bioconductor v3.9.0 BiocViews

pd <- new("PackageDetail",
Package="MyFancyPackage",
Version="1.2.3",
Title="A Fancy Package",
Description="This package does fancy things",
Author="A. Coder",
Maintainer="A. Coder <acoder@foo.bar.net>",
Depends="methods",
Imports="ASimplePackage",
Suggests="MyDataPackage",
biocViews="Infrastructure",
vignettes="vignettes/MyFancyPackage/inst/doc/MFP1.pdf,
vignettes/MyFancyPackage/inst/doc/MFP2.pdf",
vignetteScripts="vignettes/MyFancyPackage/inst/doc/MFP1.R
vignettes/MyFancyPackage/inst/doc/MFP2.R",
vignetteTitles="MFP1 Document,
MFP2 Document",
source.ver="src/contrib/MyFancyPackage_1.2.3.tar.gz",
win.binary.ver="bin/windows/contrib/3.4/MyFancyPackage_1.2.2.zip",
`mac.binary.el-capitan.ver`="bin/macosx/el-capitan/contrib/3.4/MyFancyPackage_1.2.3.tgz",
dependsOnMe=c("PackageThatExposesMe"),
importsMe=c("AnEvenFancierPackage","AMuchFancierPackage"),
suggestsMe="PackageThatUsesMeInVignette",
reposRoot="http://foo.bar.org")

html <- htmlValue(pd)
pd

RepositoryDetail_class()

Class "RepositoryDetail"

Description

Representation of R package repository index

Author

Seth Falcon

biocViewsVocab()

Bioconductor Task Views Vocabulary Data

Description

A graphNEL-class instance representing the Bioconductor Task Views as a directed graph.

Format

The format is: graphNEL instance

Usage

data(biocViewsVocab)

Details

The source for the vocabulary data is in the dot directory of the package in file biocViewsVocab.dot. This is transformed to GXL using the dot2gxl command line utility from the graphviz package. Then the fromGXL function from the graph package is used to convert to graphNEL-class .

Examples

data(biocViewsVocab)
biocViewsVocab
## If you have Rgraphviz available, you can
## plot the vocabulary with plot(biocViewsVocab)

biocViews_package()

Categorized views of R package repositories

Description

Structures for vocabularies and narratives of views. This can be used to create HTML views of the package structure in a Bioconductor repository.

Details

list(list("ll"), list(" ", "Package: ", list(), " biocViews", list(), " ", "Version: ", list(), " 1.11.4", list(), " ", "Depends: ", list(), " R (>= 2.4.0), methods, utils", list(), " ", "Imports: ", list(), " tools, Biobase, graph (>= 1.9.26), RBGL (>= 1.13.5), XML", list(), " ", "Suggests: ", list(), " Biobase", list(), " ", "License: ", list(), " Artistic-2.0", list(), " ", "URL: ", list(), " http://www.bioconductor.org/packages/release/BiocViews.html", list(), " ", "biocViews: ", list(),

" Infrastructure", list(), "

"))

Index: list(" ", "BiocView-class Class "BiocView" ", "Htmlized-class Class "Htmlized" ", "PackageDetail-class Class "PackageDetail" ", "RepositoryDetail-class ", " Class "RepositoryDetail" ", "biocViewsVocab Bioconductor Task Views Vocabulary Data ", "extractVignettes Extract pdf vignettes from local package ", " repository ", "genReposControlFiles Generate CRAN-style repository control files ", "getBiocSubViews Build a list of BiocView objects from a package ",

"                        repository

", "getBiocViews Build a list of BiocView objects from a package ", " repository ", "getPacksAndViews Parse VIEWS file for views and packages ", "getSubTerms Retrieve a term and its children from a vocab ", " DAG ", "htmlDoc Create a complete HTML document representation ", " of an object ", "htmlFilename Return a filename for an object's HTML ",

