Merge branch 'pkgsrc_2013Q4' into joyent/feature/smf/2013Q4
Fix Fortran reference for math/R (DATASET-962)
Revert "Fix R vs. gcc47-libs problem by fixing R_LD_LIBRARY_PATH"

This reverts commit 4fa6a9e1f0c542e8045aaa0a33af7eff7b19e4df.
Do not include system library paths in R_LD_LIBRARY_PATH, picking up system
libraries when previously preferring libraries from pkgsrc causes conflicts.

Fixes build on SmartOS where the platform /usr/lib/libgcc_s.so.1 for legacy
applications conflicts with GCC libraries from pkgsrc.
Exclude 64-bit system library paths on SunOS.
Update to R 3.0.2

* The NEWS files have been re-organized.

  This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
  and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2.  The
  latter files are now installed when R is installed.  An HTML
  version of news from 2.10.0 to 2.15.3 is available as
  doc/html/NEWS.2.html.

* sum() for integer arguments now uses an integer accumulator of at
  least 64 bits and so will be more accurate in the very rare case
  that a cumulative sum exceeds 2^53 (necessarily summing more than
  4 million elements).

* The example() and tools::Rd2ex() functions now have parameters to
  allow them to ignore \dontrun markup in examples.  (Suggested by
  Peter Solymos.)

* str(x) is considerably faster for very large lists, or factors
  with 100,000 levels, the latter as in PR#15337.

* col2rgb() now converts factors to character strings not integer
  codes (suggested by Bryan Hanson).

* tail(warnings()) now works, via the new `[` method.

* There is now support for the LaTeX style file zi4.sty which has
  in some distributions replaced inconsolata.sty.

* unlist(x) now typically returns all non-list xs unchanged, not
  just the "vector" ones.  Consequently, format(lst) now also works
  when the list lst has non-vector elements.

* The tools::getVignetteInfo() function has been added to give
  information about installed vignettes.

* New assertCondition(), etc. utilities in tools, useful for
  testing.

* Profiling now records non-inlined calls from byte-compiled code
  to BUILTIN functions.

* Various functions in stats and elsewhere that use non-standard
  evaluation are now more careful to follow the namespace scoping
  rules.  E.g. stats::lm() can now find stats::model.frame() even
  if stats is not on the search path or if some package defines a
  function of that name.

* If an invalid/corrupt .Random.seed object is encountered in the
  workspace it is ignored with a warning rather than giving an
  error.  (This allows R itself to rely on a working RNG, e.g. to
  choose a random port.)

* seq() and seq.int() give more explicit error messages if called
  with invalid (e.g. NaN) inputs.

* When parse() finds a syntax error, it now makes partial parse
  information available up to the location of the error.  (Request
  of Reijo Sund.)

* Methods invoked by NextMethod() had a different dynamic parent to
  the generic. This was causing trouble where S3 methods invoked
  via lazy evaluation could lose track of their generic.
  (PR#15267)

* Code for the negative binomial distribution now treats the case
  size == 0 as a one-point distribution at zero.
* abbreviate() handles without warning non-ASCII input strings
  which require no abbreviation.

* read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
  PR#15250.)

* formatC(x) no longer copies the class of x to the result, to
  avoid misuse creating invalid objects as in PR#15303.  A warning
  is given if a class is discarded.

* Dataset npk has been copied from MASS to allow more tests to be
  run without recommended packages being installed.

* The initialization of the regression coefficients for
  non-degenerate differenced models in arima() has been changed and
  in some examples avoids a local maximum.  (PR#15396)

* termplot() now has an argument transform.x to control the display
  of individual terms in the plot.  (PR#15329)

* format() now supports digits = 0, to display nsmall decimal
  places.

* There is a new read-only par() parameter called "page", which
  returns a logical value indicating whether the next plot.new()
  call will start a new page.

* Processing Sweave and Rd documents to PDF now renders backticks

* utils::modifyList() gets a new argument keep.null allowing NULL
  components in the replacement to be retained, instead of causing
  corresponding components to be deleted.

* tools::pkgVignettes() gains argument check; if set to TRUE, it
  will warn when it appears a vignette requests a non-existent
  vignette engine.

Conflicts:
	math/R/Makefile
Update couchdb to 1.5.0.

Changes since 1.4.0:
- COUCHDB-1781: The official documentation has been overhauled.
- New administration UI, included as an experimental preview.
- COUCHDB-1888: Fixed an issue where admin users would be restricted
  by the public_fields feature.
- Fixed an issue with the JavaScript CLI test runner.
- COUCHDB-1867: An experimental plugin feature has been added.
- COUCHDB-1894: An experimental Node.js-based query server runtime added.
- COUCHDB-1901: Better retry mechanism for transferring attachments during
  replication.
Stop filling stdout/stderr files (DATASET-955)
Merge branch 'joyent/feature/miscfix/2013Q4' into joyent/release/2013Q4
Merge branch 'joyent/feature/smf/2013Q4' into joyent/release/2013Q4
Update joyent and wip