaveEnvironment",
    "missingPlaceholderName",
    "moveObject",
    "processMcols",
    "processMetadata",
    "quickLoadObject",
    "quickReadCsv",
    "quickStageObject",
    "quickWriteCsv",
    "readAtomicVector",
    "readBaseFactor",
    "readBaseList",
    "readDataFrame",
    "readDataFrameFactor",
    "readLocalObject",
    "readMetadata",
    "readObject",
    "readObjectFile",
    "readObjectFunctionRegistry",
    "registerReadObjectFunction",
    "registerSaveEnvironment",
    "registerValidateObjectDerivedFrom",
    "registerValidateObjectDimensionsFunction",
    "registerValidateObjectFunction",
    "registerValidateObjectHeightFunction",
    "registerValidateObjectSatisfiesInterface",
    "removeObject",
    "restoreMetadata",
    "saveBaseListFormat",
    "saveDataFrameFormat",
    "saveLocalObject",
    "saveMetadata",
    "saveObject",
    "saveObjectFile",
    "schemaLocations",
    "searchForMethods",
    "stageObject",
    "transformVectorForHdf5",
    "useSaveEnvironment",
    "validateDirectory",
    "validateObject",
    "writeMetadata"
  ],
  "_help": [
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      "page": "absolutizePath",
      "title": "Make an absolute file path",
      "topics": [
        "absolutizePath"
      ]
    },
    {
      "page": "acquireFile",
      "title": "Acquire file or metadata",
      "topics": [
        "acquireFile",
        "acquireFile,character-method",
        "acquireMetadata",
        "acquireMetadata,character-method"
      ]
    },
    {
      "page": "altReadObject",
      "title": "Alter the reading function",
      "topics": [
        ".altLoadObject",
        ".loadObject",
        "altLoadObject",
        "altLoadObjectFunction",
        "altReadObject",
        "altReadObjectFunction"
      ]
    },
    {
      "page": "altSaveObject",
      "title": "Alter the saving generic",
      "topics": [
        ".altStageObject",
        ".stageObject",
        "altSaveObject",
        "altSaveObjectFunction",
        "altStageObject",
        "altStageObjectFunction"
      ]
    },
    {
      "page": "anyMissing",
      "title": "Find missing values",
      "topics": [
        "anyMissing",
        "is.missing"
      ]
    },
    {
      "page": "chooseMissingPlaceholderForHdf5",
      "title": "Choose a missing value placeholder",
      "topics": [
        ".addMissingStringPlaceholderAttribute",
        ".chooseMissingStringPlaceholder",
        "addMissingPlaceholderAttributeForHdf5",
        "chooseMissingPlaceholderForHdf5",
        "missingPlaceholderName"
      ]
    },
    {
      "page": "cloneDirectory",
      "title": "Clone an existing directory",
      "topics": [
        "cloneDirectory"
      ]
    },
    {
      "page": "cloneFile",
      "title": "Clone an existing file",
      "topics": [
        "cloneFile"
      ]
    },
    {
      "page": "createDedupSession",
      "title": "Deduplicate objects when saving",
      "topics": [
        "addObjectToDedupSession",
        "checkObjectInDedupSession",
        "createDedupSession"
      ]
    },
    {
      "page": "createRedirection",
      "title": "Create a redirection file",
      "topics": [
        ".createRedirection",
        "createRedirection"
      ]
    },
    {
      "page": "getSaveEnvironment",
      "title": "Track the environment used for saving objects",
      "topics": [
        "formatSaveEnvironment",
        "getSaveEnvironment",
        "loadSaveEnvironment",
        "registerSaveEnvironment",
        "useSaveEnvironment"
      ]
    },
    {
      "page": "hdf5",
      "title": "HDF5 utilities",
      "topics": [
        "h5_cast",
        "h5_create_vector",
        "h5_guess_vector_chunks",
        "h5_object_exists",
        "h5_read_attribute",
        "h5_read_vector",
        "h5_write_attribute",
        "h5_write_vector",
        "hdf5"
      ]
    },
    {
      "page": "listObjects",
      "title": "List objects in a directory",
      "topics": [
        "listDirectory",
        "listLocalObjects",
        "listObjects"
      ]
    },
    {
      "page": "loadDirectory",
      "title": "Load all non-child objects in a directory",
      "topics": [
        "loadDirectory"
      ]
    },
    {
      "page": "moveObject",
      "title": "Move a non-child object in the staging directory",
      "topics": [
        "moveObject"
      ]
    },
    {
      "page": "quickLoadObject",
      "title": "Convenience helpers for handling local directories",
      "topics": [
        "quickLoadObject",
        "quickStageObject",
        "readLocalObject",
        "saveLocalObject"
      ]
    },
    {
      "page": "quickReadCsv",
      "title": "Quickly read and write a CSV file",
      "topics": [
        ".quickReadCsv",
        ".quickWriteCsv",
        "quickReadCsv",
        "quickWriteCsv"
      ]
    },
    {
      "page": "readAtomicVector",
      "title": "Read an atomic vector from disk",
      "topics": [
        "loadAtomicVector",
        "readAtomicVector"
      ]
    },
    {
      "page": "readBaseFactor",