"                        representation

", "htmlValue HTML Representation of an Object ", "writeBiocViews Write a list of BiocView objects to HTML ", "writeHtmlDoc Write an XML DOM containing HTML to a file ", "writePackageDetailHtml ", " Write HTML files for packages in a CRAN-style ", " repository ", "writeRepositoryHtml Write package descriptions and a repository ", " index as HTML ",

"writeTopLevelView       Write the view for the root of a vocabulary to

", " disk ", "write_REPOSITORY Write a REPOSITORY control file for a ", " CRAN-style package repository ", "write_SYMBOLS Write a SYMBOLS file ", "write_VIEWS Write a VIEWS control file for a CRAN-style ", " package repository ")

The terms of the vocabulary are stored in a DAG, which can be loaded as the serialized data object biocViewsVocab . For listing of available terms use function getSubTerms .

Further information is available in the following two vignettes: list(list("ll"), list(" ", list("HOWTO-BCV"), " ", list(), " Basic package usage", list(), " ", list("createReposHtml"), " ", list(), " Further information for repository admins", list(), " "))

Author

VJ Carey stvjc@channing.harvard.edu, BJ Harshfield rebjh@channing.harvard.edu, S Falcon sfalcon@fhcrc.org

Maintainer: Biocore Team c/o BioC user list bioconductor@stat.math.ethz.ch

Examples

data(biocViewsVocab)
getSubTerms(biocViewsVocab, "Technology")

extractManuals()

Extract Rd man pages and build pdf reference manuals from local package repository

Description

This function extracts Rd man pages and builds pdf reference manuals from the man subdirectory of R source packages archives ( .tar.gz ) found in a local package repository.

All Rd files found in man will be extracted and used during the pdf construction process. Only source package archives will be processed. The constructed pdf files will be extracted under destDir and will be found in PKGNAME/man/*.pdf .

Prior to extraction, all Rd and pdf files in destDir/PKGNAME/man will be removed.

Usage

extractManuals(reposRoot, srcContrib, destDir)

Arguments

Argument	Description
`reposRoot`	character vector giving the path to the root of the local CRAN-style package repository
`srcContrib`	character vector giving the relative path from the `reposRoot` to the source packages. In a standard CRAN-style repository, this will be `src/contrib` .
`destDir`	character vector specifying the directory in which the extracted files will be written. If missing, files will be written to `<reposRoot>/manuals` .

Author

Patrick Aboyoun

extractNEWS()

Extract NEWS files from source package tarballs

Description

Extracts NEWS files from source tarballs of packages.

Usage

extractNEWS(reposRoot, srcContrib, destDir)

Arguments

Argument	Description
`reposRoot`	Top level path for CRAN-style repos
`srcContrib`	Location of source packages
`destDir`	where to extract

extractTopLevelFiles()

Extract files from the top level of source package tarballs

Description

Extracts files from source tarballs of packages.

Usage

extractTopLevelFiles(reposRoot, srcContrib, destDir, fileName)

Arguments

Argument	Description
`reposRoot`	Top level path for CRAN-style repos
`srcContrib`	Location of source packages
`destDir`	where to extract
`fileName`	name of file to extract

extractVignettes()

Extract pdf vignettes from local package repository

Description

These functions extract pdf or HTML files from the inst/doc subdirectory of R source packages archives ( .tar.gz ) found in a local package repository.

All pdf files found in inst/doc will be extracted. With extractHTMLDocuments , all HTML files except index.html will be extracted. Only source package archives will be processed. The extracted pdf or HTML files will be extracted under destDir and will be found in PKGNAME/inst/doc/ .

Prior to extraction, all pdf files in destDir/PKGNAME/inst/doc will be removed.

Usage

extractVignettes(reposRoot, srcContrib, destDir)
extractHTMLDocuments(reposRoot, srcContrib, destDir)

Arguments

Argument	Description
`reposRoot`	character vector giving the path to the root of the local CRAN-style package repository
`srcContrib`	character vector giving the relative path from the `reposRoot` to the source packages. In a standard CRAN-style repository, this will be `src/contrib` .
`destDir`	character vector specifying the directory in which the extracted files will be written. If missing, files will be written to `<reposRoot>/vignettes` .

