BiocContributions (version 0.99.70)

clean: Convenience functions for managing behind the scenes operations involved in adding packages to Bioconductor Repositories.

Description

There are several convenience functions in this package that are useful for different things. I will enumerate them below

clean: used for removing cruft that is added to tarball by R CMD build. This is normally run before adding a new tarball to the svn repository.

makeBins: used for making tarballs that don't contain source code into mac and windows binaries.

emailExistingUser: used to send an instructional email to a user who already has an existing svn account.

emailNewUser: used to print out a customized instructional email for a user who has a new svn account. Since there is currently no way to get the credentials, these will have to be pasted in, but at least the rest of the message will be put together.

emailNewSvnAccount: used to send an email to Carl (with a custom guess for the proposed username) so that he can make a new svn account. If a user like this already exists, then you can refuse to send the email and it will instead print a message out so that you can just change one character manually and then send it. Again, this could be improved if we had access to a local copy of the the svn credentials file.

existingSvnUsers: used to list all existing svn accounts that look like the user you would expect to generate based on a taball. It searches the maintainer field of a tarball, generates a user name and then looks at all the svn users to see if any are similar to that.

getPackageTotals: looks at the manifests and gives package counts for each. This may need to be updated to reflect new manifests...

getPackageDeltas: looks at the manifests and gives package the deltas for each manifest transition. So you can see how many packages were added with each release. plotPackageTotals: makes a simple plot of package growth over time.

installDeps: Given a tarball or package directory, this will install all its dependencies using biocLite(). This works even for tarballs/directories that are not yet available themselves via biocLite().

generatePermissionEdits: Takes a vector of tarball paths, and prints output that can be pasted (after some scrutiny) into the permissions file.

rebuildIssueTarball: A helper so that you don't have to bother Dan to rebuild a tarball when the tracker fails to do so for some reason. This function does require that you have access to habu

removeDeadTrackerIssue: Another helper that will remove an issue completely from the tracker. Use this with caution! This also requires access to habu

filterIssues: This function will get issue IDs and even tarballs that match certain date and status criteria. So you want to know what packages were accepted in march of 2014? Or maybe just which packages are classified as 'new-package' status from last month? This function should help with that. coneOfShame: This function is named after the 'cone of shame' from UP. Because sometimes you might get a false positive of the end user just writes 'thank you' and has not bounced the ball back into your court... But its still a useful funtion to seeing which packages are getting neglected and by how much. The hope is that this should spare all of us the embarrassment of packages getting too far behind.

readyToAdd: This is just a convenience for listing those packages that are accepted in the tracker but still not yet in the latest bioc manifest. IOW this is to list out packages that need to be added so that we don't miss any. We need to use this because that has happened before! One issue is that this function has to rely on the package name in the title being accurate. If those values are wrong, then this will give false positives. creditworthy: gives credit to core Seattle members and finds out whose done what in the last 30 days with respect to packages getPackageRange: Every 6 months, core Seattle members are given a range and they need to ensure that all packages in that range pass without any errors and warnings. This helper function takes in the name of reviewer and gives back the number of packages assigned to them, number of packages with errors and number of packages with warnings. getEmailAddressesToWarnPkgMaintainers: just a convenience wrapper that calls getPackageRange and produces a list of emails addresses to bother with a form message. Like getPackageRange, it takes a userName argument that it then uses to restrict which authors it will bother...

compareReleases: given an 'old' and 'new' release, what packages were added and what packages were removed?

getDescriptions: given a list of packages (maybe returned by compareReleases), get the Description fields of each and return as a string suitable for pasting into a release announcement.

preacceptedToAccepted: finds the packages on the tracker with pre-accepted status and checks if the build report for them has any warnings or errors

failmail: Sends email to maintainers whose packages are broken in the build system. All you have to provide is the package name, though you are able to customize the email that's sent.

Usage

clean(tarball, svnDir="~/proj/Rpacks/", copyToSvnDir=TRUE,
        svnAccountExists=FALSE)
  cleanDataPkg(tarball,
               svnDir1="~/proj/experiment/pkgs",
               svnDir2="~/proj/experiment/data_store",
               copyToSvnDir=TRUE,
               svnAccountExists=FALSE)
  makeBins(tarball)
  emailExistingUser(tarball, sendMail=FALSE)
  emailNewUser(tarball)
  requestNewSvnAccountFromScicomp(tarball, sendMail=FALSE)
  existingSvnUsers(tarballsPath=".", suffix=".tar.gz$")
  svnUserMatches(names)
  generatePermissionEdits(tarballsPath=".", suffix=".tar.gz$")
  rebuildIssueTarball(issueNumber,tarballUrlPath)
  removeDeadTrackerIssue(issueNumber)
  filterIssues(status=c('new-package'),datePrefix='2015',getUserFiles=FALSE)
  coneOfShame(daysNeglected=14, userName=NULL, daysToForget=30,lastTouchedFilter=TRUE)
  readyToAdd(datePrefix='2015',svnDir="~/proj/Rpacks/",
             svnDir1="~/proj/experiment/pkgs/", getUserFiles=FALSE)
  creditworthy(creditDays=30, userName)
  getPackageRange(userName = "sarora", biocVersion = "3.1")
  getEmailAddressesToWarnPkgMaintainers(userName)
  compareReleases(path = "~/proj/Rpacks/", oldRel="3.0", newRel="3.1")
  getDescriptions(path = "~/proj/Rpacks/", pkgs)
  preacceptedToAccepted()
  failmail(package, software=TRUE, 
    from=getOption("fromEmail", "[e-mail]"),
    sig=getOption("mail.sig", "Dan"), subject=sprintf("%s build problem", package),
    preview=TRUE, bccme=TRUE)

