R/tallyManifests.R

In Bioconductor/BiocContributions: Convenience functions for adding packages to the svn repository

## Used to count and plot the amount of packages in the respos.

## helper that generates names for manifests.  You have to update this
## each release in order to get the current totals!
.makeManifestNames <- function(path, appendPath=TRUE){
    files <- dir(path)[grepl(glob2rx("bioc_*.manifest"),dir(path))]
    if(appendPath==TRUE){
        paste0(path,files)
    }else{
        files
    }
}

.makeExpManifestNames <- function(path, appendPath=TRUE){
    files <- dir(path)[grepl(glob2rx("bioc-data-experiment.*.manifest"),
                             dir(path))]
    if(appendPath==TRUE){
        paste0(path,files)
    }else{
        files
    }
}

.getManifestFilenameFromVersion <- function(path, version)
{
    file.path(path, paste0("bioc_", version, ".manifest"))
}


## Helper to just read in one manifest and get the total number of packages.
.scanMani <- function(file){
    res <- scan(file, what="character",skip=1, quiet=TRUE)
    table(grepl("Package", res))[["TRUE"]]
}

.getPkgs <- function(file) 
{
    lines <- readLines(file)
    lines <- lines[grepl("^Package:", lines)]
    lines <- gsub("^Package:", "", lines)
    lines <- trimws(lines)
}


## This extracts the package totals based on existing manifests
getPackageTotals <-
    function(path = proj_path("Rpacks"))
{
    manis <- .makeManifestNames(path)
    maniNames <- .makeManifestNames(path, appendPath=FALSE)
    ## Always update the most recent manifest file (at the very least)
    lastMani <- manis[length(manis)]
    system(paste0("svn up ", lastMani))
    res <- setNames(unlist(lapply(manis, .scanMani)), maniNames)
    res[order(res)] ## assumption: that the size will always grow...
}

## getPackageTotals()


## And this plots the package totals based on existing manifests
plotPackageTotals <-
    function(path = proj_path("Rpacks"))
{
    totals <- getPackageTotals(path)
    plot(totals)
    abline(a=100,b=20,col="red")
}

## plotPackageTotals()


getPackageDeltas <-
    function(path = proj_path("Rpacks"))
{
    tots <- getPackageTotals(path)
    res <- integer()
    names <- character()
    for(i in seq_along(tots)){
        res[i] <- tots[i+1] - tots[i]
        names[i] <- paste0(names(tots[i]),"_TO_",names(tots[i+1]))
        names(res) <- names
    }
    res <- res[1:(length(res)-1)]
    res
}

compareReleases <-
    function(path = proj_path("Rpacks"), oldRel="3.0", newRel="3.1")
{
    oldPkgs <- .getPkgs(.getManifestFilenameFromVersion(path, oldRel))
    newPkgs <- .getPkgs(.getManifestFilenameFromVersion(path, newRel))
    list(removed=sort(setdiff(oldPkgs, newPkgs)),
      added=sort(setdiff(newPkgs, oldPkgs)))
}

getDescriptions <-
    function(path = proj_path("Rpacks", pkgs))
{
    ret <- ""
    for (pkg in pkgs)
    {
        desc <- file.path(path, pkg, "DESCRIPTION")
        dcf <- read.dcf(desc)
        if ("Description" %in% colnames(dcf))
        {
            val <- unname(dcf[, "Description"])
            val <-  gsub("\n", " ", val)
            val <- paste0(pkg, " - ", val)
            val <- paste(strwrap(val, width=60), collapse="\n")
            ret <- paste0(ret, val, "\n\n")
        }
    }
    ret
}