      "title": "Read a factor from disk",
      "topics": [
        "loadBaseFactor",
        "readBaseFactor"
      ]
    },
    {
      "page": "readBaseList",
      "title": "Read a base list from disk",
      "topics": [
        "loadBaseList",
        "readBaseList"
      ]
    },
    {
      "page": "readDataFrame",
      "title": "Read a DataFrame from disk",
      "topics": [
        "loadDataFrame",
        "readDataFrame"
      ]
    },
    {
      "page": "readDataFrameFactor",
      "title": "Read a DataFrame factor from disk",
      "topics": [
        "loadDataFrameFactor",
        "readDataFrameFactor"
      ]
    },
    {
      "page": "readMetadata",
      "title": "Read R-level metadata",
      "topics": [
        ".restoreMetadata",
        "readMetadata",
        "restoreMetadata"
      ]
    },
    {
      "page": "readObject",
      "title": "Read an object from disk",
      "topics": [
        ".loadObjectInternal",
        "customloadObjectHelper",
        "loadObject",
        "readObject",
        "readObjectFunctionRegistry",
        "registerReadObjectFunction",
        "schemaLocations"
      ]
    },
    {
      "page": "readObjectFile",
      "title": "Utilities to read and save the object file",
      "topics": [
        "readObjectFile",
        "saveObjectFile"
      ]
    },
    {
      "page": "removeObject",
      "title": "Remove a non-child object from the staging directory",
      "topics": [
        "removeObject"
      ]
    },
    {
      "page": "Rfc3339",
      "title": "Representing Internet date/times",
      "topics": [
        "as.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"
      ]
    },
    {
      "page": "saveAtomicVector",
      "title": "Save atomic vectors to disk",
      "topics": [
        "saveAtomicVector",
        "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"
      ]
    },
    {
      "page": "saveBaseFactor",
      "title": "Save a factor to disk",
      "topics": [
        "saveBaseFactor",
        "saveObject,factor-method",
        "stageObject,factor-method"
      ]
    },
    {
      "page": "saveBaseList",
      "title": "Save a base list to disk",
      "topics": [
        ".saveBaseListFormat",
        "saveBaseList",
        "saveBaseListFormat",
        "saveObject,List-method",
        "saveObject,list-method",
        "stageObject,List-method",
        "stageObject,list-method"
      ]
    },
    {
      "page": "saveFormats",
      "title": "Choose the format for certain objects",
      "topics": [
        ".saveDataFrameFormat",
        "saveDataFrameFormat",
        "saveFormats"
      ]
    },
    {
      "page": "saveMetadata",
      "title": "Save R-level metadata to disk",
      "topics": [
        ".processMcols",
        ".processMetadata",
        "processMcols",
        "processMetadata",
        "saveMetadata"
      ]
    },
    {
      "page": "saveObject",
      "title": "Save objects to disk",
      "topics": [
        ".searchForMethods",
        "saveObject",
        "searchForMethods",
        "stageObject",
        "stageObject,ANY-method"
      ]
    },
    {
      "page": "stageDataFrame",
      "title": "Save a DataFrame to disk",
      "topics": [
        "saveObject,data.frame-method",
        "saveObject,DataFrame-method",
        "stageObject,DataFrame-method"
      ]
    },
    {
      "page": "saveDataFrameFactor",
      "title": "Stage a DataFrameFactor object",
      "topics": [
        "saveObject,DataFrameFactor-method",
        "stageObject,DataFrameFactor-method"
      ]
    },
    {
      "page": "transformVectorForHdf5",
      "title": "Transform a vector to save in a HDF5 file",
      "topics": [
        "transformVectorForHdf5"
      ]
    },
    {
      "page": "validateDirectory",
      "title": "Validate a directory of objects",
      "topics": [
        "checkValidDirectory",
        "validateDirectory"
      ]
    },
    {
      "page": "validateObject",
      "title": "Validate an object's on-disk representation",
      "topics": [
        "registerValidateObjectDerivedFrom",
        "registerValidateObjectDimensionsFunction",
        "registerValidateObjectFunction",
        "registerValidateObjectHeightFunction",
        "registerValidateObjectSatisfiesInterface",
        "validateObject"
      ]
    },
    {
      "page": "vls",
      "title": "VLS saving utilities",
      "topics": [
        "h5_read_vls_array",
        "h5_use_vls",
        "h5_write_vls_array",
        "vls"
      ]
    },
    {
      "page": "writeMetadata",
      "title": "Saving the metadata",
      "topics": [
        ".writeMetadata",
        "writeMetadata"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/alabaster.base/raw/RELEASE_3_23/README.md",
  "_rundeps": [
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    "assorthead",
    "BiocGenerics",
    "biocmake",
    "curl",
    "dir.expiry",
    "filelock",
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    "jsonvalidate",
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