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. > > ______________________________________________ > r-h...@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
David Winsemius Alameda, CA, USA ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel