updateBiocPackageRepoObjects: Update the serialized objects contained in a Bioconductor...

In Bioconductor/updateObject: Find/fix old serialized S4 instances

Update the serialized objects contained in a Bioconductor package Git repository or in a set of Bioconductor package Git repositories

Description

updateBiocPackageRepoObjects() and updateAllBiocPackageRepoObjects() are wrappers to updatePackageObjects() and updateAllPackageObjects() that take care of committing and pushing the changes made to the package(s).

Usage

updateBiocPackageRepoObjects(repopath=".", branch=NULL, filter=NULL,
        commit_msg=NULL, push=FALSE, remove.clone.on.success=FALSE,
        git=NULL, use.https=FALSE, user_name=NULL, user_email=NULL)

updateAllBiocPackageRepoObjects(all_repopaths=".", skipped_repos=NULL, ...)

Arguments

repopath	The path (as a single string) to the local Git repository of a Bioconductor package. See ?prepare_git_repo_for_work for more information.
branch	The branch (as a single string) of the Git repository to work on. See ?prepare_git_repo_for_work for more information.
filter	See ?updatePackageObjects.
commit_msg	The Git commit message. By default "Pass serialized S4 instances thru updateObject()" is used.
push	Whether to push the changes or not. Changes are committed but not pushed by default. You need push access to the package Git repository at git.bioconductor.org in order to use push=TRUE.
remove.clone.on.success	Whether to remove the Git clone on success or not. Only applies if repopath does not exist and needs to be cloned.
git, use.https	See ?prepare_git_repo_for_work.
user_name, user_email	See ?git_commit.
all_repopaths	Character vector of paths to local Git repositories of Bioconductor packages.
skipped_repos	Character vector of repository paths to ignore.
...	updateAllBiocPackageRepoObjects() walks over the all_repopaths vector and calls updateBiocPackageRepoObjects() on each repository path. All the arguments in ... are passed down to updateBiocPackageRepoObjects().

Value

updateBiocPackageRepoObjects() and updateAllBiocPackageRepoObjects() are wrappers to updatePackageObjects() and updateAllPackageObjects(), respectively, and return the same value.

See Also

• updatePackageObjects and updateAllPackageObjects.

• Utility functions prepare_git_repo_for_work and git_commit which are used internally by updateBiocPackageRepoObjects to perform the Git operations.

Examples

## ---------------------------------------------------------------------
## updateBiocPackageRepoObjects()
## ---------------------------------------------------------------------

## Typical use, assuming MyPackage is a Bioconductor package that you
## maintain:
## Not run: 
  repopath <- file.path(tempdir(), "MyPackage")
  updateBiocPackageRepoObjects(repopath, push=TRUE)

## End(Not run)

## Note that by default `updateBiocPackageRepoObjects()` does NOT try
## to push the changes to git.bioconductor.org. Only the authorized
## maintainers of MyPackage can do that. In the examples below we
## must use HTTPS access to clone the package because we are not
## maintainers of the CellBench or BiocGenerics packages. Also we
## don't use 'push=TRUE' because we are not allowed to do that (it
## wouldn't work anyways).

## On a package with a mix of RDS and RDA files:
repopath <- file.path(tempdir(), "CellBench")
updateBiocPackageRepoObjects(repopath, branch="RELEASE_3_13",
                             remove.clone.on.success=TRUE,
                             use.https=TRUE)

## On a package with no serialized objects:
repopath <- file.path(tempdir(), "BiocGenerics")
updateBiocPackageRepoObjects(repopath, branch="RELEASE_3_13",
                             remove.clone.on.success=TRUE,
                             use.https=TRUE)

## Note that the RELEASE_3_13 branch of all Bioconductor packages got
## frozen in October 2021. The above examples are for illustrative
## purpose only. A more realistic situation would be to use
## updateBiocPackageRepoObjects() on the development version (i.e.
## the master branch) of a package that you maintain, and to push the
## changes by calling the function with 'push=TRUE'.

## ---------------------------------------------------------------------
## updateAllBiocPackageRepoObjects()
## ---------------------------------------------------------------------

## Let's assume that the current directory is populated with the
## Git repositories of all Bioconductor software packages and that
## we have push access to them:

ALL_REPOS <- dir()  # get list of package repos to update

READ_RDS_FAILURE <- c(
    "BindingSiteFinder",
    "ChIPpeakAnno",
    "drugTargetInteractions"
)

LOAD_FAILURE <- c(
    "AlphaBeta",
    "CellaRepertorium",
    "CNVRanger",
    "gscreend",
    "HiLDA",
    "immunotation",
    "MAST",
    "midasHLA",
    "mixOmics",
    "oligoClasses",
    "TitanCNA",
    "Uniquorn"
)

UPDATEOBJECT_FAILURE <- c(
    "ACE",
    "AnnotationHubData",
    "arrayMvout",
    "Autotuner",
    "BASiCS",
    "bigmelon",
    "Biobase",
    "CAMERA",
    "categoryCompare",
    "cellHTS2",
    "cellmigRation",
    "CEMiTool",
    "CeTF",
    "cleanUpdTSeq",
    "CoGAPS",
    "CoreGx",
    "CrispRVariants",
    "crlmm",
    "decompTumor2Sig",
    "DIAlignR",
    "enhancerHomologSearch",
    "fcoex",
    "geNetClassifier",
    "GreyListChIP",
    "GSgalgoR",
    "hmdbQuery",
    "iCOBRA",
    "MassArray",
    "midasHLA",
    "MinimumDistance",
    "MSnbase",
    "msPurity",
    "multiHiCcompare",
    "musicatk",
    "MutationalPatterns",
    "openPrimeR",
    "OSAT",
    "PharmacoGx",
    "pipeFrame",
    "ProteoDisco",
    "puma",
    "qcmetrics",
    "QDNAseq",
    "r3Cseq",
    "RadioGx",
    "RTN",
    "sangeranalyseR",
    "synapter",
    "tigre",
    "topGO",
    "ToxicoGx",
    "VariantFiltering",
    "wateRmelon",
    "xcms"
)

## Contain files to push larger than 5 Mb.
PUSH_FAILURE <- c(
    "BiocSklearn",
    "BubbleTree",
    "CINdex",
    "erma",
    "ivygapSE",
    "SplicingGraphs",
    "vtpnet"
)

## Skipped for other reasons e.g. contain objects for which
## updateObject() takes forever or the package needs to be
## installed but cannot at the moment.
OTHER_SKIPPED_REPOS <- c(
    "BaalChIP", "BiGGR", "CytoTree", "gwascat",
    "mirIntegrator", "oposSOM", "PFP", "ROntoTools", "SLGI"
)

SKIPPED_REPOS <- c(
    READ_RDS_FAILURE,
    LOAD_FAILURE,
    UPDATEOBJECT_FAILURE,
    PUSH_FAILURE,
    OTHER_SKIPPED_REPOS
)

FILTER <- "\bDataFrame\b"

## Not run: 
system.time(
    codes <- updateAllBiocPackageRepoObjects(ALL_REPOS,
                                             skipped_repos=SKIPPED_REPOS,
                                             branch="master",
                                             filter=FILTER,
                                             push=TRUE)
)

## End(Not run)

Bioconductor/updateObject documentation built on May 1, 2024, 9:29 p.m.