Author

Seth Falcon

genReposControlFiles()

Generate CRAN-style repository control files

Description

This function generates control files for CRAN-style repositories. For each path specified in contribPaths a PACKAGES file is written. In addition, two top-level control files are created:

REPOSITORY contains information about the specified contrib paths.

VIEWS contains metadata for all packages in the repository including the paths to any extracted vignettes, if found. This file is useful for generating HTML views of the repository.

Usage

genReposControlFiles(reposRoot, contribPaths, manifestFile = NA,
  meatPath = NA)

Arguments

Argument	Description
`reposRoot`	character vector containing the path to the CRAN-style repository root directory.
`contribPaths`	A named character vector. Valid names are `source` , `win.binary` , `mac.binary` , `mac.binary.mavericks` , and `mac.binary.el-capitan` . Values indicate the paths to the package archives relative to the `reposRoot` .
`manifestFile`	character(1). File path location to Bioconductor formatted manifest file that lists all current packages. This file will be used in the write_VIEWS function to cross check successfully built packages with all expected packages. Packages that have not built will be given dummy entry for complete listing in bioc_VIEWS. If NA cross check is skipped and packages not built on any system will be missing from biocVIEWS
`meanPath`	character(1). File path location to the directory containing cloned repositories of Bioconductor packages. If manifestFile is used for cross checking and the meatPath is provided, entries from the DESCRIPTION file are manually entered into biocVIEWS information. If NA dummy values for minimal fields for landing page generation are included with ERROR. This attempts to fill in as much information as possible for packages that have failed to build.

Author

Seth Falcon

getBiocSubViews()

Build a list of BiocView objects from a package repository

Description

This function returns a list of BiocView-class objects corresponding to the subgraph of the views DAG induced by topTerm . In short, this does the same thing as getBiocViews , but limits the vocabulary to topTerm and all of its decendents.

Usage

getBiocSubViews(reposUrl, vocab, topTerm, local = FALSE, htmlDir = "")

Arguments

Argument	Description
`reposUrl`	URL for a CRAN-style repository that hosts a `VIEWS` file at the top-level.
`vocab`	A `graph-class` object representing the ontologyof views. This graph should be a directed acyclic graph (DAG).
`topTerm`	A string giving the name of the subview DAG. This view and all of its decendents will be included in the result.
`local`	logical indicating whether to assume a local package repository. The default is `FALSE` in which case absolute links to package detail pages are created.
`htmlDir`	if the `local` argument is `TRUE` , this will be used as the relative path for package HTML files.

Details

The root of the vocabulary DAG is implicitly included in the view creation process order to build views with a link back to the top. It is removed from the return list.

This function is tailored to generation of Bioconductor Task Views. With the current vocabulary, it probably only makes sense to call it with topView set to one of "Software" , "AnnotationData" , or "ExperimentData" . This is a hack to allow the biocViews code to manage HTML views across more than one repository.

Value

A list of BiocView-class objects. The names of the list give the name of the corresponding view.

Author

Seth Falcon

Examples

data(biocViewsVocab)
reposPath <- system.file("doc", package="biocViews")
reposUrl <- paste("file://", reposPath, sep="")
biocViews <- getBiocSubViews(reposUrl, biocViewsVocab, "Software")
print(biocViews[1:2])

getBiocViews()

Build a list of BiocView objects from a package repository

Description

Given the URL to a CRAN-style package repository containing a VIEWS file at the top-level and a graph-class object representing a DAG of views, this function returns a list of BiocView-class objects.

