R devel - Jan 2015 - updated R-cairo bridge, official R-3.1.*-mavericks.pkg crippled, snpMatrix 1.19.0.20

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':

3918832
./R-3.1.2-snowleopard/R.framework/Versions/3.1/Resources/library/grDevices/libs/cairo.so
3778144
./R-3.0.3/R.framework/Versions/3.0/Resources/library/grDevices/libs/cairo.so
3170596
./R-3.1.2-mavericks/R.framework/Versions/3.1/Resources/library/grDevices/libs/cairo.so
3252656
./R-2.15.3/R.framework/Versions/2.15/Resources/library/grDevices/libs/i386/cairo.so
3539992
./R-2.15.3/R.framework/Versions/2.15/Resources/library/grDevices/libs/x86_64/cairo.so

"R-3.1.2-mavericks/R.framework/Versions/3.1/Resources/library/grDevices/libs/cairo.so"
is so much smaller,
not because it is built with a better and newer compiler, but because tiff
functionality is
missing.

The official R-3.1.*-mavericks.pkg is about 14MB smaller than
R-3.1.*-snowleopard.pkg (from 55MB-ish to 70MB-ish). Looking carefully, the size
differently did
not come from better compilation - it is in 3 unrelated areas, one of the
problematic:

- the snowleopard builds come the manuals in pdf's, mavericks don't.
That's about 14MB.
- a few bundled gcc runtime libraries (libgcc/libfortran...) are quad arch in
the former, and biarch in the latter.
  That's another 6 MB.
- the missing tiff functionality. That affects both R_X11.so and cairo.so, and
add up to about 1.5MB.

And the 18-20MB difference compress down to 14MB.

I don't know whether it actually offers any speed advantage, but I'd
probably suggest stay away from
the official mavericks builds, just because of missing functionality. It is
missing from all of R 3.1.0, 3.1.1, and 3.1.2.

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.