[BioC] [R] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x
David Winsemius
dwinsemius at comcast.net
Fri Dec 13 17:29:41 CET 2013
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.
First: Sorry for the blank message. Need more coffee.
Second: Does this mean that only Mac users who are still using 2.15.x need to worry about this issue?
Third: I'm reading this (and Terry's comment about singularity conditions) to mean that a numerical discrepancy between vignette output when code was run being from what was expected was causing a segfault under some situation that I cannot quite reconstruct. Was the implication that Mac users (of 2.15.x) need to build from sources only if they wanted to build the survival package from source? Does this have any implications for those of us who use the survival package as the binary? (And I'm using 3.0.2, so a split answer might be needed to cover 2.15.x and the current versions separately)
--
David.
>
> 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
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