[Rd] updated R-cairo bridge, official R-3.1.*-mavericks.pkg crippled, snpMatrix 1.19.0.20

[Hin-Tak Leung]

The windows replacement is 
R-library-grDevices-libs-winCairo_20150122.zip
in
http://sourceforge.net/projects/outmodedbonsai/files/R/

The cairo replacements are just two bundles, windows or OS X - containing
replacements for R 2.15.3, 3.0.3 and 3.1.2. You just extract the relevant one
for your R version.

The windows builds of R packages snpStats x.x.x.8 and snpMatrix 1.19.0.20
were done with link-time optimization. (uploaded last weekend). I'd be interested
if anybody wants to compare the speed of the 1000 genome code
vs 1.19.0.19 on windows. LTO on linux is 10+% faster.

There is a new bug fix in GLM related stuff in snpStats x.x.x.8 . I'd be interested
in anybody supplies an example to demonstrate snpStats 1.17.0 being buggy also.

I haven't decided what to do with link-time optimization of the OS X build -
Xcode/Clang  is the default on OS X though gcc is more familiar 
(https://gcc.gnu.org/ml/gcc-testresults/2014-11/msg00268.html) so I probably
will do both and see which one is better at some point.

The package uploads (12 in all, 2 packages x 3 R versions x 2 builds)
are now divided by R versions - those in unversion'ed directories are still for R 2.x. 

--------------------------------------------
On Wed, 21/1/15, Hin-Tak Leung <htl10 at users.sourceforge.net> wrote:

 R.framework-Versions-Resources-library-grDevices-libs-cairo_20150120.tgz
 in
 http://sourceforge.net/projects/outmodedbonsai/files/R/
 are dropped in replacement to the cairo.so's in the official
 R binaries (2.15.3, 3.0.3, 3.1.2).

 updated to cairo-1.12.18 and freetype-2.5.4. The official R
 binaries' were
 built with early freetype 2.4.x and cairo 1.11(?) and had a
 number of issues
 with some windows and mac system fonts; also the one in the
 official binaries
 were built with a freetype that's built differently from
 apple's and
 and therefore can interfere with other GUI applications' use
 of dfonts on Mac OS X. (that
 unfortunately means the most common typefaces like Time and
 Helvetica!).

 While doing that, I found that the official
 R-3.1.*-mavericks.pkg are crippled, compared
 to R-3.1.*-snowleopard.pkg. They have tiff functionality
 missing. Here are the sizes of
 the official binaries':

...

 The next thing I am doing is building the replacement for
 the cairo.dll's in the offical R windows binaries.
 Just watch out in the next few days in the same directory.

 ---------- not R-devel related below this point ------

 I have finished with snpMatrix 1.19.0.20 5 days ago. Some of
 you may notice the documentations
 are already out - 19 months about 400 commit since
 1.19.0.19, it comes with a snpStats compatibility
 mode; when that mode is on, about 1/3 of its internals are
 swapped to their snpStats-equivalent
 versions. Initially synchronized to snpStats x.x.x.8 - and I
 already mentioned that it is because of another
 GLM related bug, found on top of x.x.x.7. Sigh.

 snpMatrix 1.19.0.20 and snpStats x.x.x.8 are now really just
 waiting for me to finish with the cairo
 stuff (for R 3.1.x). The impatient can just read the new
 vignettes.