Usage

getBiocViews(reposUrl, vocab, defaultView, local = FALSE, htmlDir = "")

Arguments

Argument	Description
`reposUrl`	URL for a CRAN-style repository that hosts a `VIEWS` file at the top-level.
`vocab`	A `graph-class` object representing the ontology of views. This graph should be a directed acyclic graph (DAG).
`defaultView`	A string giving the term to use for packages that do not list a term of their own via the `biocViews` field in the DESCRIPTION file.
`local`	logical indicating whether to assume a local package repository. The default is `FALSE` in which case absolute links to package detail pages are created.
`htmlDir`	if the `local` argument is `TRUE` , this will be used as the relative path for package HTML files.

Value

A list of BiocView-class objects. The names of the list give the name of the corresponding view.

Author

Seth Falcon

Examples

data(biocViewsVocab)
reposPath <- system.file("doc", package="biocViews")
reposUrl <- paste("file://", reposPath, sep="")
biocViews <- getBiocViews(reposUrl, biocViewsVocab, "NoViewProvided")
print(biocViews[1:2])

getCurrentbiocViews()

Get a list of biocViews for each branch

Description

This function looks returns a list containing all the biocViews that are present on the Bioconductor website.

Usage

getCurrentbiocViews()

Details

It parses the dot file present inside the biocViews package.

Value

It returns a named list with 3 components.

Author

Sonali Arora

Examples

ans <- getCurrentbiocViews()
## only the first 6 from each branch are shown here.
lapply(ans, head)

getPackageNEWS()

Retrieve and print package NEWS

Description

These functions visit two Bioconductor releases, identifying packages that are present in the current repository and have NEWS since the base version of the same package in the previous release. All NEWS is reported for packages only in the current repository.

Usage

getPackageNEWS(prevRepos="3.6", 
               currRepos="3.7", 
               repo=c("bioc", "data/experiment", "workflows"))
printNEWS(dbs, destfile, overwrite = FALSE, width = 68,
          output=c("md", "text"), ...)

Arguments

Argument	Description
`prevRepos`	`character(1)` Bioconductor version from which NEWS starts.
`currRepos`	`character(1)` Bioconductor version for current packages.
`repo`	`character(1)` Which repository to get NEWS for. bioc is software packages, data/experiment is for data experiment packages and workflows for workflow packages
`dbs`	A list of `news_db` elements, as returned by `getPackageNEWS` .
`destfile`	`character(1)` file path to the location where NEWS will be printed.
`overwrite`	`logical(1)` indicating whether `destfile` can be over-written, if it exists.
`width`	`numeric(1)` number of characters news items are to be wrapped to, excluding indent.
`output`	`character(1)` output to text or markdown format.
`...`	additional arguments, unused.

Value

A list of news_db files, as returned by utils::news , for each package for which relevant NEWS is available.

Author

Martin Morgan mtmorgan@fhcrc.org and Lori Shepherd

getPackageTitles()

Retrieve list of package titles and print package Description

Description

These functions visit two Bioconductor releases branches, identifying differnt packages that are present in the current repository from the previous release. Utilizes the devel branch of bioconductor to retrieve description.

Usage

getPackageTitles(prevBranch="RELEASE_3_6",
                 currBranch="master",
                 manifest=c("software.txt", "data-experiment.txt", "workflows.txt"),
                 status = c("new", "removed"))
getPackageDescriptions(pkgs, outfile, output=c("md", "text"))

Arguments

Argument	Description
`prevBranch`	`character(1)` Bioconductor branch to compare to
`currBranch`	`character(1)` Bioconductor branch for current packages.
`manifest`	`character(1)` Which repository of pakcages to compare. software.txt is software packages, data-experiment.txt is for data experiment packages and workflows.txt for workflow packages
`status`	get new or removed package list comparing currBranch to prevBranch
`pkgs`	character() A list of packages to retrieve DESCRIPTION
`outfile`	`character(1)` file path to the location where DESCRIPTIONS will be printed.
`output`	`character(1)` output to text or markdown format.

Value

A list of package titles.

