From htl10 at users.sourceforge.net  Thu Dec 12 04:30:31 2013
From: htl10 at users.sourceforge.net (Hin-Tak Leung)
Date: Thu, 12 Dec 2013 03:30:31 +0000
Subject: [Rd] freetype 2.5.2, problem with the survival package,
 build R 2.15.x with gcc 4.8.x
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Here is a rather long discussion etc about freetype 2.5.2, problem with the 
survival package, and build R 2.15.x with gcc 4.8.x. Please feel free to skip 
forward.

- freetype 2.5.2:

the fix to cope with one of the Mac OS X's system fonts just before the release 
of freetype 2.5.1 caused a regression, crashing over one of Microsoft windows' 
system fonts. So there is a 2.5.2. There are new 2.5.2 bundles for windows & Mac 
OS X. The official win/mac binaries of R were built statically with 2+-years-old 
freetype with a few known problems. Most should upgrade/rebuild.

http://sourceforge.net/projects/outmodedbonsai/files/R/

- problem with the survival package:

Trying to re-run a vignette to get the same result as two years ago
reveal a strange change. I went and bisected it down to
r11513 and r11516 of the survival package.

-------------- r11513 --------------------
clogit(cc ~ addContr(A) + addContr(C) + addContr(A.C) + strata(set))


                    coef exp(coef) se(coef)     z      p
addContr(A)2     -0.620     0.538    0.217 -2.86 0.0043
addContr(C)2      0.482     1.620    0.217  2.22 0.0270
addContr(A.C)1-2 -0.778     0.459    0.275 -2.83 0.0047
addContr(A.C)2-1     NA        NA    0.000    NA     NA
addContr(A.C)2-2     NA        NA    0.000    NA     NA

Likelihood ratio test=26  on 3 df, p=9.49e-06  n= 13110, number of events= 3524
------------------------------------------

------------- r11516 ---------------------
clogit(cc ~ addContr(A) + addContr(C) + addContr(A.C) + strata(set))


                      coef exp(coef) se(coef)         z  p
addContr(A)2     -0.14250     0.867   110812 -1.29e-06  1
addContr(C)2      0.00525     1.005   110812  4.74e-08  1
addContr(A.C)1-2 -0.30097     0.740   110812 -2.72e-06  1
addContr(A.C)2-1 -0.47712     0.621   110812 -4.31e-06  1
addContr(A.C)2-2       NA        NA        0        NA NA

Likelihood ratio test=26  on 4 df, p=3.15e-05  n= 13110, number of events= 3524
------------------------------------------

r11514 does not build, and r11515 have serious memory hogs, so the survival
package broke somewhere between r11513 and r11516. Anyway, here is the diff in
the vignette, and the data, etc is in the directory above. If somebody want to
fix this before I spend any more time on this particular matter, please feel 
free to do so.

http://sourceforge.net/projects/outmodedbonsai/files/Manuals%2C%20Overviews%20and%20Slides%20for%20talks/2013SummerCourse/practicals/with-answers/practical8_survival-clogit-diff.pdf/download

That's the one problem from David's 10 practicals which are not due to bugs in 
snpStats. Some might find it reassuring that only 3 of the 4 problems with the 
practicals are due to snpStats bugs.

http://sourceforge.net/projects/outmodedbonsai/files/Manuals%2C%20Overviews%20and%20Slides%20for%20talks/2013SummerCourse/practicals/with-answers/practical7_snpStatsBug-diff.pdf/download
http://sourceforge.net/projects/outmodedbonsai/files/Manuals%2C%20Overviews%20and%20Slides%20for%20talks/2013SummerCourse/practicals/with-answers/practical6_snpStatsBug-diff.pdf/download
http://sourceforge.net/projects/outmodedbonsai/files/Manuals%2C%20Overviews%20and%20Slides%20for%20talks/2013SummerCourse/practicals/with-answers/practical3_snpStatsBug-diff.pdf/download

- build R 2.15.x with gcc 4.8.x

I wish the R commit log was a bit more detailed with r62430 than just
"tweak needed for gcc 4.8.x". Anyway, building R 2.15.x with gcc 4.8.x
could result in segfaults in usage as innocent and essential
as running summary() on a data.frame:

--------------------------------
  *** caught segfault ***
address 0x2f8e6a00, cause 'memory not mapped'

Traceback:
  1: sort.list(y)
  2: factor(a, exclude = exclude)
  3: table(object, exclude = NULL)
  4: summary.default(X[[3L]], ...)
  5: FUN(X[[3L]], ...)
  6: lapply(X = as.list(object), FUN = summary, maxsum = maxsum, digits = 12, 
   ...)
  7: summary.data.frame(support)
...
--------------------------------

r62430 needs a bit of adapting to apply to R 2.15.x , but you get the idea.
I hope this info is useful to somebody else who is still using R 2.15.x , no 
doubt for very good reasons.

Hin-Tak Leung wrote:
> The freetype people fixed the 2nd set of issues with system fonts shipped with
> Mac OS X, and released 2.5.1 almost immediately after that. So there are
> new bundles under http://sourceforge.net/projects/outmodedbonsai/files/R/ .
>
> Just a reminder that the official R binaries for windows/mac OS X are statically
> linked with rather dated versions of freetype with a few known issues. This
> affects the cairo-based functionalities in R. So a rebuild is needed.
>
> Most unix users should just upgrade their system's libfreetype, and
> dynamic-linking should take care of the rest.



[Rd] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x
Hin-Tak Leung