Arguments

tarball

The tarball (as built by R CMD build). In installDeps, this can also be a directory.

svnDir

The dir where the svn repos is located

svnDir1

The dir where the pkgs repos if located (data pkgs)

svnDir2

The dir where the data repos is located (data pkgs)

copyToSvnDir

TRUE/FALSE do we copy the cleaned dir to svnDir?

svnAccountExists

TRUE/FALSE does the maintainer of this tarball have an svn account alread?

sendMail

TRUE/FALSE do we call sendmail or do we print out a file to send later?

names

A character vector of strings that you think might be user names.

tarballsPath

The path to a group of tarballs to process

suffix

The suffix to use for recognizing tarball files (normally '.tar.gz' - so no need to specify it)

issueNumber

The roundup tracker issue number

tarballUrlPath

The url for a tarball that is to be checked

status

Any of the following tracker based states: 'new-package', 'preview-in-progress', 'sent-back', 'modified-package', 'review-in-progress', 'accepted', 'rejected'

datePrefix

Tracker dates are formatted like this: 'YYYY-MM-DD timestamp', so provide a string that is formatted to match the amount of date that you intend to exactly match. For example '2007-05' would match things from may of 2007. It probably won't be useful to be more specific than that.

getUserFiles

TRUE/FALSE get the tarball names associated with issues that match?

daysNeglected

Number of days to wait before including in a cone of shame list

userName

username for a person whos activity you want to see

daysToForget

Number of days before something is old enough that we always want to exclude if from a cone of shame list

lastTouchedFilter

TRUE/FALSE Filter based on whether the author was the last person to touch it?

creditDays

Number of days for which you want to find out which reviewer has done what

biocVersion

What version of BiocConductor

oldRel

old release

newRel

new release

pkgs

a character vector of package names

package

The package to email the maintainer about.

software

TRUE for software packages, FALSE for experiment data packages.

from

From address for maintainer email.

sig

String to sign maintainer email with.

subject

Subject of maintainer email.

preview

Show a preview of maintainer email before sending?

bccme

If TRUE, copy maintainer email to 'from' address via BCC.

Value

• This varies with the function.

Details

In order to use the email functions you should put a line in your .Rprofile file that looks like this:

options( fromEmail = '[e-mail]')

The 'failmail' function works a bit differently and requires that you have something like this in your .Rprofile:

options(email.options= list(host.name = "hostname", port = 25, tls = TRUE, authenticate = TRUE, user.name = "username", passwd = "password", debug=FALSE, ssl = TRUE) )

Examples

library(BiocContributions)
  tarball <- system.file("testpackages", "AnnotationHub_1.3.18.tar.gz",
                         package="BiocContributions")

  ## interactive() here is to protect me from example spam etc.
  if(interactive()){
    ## clean up a tarball and copy it to the repos
    clean(tarball)

    ## clean up a data tarball and copy it to the svn repositories.
    cleanDataPkg(tarball)

    ## email someone who has an account
    emailExistingUser(tarball)

    ## generate an email for someone who needs svn credentials
    emailNewUser(tarball)

    ## send an email to Scicomp asking for a new account.
    requestNewSvnAccountFromScicomp(tarball)


    ## make mac and windows binaries for a package.
    tarball <- system.file("testpackages", "hgu95av2.db_2.10.1.tar.gz",
                           package="BiocContributions");
    makeBins(tarball)

    ## list existing svn users that are similar to tarball maintainers
    ## for all the tarballs in the working directory
    existingSvnUsers()

    ## list svn users like 'carlson'
    svnUserMatches('carlson')

    ## list how many packages are in each known release of Bioconductor
    getPackageTotals()

    ## Install all the dependencies for a tarball you need to review
    ## (but that isn't yet in biocLite itself)
    installDeps(tarball)

    ## Generate permission edits for a directory of new tarballs
    generatePermissionEdits()

    ## rebuild tarball issue 558 (URL indicates which tarball to rebuild)
    rebuildIssueTarball(558,
          'https://tracker.bioconductor.org/file4845/spbtest_0.99.0.tar.gz')

    ## remove issue 1114 from the tracker
    removeDeadTrackerIssue('1114')

    ## get issues that are from 2015 and that are either new or in
    ## preview
    filterIssues(status=c('new-package','preview-in-progress'),
                 datePrefix='2015')

    ## get similar issues that are from December of 2014
    filterIssues(status=c('new-package','preview-in-progress'),
                 datePrefix='2014-12')

    ## list users who may be currently behind on their package reviews
    ## by two weeks but not more than a month.
    coneOfShame()
    ## use coneOfShame to only see which issues mcarlson has not touched for
    ## more than one week
    coneOfShame(7, 'mcarlson')
    ## use coneOfShame to just see all issues assigned to mcarlson period:
    coneOfShame(1, 'mcarlson', lastTouchedFilter=FALSE)

    ## list packages that may be ready to be added to the repos.
    readyToAdd('2015')

    ## give credit to people for what they've worked on in the past 30 days
    df <- creditworth()

    diff <- compareReleases()
    descs <- getDescriptions(pkgs<-diff$added)
  }

  failmail("xps")