Author

Martin Morgan mtmorgan@fhcrc.org and Lori Shepherd

Examples

# At release time get a list of new or removed or deprecated packages

# get new packages in release 3.7 that are not in 3.6
newSoft = getPackageTitles()
# get removed packages from 3.6
rmSoft = getPackageTitles(currBranch="RELEASE_3_7", status="removed")
# get depreacted package for 3.7
deprecatedSoft = setdiff(getPackageTitles(status="removed"), rmSoft)

# repeated above for data-experiment packages
newData = getPackageTitles(manifest="data-experiment.txt")
rmData = getPackageTitles(currBranch="RELEASE_3_7", manifest="data-experiment.txt", status="removed")
deprecatedData = setdiff(getPackageTitles(manifest="data-experiment.txt", status="removed"), rmData)

getPacksAndViews()

Parse VIEWS file for views and packages

Description

Given a repository URL, download and parse the VIEWS file.

Usage

getPacksAndViews(reposURL, vocab, defaultView, local=FALSE)

Arguments

Argument	Description
`reposURL`	character vector giving the URL of a CRAN-style repository containing a VIEWS file at the top-level.
`vocab`	A `graph-class` object representing the ontologyof views. This graph should be a directed acyclic graph (DAG).
`defaultView`	A string giving the term to use for packages that do not list a term of their own via the `biocViews` field in the DESCRIPTION file.
`local`	logical indicating whether certain links should be absolute (using `reposURL` ) or relative.

Value

A list with named elements:

views : Vector of view memberships. Names are package names.

pkgList : A list of PackageDetail-class objects.

Author

Seth Falcon

getSubTerms()

Retrieve a term and its children from a vocab DAG

Description

Given a Directed Acyclic Graph (DAG) represented as a graphNEL instance, return a character vector consisting of the specified term and all of its descendants. That is, give the list of terms for which a path exists starting at term .

Usage

getSubTerms(dag, term)

Arguments

Argument	Description
`dag`	A `graphNEL` representing a DAG
`term`	A string giving a term in the vocabulary (a node in `dag` )

Value

A character vector of term names.

Author

S. Falcon

Examples

data(biocViewsVocab)
getSubTerms(biocViewsVocab, "Software")

guessPackageType()

Guess Package Type (Software, ExperimentData, AnnotationData) using existing biocViews.

Description

biocViews are "keywords" which are used to describe a given package. They are broadly divided into three categories, representing the type of packages present in the Bioconductor Project - Software, Annotation Data and Experiment Data. biocViews are supposed to come from only one of the three fields, but this function will check the list of biocViews and guess the package type based on how many biocViews came from each field.

Usage

guessPackageType(biocViews)

Arguments

Argument	Description
`biocViews`	A character vector containing a list of biocViews.

Value

A character(1) of package type: either "Software", "ExperperimentData", or "AnnotationData".

Author

Lori Shepherd

Examples

guessPackageType(c("clustering", "classification"))
guessPackageType(c("Organism", "Homo Sapien"))

htmlDoc()

Create a complete HTML document representation of an object

Description

This generic function should return an XMLNode instance representing the specified object in HTML as a complete HTML document.

Usage

htmlDoc(object, ...)

Arguments

Argument	Description
`object`	An object
`list()`	Not currently used.

Value

An instance of XMLNode from the XML package.

Author

Seth Falcon

htmlFilename()

Return a filename for an object's HTML representation

Description

This function returns a string containing an appropriate filename for storing the object's HTML representation.

Usage

htmlFilename(object, ...)

Arguments

Argument	Description
`object`	An object.
`list()`	Not currently used

Value

A character vector of length one containing the filename.

Author

Seth Falcon

htmlValue()

HTML Representation of an Object

Description

This generic function should return an XMLNode instance representing the specified object in HTML

Usage

htmlValue(object)

Arguments

Argument	Description
`object`	An object

Value

An instance of XMLNode from the XML package.

Author

Seth Falcon

recommendBiocViews()

Recommend biocViews for an existing Package.

