[BioC] [R] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x

[David Winsemius]

On Dec 11, 2013, at 7:30 PM, Hin-Tak Leung wrote:

> 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.
> 
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David Winsemius
Alameda, CA, USA