The package tools has a non-exported function tools:::.split_dependencies.

A copy of this function exists in pkgDepTools.R

addPackages, updatePackages, makeRepo, etc. currently specify the package type as an argument.

Either:

1. Create wrappers to these functions to be able to quickly add packages for all three types (.tar.gz, .zip, .tgz)
2. Ensure these functions can handle a vector, e.g., type=c("source", "win.binary", ...)

I prefer the second option.

With R CMD check I get

* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'oldPackages.Rd':
  'pkgAvail(repos=path, type=type)'

CRAN requires all tests to run in fairly short amount of time.

• Use devtools::skip_on_cran to test locally, but skip on CRAN.
• Carefully choose package list to minimise dependencies, e.g. by using Matrix rather than raster in example_checkVersions.R

Need to import is from methods otherwise this function doesn't work when called from the commandline (e.g., using Rscript).

However, travis-ci autobuilds fail when methods::is is imported:

Namespace dependency not required: ‘methods’

Once addPackage is updated, addGithub should be too to perform the corresponding tasks but using a GitHub package instead of CRAN-like repo.

We need a simple wrapper around tools::write_PACKAGES

The use of the Rversion=... argument in addPackages() is inconsistent with use elsewhere in package, particularly makeRepo()

1. new argument: download=TRUE specifies whether the package files should be downloaded from a CRAN-like repo.
2. new argument: reindex.all=FALSE specifies whether the entire package index should be rebuilt based on the contents of the miniCRAN repo, or whether the index should simply be modified directly (more efficient).

miniCRAN can use any CRAN-like repository as a source, including:

• R-forge
• BioConductor
• MRAN

Sample code at https://gist.github.com/andrie/f826769f023b87799541

The package index files should be written in the tips of the directory structure, in the same dir as the packages themselves.

In makeRepo.R:

#' @section Repo folder structure:
#' The folder structure of a repository

Specifies the structure as

• root/
  • bin/
    • macosx/contrib/
    • windows/contrib/{version}
  • src/
    • contrib/
  • PACKAGES

But it should be:

• root/
  • bin/
    • macosx/contrib/
      • PACKAGES
    • windows/contrib/{version}
      • PACKAGES
  • src/
    • contrib/
      • PACKAGES

Features that would be useful in dependency graph include displaying information about:

• "top level" packages
• suggests, imports and depends
• License

Hi @andrie Should users have the option of asking for pkgs listed in the Enhances field of a pkg DESCRIPTION file? Doesn't seem to work when I do e.g. tools::package_dependencies("PivotalR", pdb, which="Enhances", recursive=TRUE)

The documentation can be improved with clear instruction on how to use a local repository, i.e. how to modify .Rprofile or how to set default repo.

Demonstrate use of:

• oldPackages
• upatePackages

Currently only @family miniCRAN functions is used for documentation. Since all of the package functions are included in the package help index, it makes more sense to specify more specific function groupings, such as "adding new packages", "dependency checking", etc.

Related: I really like the way the raster package groups their functions in the package documentation (see ?"raster-package").

Currently using backslashes to specify paths to examples in inst/examples/, which Windows is OK with but OSX and Linux are unable to build the package unless forward slashes are used.

However, travis-ci automated builds fail when forward slashes are used.

General improvements:

• Fix package title to comply with new CRAN rules (60 chars, title case, no ending period)
• Expand description
• Categorise functions in package documentation #19
• Use @inheritParams to simplify documentation

I'm working on a mac now, with Mavericks OS. In the example I'm playing with I had rgdal as a package to use in the project. However, there is no binary available for my OS http://cran.r-project.org/web/packages/rgdal/index.html

Perhaps pkgDep() can have a parameter to optionally grab pkg information via available.packages(type="source") or similar, to then be able to get dependencies.

Or is there already a way to do this?

This broke the addPackageGithub() example.

For example,

makeDepGraph("Rcpp")

throws an error

Currently these tests each creates a new miniCRAN repo, which is possibly inefficient.

Tasks:

• Combine tests into a single testthat context
• Use MRAN snapshots to test updates to binaries, in addition to source

Supersedes #25, #26, #27, #28, #29, #34 and relates to #43

It's easier to edit and review roxygen if the documentation runs on a single line.

Most IDEs, and particularly RStudio allows soft line wrapping.

Having a single line makes it much easier to edit documentation, rather than having to continually re-split on edits.

Note: actual code should be split at ~80 chars

Add helper functions to read DESCRIPTION from any package on github.

This is the logical next step after completing #9

Remove package names in Roxygen documentation links, to install without warnings.

For example, use

#' \code{\link{write_PACKAGES}}

instead of

#' \code{\link[tools]{write_PACKAGES}}

Great package @andrie !

I have been trying to create a miniCRAN repo for mavericks. When I use makeRepo, however, I get the following error:

Error in match.arg(type) :
'arg' should be one of “source”, “mac.binary”, “win.binary”

From the install.packages help file: Possible values are (currently) "source", "mac.binary", "mac.binary.mavericks" and "win.binary"

mac.binary.mavericks files are collected but the PACKAGES files is not. This is probably an issue in write_PACKAGES but I couldn't see how to fix it.

On my system, getOption("repos") is just a simple string:

> getOption("repos")
[1] "http://cran.revolutionanalytics.com"

This causes pkgDep to fail:

> miniCRAN:::pkgDep("ggplot2")
Error in if (repos["CRAN"] == "@CRAN@") { : 
  missing value where TRUE/FALSE needed

This command fixes the problem for me:

options(repos=c(CRAN="http://cran.revolutionanalytics.com"))

This is a feature that gets requested often

Related to:

• #23 new function to add a local package
• #9 Add capability to read package data from local file
• #10 Add capability to read package data from github

Right now, this function creates a duplicate and throws a warning

This may leave the repository in an inconsistent state.

Should we remove the duplicate?

If the user simply wants a local library of packages, then makeRepo() is overkill.

Create the ability to download packages into a specified library location without creating the PACKAGES file.

Revolution Analytics keeps historic snapshots of CRAN at the MRAN site:

http://mran.revolutionanalytics.com/snapshot/

We can use this to create unit tests for updating packages. It works as follows:

• Install packages from snapshot date t
• Set repos to snapshot date t + x
• Update packages

The repo for source folders should have the structure

/root/src/contrib/pkg_0.0.0

Supplements adding packages from CRAN-like repo and GitHub.

Can be used with addOldPackage(..., writePACKAGES=FALSE) and, after a build of the package binaries on a local machine, should add the local files to the miniCRAN repo.

"local" packages here could mean package files on the local harddrive, a network location, and possibly a non-CRAN-like web location (so this would also work with prebuilt packages from Github or other site).

Separate vignettes into:

• Building a private repository using makeRepo
• Using miniCRAN to identify package dependencies

Given some recent reports of difficulties installing igraph, is it possible to modify the Imports to Enhances or `Suggests?

Having contrib.url as an argument introduces unnecessariy complexity from the user's point of view, since one has to add type=... in multiple places.

This means that the user can't specify the R version to use. Need to create a version of contrib.url() that includes user-specified R.version

[pending rename/merge as addPackage]

Add helper functions to read DESCRIPTION from any local package and use this information to build the graph in makeDepGraph()

This question at StackOverflow provides a hint:

http://stackoverflow.com/questions/26104401/character0-warnings-when-running-devtoolsload-all-in-rstudio

empty warnings that load_all is giving you are actually initiated when loading the package because of function name conflicts

Conflicts exist in @import tools and we should use @importFrom tools ... instead.