Description

Packages being added to the Bioconductor Project require biocViews in their DESCRIPTION file.(Note that the field name "biocViews" is case-sensitive and must begin with a lower-case 'b'.)biocViews are "keywords" which are used to describe a given package. They are broadly divided into three categories, representing the type of packages present in the Bioconductor Project - Software, Annotation Data and Experiment Data.

Usage

recommendBiocViews(pkgdir, branch)

Arguments

Argument	Description
`pkgdir`	The path of the package Directory.
`branch`	The branch which your package will belong to. It can be either 'Software', 'AnnotationData' or 'ExperimentData'.

Details

This function parses the package directory provided by the user to recommend biocViews to the user. The output is a suggested list - the user of this function is expected to go through this list and find which biocViews best describe his or her package. It uses the following strategies.

It parses the "Description", "Title", "Package" of the DESCRIPTION page to find biocViews.
It looks up the biocViews of the packages in the "Depends" field of the given package to recommend biocViews
It parses the text from the man pages and the vignettes to suggest biocViews. Please note the following:
Do not make up your own biocViews.
Double check the spelling and case of the biocViews added.
Please add biocViews only from the appropriate branch. eg: Software packages should have only Software biocViews.

Value

A list is returned with 3 characters - current , recommended and remove.

"current" contains the biocViews from the package's DESCRIPTION file.
"recommended" are the recommended biocViews - This is a suggested list which the user can add in addition to "current" biocViews - the user is expected to go through this list and find which biocViews best describe their package.
"remove" are those biocViews which are inconsistent with the Bioconductor biocViews. (Hint - check for spelling, cases and plural)

Author

Sonali Arora.

recommendPackages()

Recommend Packages using existing biocViews.

Description

biocViews are "keywords" which are used to describe a given package. They are broadly divided into three categories, representing the type of packages present in the Bioconductor Project - Software, Annotation Data and Experiment Data. One can find packages which are tagged with biocViews using this function.

Usage

recommendPackages(biocViews, use.release=TRUE, intersect.views=TRUE)

Arguments

Argument	Description
`biocViews`	A character vector containing a list of biocViews. Currently only biocViews from the software branch are supported.
`use.release`	A logical character indicating if you want packages recommended from the release branch of Biocondutor.
`intersect.views`	A logical character indicating if you want packages which are tagged with all the input biocViews or packages tagged with any one or more of the biocViews.

Value

A character vector containing a list of packages. If multiple biocViews are given as input, the result returns packages tagged with all or atleast one of the input biocViews.

Author

Sonali Arora.

Examples

recommendPackages(c("clustering", "classification"))

validation_tests()

Validate a package's biocViews.

Description

Ensures that a package has biocViews and that they are valid. Function is designed to be called from the unit tests of another package.

Usage

validate_bioc_views(pkg)

Arguments

Argument	Description
`pkg`	`character(1)` Name of package to validate.

Value

invisible(NULL) if tests pass.

Author

Dan Tenenbaum dtenenba@fhcrc.org

Examples

validate_bioc_views("biocViews")

writeBiocViews()

Write a list of BiocView objects to HTML

Description

This function serializes a list of BiocView-class objects to a series of HTML files.

Usage

writeBiocViews(bvList, dir, backgroundColor="transparent")

Arguments

Argument	Description
`bvList`	A list of `BiocView-class` objects
`dir`	A character vector giving the directory where the HTML files will be written.
`backgroundColor`	A character vector giving the background color for the body in the CSS file.

Author

Seth Falcon

writeHtmlDoc()

Write an XML DOM containing HTML to a file

Description

Given a DOM tree from the XML package and a filename, write the DOM to disk creating an HTML file.

Usage

writeHtmlDoc(html, file)

Arguments

Argument	Description
`html`	A DOM object from the XML package
`file`	A string giving the filename

Author

S. Falcon

writePackageDetailHtml()

Write HTML files for packages in a CRAN-style repository

Description

This function creates package "homepages" that describe the package and provide links to download package artifacts in the repository.

