R dataset

[unutbu]

Motivation for this pull request came from this problem: http://stackoverflow.com/q/19039356/190597.

The problems:

• pandas.rpy.common.load_data currently fails to load high-dimensional arrays such as the "Titanic" dataset. load_data prints an error to stdout and returns None.
• Applying load_data to "iris3", "state.division" or "state.region" R datasets currently raise a TypeError.
• Timeseries R data is currently converted to lists that lack a time series index.
• Factor data is converted to a list of index numbers without any levels information.

This pull request:

• Provides code which allows load_data to convert the "Titanic" dataset (and similar high-dimensional arrays) to "melted" DataFrames. The code does not use R's melt function, since that would introduce a new dependency.
• load_data now returns a DataFrame for arrays like "iris3".
• load_data converts R factors like "state.division" and "state.region" to lists which use the levels as values.
• load_data converts ts (timeseries) R data, like "airmiles" to Series with an index showing the times. Note however I wasn't able to convert the index to a DatetimeIndex since the same code is used to convert numeric R data (like "euro") which does not have a time-related index.
• moves already existant tests from rpy/common.py to tests/test_rpy.py
• adds new unit tests which highlight the problems mentioned above, and tests for what I think is more desireable behavior as described above.

[jreback]

add rpy2 in ci/requirements

2.7, 3.3 maybe

[cpcloud]

i think need to add R in ci/install.sh as well

[cpcloud]

problem is that is a huge honking install on ubuntu

[cpcloud]

all this for r-base on ubuntu 12.04:

autoconf automake autotools-dev cdbs dh-translations dpatch fakeroot fontconfig fontconfig-config intltool libbz2-dev libcairo2 libdatrie1 libencode-locale-perl libfile-basedir-perl libfile-desktopentry-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libfontconfig1 libfontenc1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libio-socket-inet6-perl libio-socket-ssl-perl libllvm3.0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmailtools-perl libncurses5-dev libnet-http-perl libnet-ssleay-perl libpango1.0-0 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpixman-1-0 libsm6 libsocket6-perl libthai-data libthai0 libtiff4 liburi-perl libutempter0 libwww-perl libwww-robotrules-perl libx11-xcb1 libxaw7 libxcb-glx0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 libxml-parser-perl libxmu6 libxpm4 libxrandr2 libxrender1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 m4 patchutils python-scour r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended shared-mime-info tcl8.5 tk8.5 ttf-dejavu-core unzip x11-common x11-utils x11-xserver-utils xbitmaps xdg-utils xterm zip 

[jreback]

any way to have it skip all of the display stuff ?

[cpcloud]

someone more knowledgeable than me about apt-get may know the answer to that question. @yarikoptic can you grace us with your debian wisdom? is something like this possible?

[cpcloud]

It's simply not the case that all of those deps are required to install R. On Arch Linux, these are the dependencies:

blas lapack bzip2 libpng libjpeg libtiff ncurses pcre readline zlib perl gcc-libs libxt libxmu pango xz desktop-file-utils

[jtratner]

why do you need to build R, can't you just use apt-get to get the package
without build-dep?

On Sun, Sep 29, 2013 at 12:12 AM, Phillip Cloud notifications@github.comwrote:

It's simply not the case that to build R this is required. On Arch Linux,
these are the following dependencies:

blas lapack bzip2 libpng libjpeg libtiff ncurses pcre readline zlib perl gcc-libs libxt libxmu pango xz desktop-file-utils

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/5036#issuecomment-25314107
.

[cpcloud]

those ubuntu deps i listed above are from calling apt-get, shouldn't have said "build". meant "install"

[yarikoptic]

well -- it feels that list a bit bloated due to recommends -- what if you do apt-get install r-base --no-install-recommend? that still would need x11-common xdg-utils though, but most probably that is unavoidable... I would recommend on your box to run sudo apt-get install debtree; debtree --no-recommends r-base | dot -Tsvg > /tmp/r-basedepends.svg; firefox /tmp/r-basedepends.svg which would give you a nice graph of dependencies so you could clearly see how they are pulled in.

[unutbu]

Installing R on Travis seems like an unsolved problem for many people: http://yihui.name/en/2013/04/travis-ci-general-purpose/. Would it be helpful if I move the unit tests back into rpy/common.py so those with R installed could run the tests, but not have it part of the official test suite?

[jtratner]

just add a raise nose.SkipTest("R not installed") at the top of the file
instead. (and, you know, check for that too :))

[jreback]

can you change to nose.SkipTest('R not installed') thxs....then squash to smaller num of commits