Usage

writePackageDetailHtml(pkgList, htmlDir = "html", backgroundColor="transparent")

Arguments

Argument	Description
`pkgList`	A list of `PackageDescription` objects.
`htmlDir`	The files will be written to this directory.
`backgroundColor`	A character vector giving the background color for the body in the CSS file.

Author

Seth Falcon

writeRFilesFromVignettes()

Write R files from vignettes

Description

Ensures that .R files from vignette code chunks are written out.

Usage

writeRFilesFromVignettes(reposRoot, reposUrl="..",
                                    viewUrl="../..", reposFullUrl=reposUrl,
                                    downloadStatsUrl="", devHistoryUrl="")

Arguments

Argument	Description
`reposRoot`	Root directory of a CRAN-style repository
`reposUrl`	URL of repository
`viewUrl`	url of VIEWS file
`reposFullUrl`	Full URL of VIEWS file
`downloadStatsUrl`	URL to download stats page
`devHistoryUrl`	Dev history URL

writeRepositoryHtml()

Write package descriptions and a repository index as HTML

Description

This function generates an HTML file for each package in a repository and generates an index.html file that provides an alphabetized listing of the packages.

Usage

writeRepositoryHtml(reposRoot, title, reposUrl = "..", viewUrl = "../..",
                    reposFullUrl=reposUrl, downloadStatsUrl="",
                    devHistoryUrl="", link.rel = TRUE,
                    backgroundColor="transparent")

Arguments

Argument	Description
`reposRoot`	string specifying the path to the root of the CRAN-style package repository.
`title`	string giving the title for the repository
`reposUrl`	string giving the prefix for URL in links generated on the package description pages. The default is `"..."` which works well if the package description HTML files are written to an `html` subdirectory under the root of the repository.
`viewUrl`	string giving the prefix for the URL in links to the view pages. The biocViews terms will be linked to views summary pages with this prefix.
`reposFullUrl`	string giving the full prefix for URL in links generated on the package description pages. The default is `reposUrl` .
`downloadStatsUrl`	string giving the prefix for the URL in links to the download history statistics pages.
`devHistoryUrl`	string giving the prefix for the URL in links to the development changelog.
`link.rel`	logical indicating whether the index page should generate relative URL links. The default is `TRUE` . If you are generating HTML for a remote repository, you will want to set this to `FALSE` .
`backgroundColor`	A character vector giving the background color for the body in the CSS file.

Author

Seth Falcon

writeTopLevelView()

Write the view for the root of a vocabulary to disk

Description

Given a directory and a vocabulary represented as a graphNEL containing a DAG of terms, write the top-level term to disk as HTML.

This assumes your vocabulary has a single term with no parents.

Usage

writeTopLevelView(dir, vocab)

Arguments

Argument	Description
`dir`	A string giving a directory in which to write the HTML file
`vocab`	A `graphNEL` instance giving the DAG of terms. It should have a root node. That is, there should be exactly one node with no incoming edges.

Author

S. Falcon

write_REPOSITORY()

Write a REPOSITORY control file for a CRAN-style package repository

Description

This function writes a REPOSITORY file at the top-level of a CRAN-style repository. This file is DCF formatted and describes the location of packages available in the repository. Here is an example for a repository containing source packages, and Windows and Mac binary packages:

list(" ", " source: src/contrib ", " win.binary: bin/windows/contrib/3.4 ", " mac.binary.el-capitan: bin/mac/el-capitan/contrib/3.4 ", " provides: source, win.binary, mac.binary.el-capitan ", " ")

Usage

write_REPOSITORY(reposRootPath, contribPaths)

Arguments

Argument	Description
`reposRootPath`	character vector containing the path to the CRAN-style repository root directory.
`contribPaths`	A named character vector. Valid names are `source` , `win.binary` , `mac.binary` , `mac.binary.mavericks` , and `mac.binary.el-capitan` . Values indicate the paths to the package archives relative to the `reposRoot` .

Author

Seth Falcon

write_SYMBOLS()

Write a SYMBOLS file

Description

Writes a DCF formatted file, SYMBOLS, containing the symbols exported by each package in a directory containg R package source directories.

Usage

write_SYMBOLS(dir, verbose = FALSE, source.dirs=FALSE)

Arguments

Argument	Description
`dir`	The root of a CRAN-style package repository containing source packages. When `source.dirs` is `TRUE` , `dir` should be a directory containing R package source directories
`verbose`	Logical. When `TRUE` , progress is printed to the standard output.
`source.dirs`	Logical. When `TRUE` , interpret `dir` as a directory containing source package directories. When `FALSE` , the default, `dir` is assumed to be the root of a CRAN-style package repository and the function will operate on the source package tarballs in `dir/src/contrib` .

Value

Returns NULL . Called for the side-effect of creating a SYMBOLS file in dir .

Author

S. Falcon

write_VIEWS()

Write a VIEWS control file for a CRAN-style package repository

Description

This function writes a VIEWS file to the top-level of a CRAN-style package repository. The VIEWS file is in DCF format and describes all packages found in the repository.

The VIEWS file contains the complete DESCRIPTION file for each source package in the repository. In addition, metadata for available binary packages and vignettes is centralized here.

Usage

write_VIEWS(reposRootPath, fields = NULL,
          verbose = FALSE, vignette.dir = "vignettes",
          manifestFile = NA, meatPath = NA)

Arguments

Argument	Description
`reposRootPath`	character vector containing the path to the CRAN-style repository root directory.
`fields`	Any additional fields to include. You shouldn't need this, but if you have added fields to the DESCRIPTION files of the packages in the repository, you may want it.
`type`	One of `source` , `win.binary` , `mac.binary` , `mac.binary.mavericks` , or `mac.binary.el-capitan` indicating which set of packages should be used to build up the "shared" information. Since a repository can contain different versions of the same package (source vs binary) the shared information may not be reliable.
`verbose`	logical, if `TRUE` , print progress messages.
`vignette.dir`	character specifying where to look for vignettes.
`manifestFile`	character(1). File path location to Bioconductor formatted manifest file that lists all current packages. This file will be used in the write_VIEWS function to cross check successfully built packages with all expected packages. Packages that have not built will be given dummy entry for complete listing in bioc_VIEWS. If NA cross check is skipped and packages not built on any system will be missing from biocVIEWS
`meanPath`	character(1). File path location to the directory containing cloned repositories of Bioconductor packages. If manifestFile is used for cross checking and the meatPath is provided, entries from the DESCRIPTION file are manually entered into biocVIEWS information. If NA dummy values for minimal fields for landing page generation are included with ERROR. This attempts to fill in as much information as possible for packages that have failed to build.

Author

Seth Falcon

v3.9.0

bioconductor v3.9.0 BiocViews

Link to this section Summary

Functions

Link to this section Functions

BiocView_class()

Description

Author

Htmlized_class()

Description

Author

PackageDetail_class()

Description

Author

Examples

RepositoryDetail_class()

Description

Author

biocViewsVocab()

Description

Format

Usage

Details

Examples

biocViews_package()

Description

Details

Author

Examples

extractManuals()

Description

Usage

Arguments

Author

extractNEWS()

Description

Usage

Arguments

extractTopLevelFiles()

Description

Usage

Arguments

extractVignettes()

Description

Usage

Arguments

Author

genReposControlFiles()

Description

Usage

Arguments

Seealso

Author

getBiocSubViews()

Description

Usage

Arguments

Details

Value

Seealso

Author

Examples

getBiocViews()

Description

Usage

Arguments

Value

Seealso

Author

Examples

getCurrentbiocViews()

Description

Usage

Details

Value

Author

Examples

getPackageNEWS()

Description

Usage