On Nov 8, 2007, at 2:22 AM, Prof Brian Ripley wrote: > I am not sure why Simon thought you should ask here
mainly because of the d-p-q-r-test - I was wondering whether it falls in the category of too strict tests or is a more serious issue. I can't look into it myself right now, so I was hoping someone might have an idea ... Thanks, Simon > (and not on R-sig-mac, > say): it is almost certain these are problems with your system not R. > For the first, use your debugger to find where the segfault > occurred (it > might be inadequate stack space). For the second, look at the > values of > dbeta(0, 0.9, 2.2, ncp = c(0, a)), and trace the C code to find out > why > you are not getting Inf (it is probably a broken libm function). > > I'd be worried about the first: the second is probably esoteric. > > On Wed, 7 Nov 2007, Steven McKinney wrote: > >> Hi all, >> >> I compiled 64-bit R on an Apple Mac G5 running OS X, but it failed >> make check. Simon Urbanek suggested I post results to R-devel. >> >>> On Nov 6, 2007, at 10:23 PM, Steven McKinney wrote: >>> >> >>>> Hi Simon, >>>> >>>> Would you be able to give more guidance on how to compile 64-bit >>>> libiconv for Tiger, >>> >>> You can get the sources from Apple and compile it: >>> http://www.opensource.apple.com/darwinsource/tarballs/other/ >>> libiconv-13.2.tar.gz >>> >>> If you want to save yourself the hassle, my 64-bit build can be >>> obtained and installed as follows: >>> curl -s http://r.research.att.com/libiconv-quad.tar.gz | \ >>> sudo tar fvxz - -C /usr/lib >> >> Many thanks to Simon Urbanek for providing a 64-bit libiconv for >> use on the Apple Mac OS X platform. This allowed compilation >> on the Mac without having to use the '--without-iconv' switch >> (for those of us who are not yet proficient at compiling 64-bit >> libraries on the Mac). >> >> Compilation of 64-bit R succeeded, but make check did not. >> >> First failure was in ok-errors.R, and generated this output >> in ok-errors.Rout.fail >> >>> ## bad infinite recursion / on.exit / ... interactions >>> bar <- function() 1+1 >>> foo <- function() { on.exit(bar()); foo() } >>> foo() # now simple "infinite recursion" >> >> *** caught segfault *** >> address 0x7fffeff7ffe30, cause 'memory not mapped' >> >> Traceback: >> 1: foo() >> 2: foo() >> 3: foo() >> ... >> 2154: foo() >> 2155: foo() >> 2156: foo() >> aborting ... >> >> Second error was in d-p-q-r-tests.Rout from this test: >> ## dbeta(*, ncp): >> a <- rlnorm(100) >> stopifnot(All.eq(a, dbeta(0, 1, a, ncp=0)), >> dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf >> ) >> ## the first gave 0, the 2nd NaN in R <= 2.3.0 >> >> and generated this >> output in d-p-q-r-tests.Rout.fail >> >>> >>> ## dbeta(*, ncp): >>> a <- rlnorm(100) >>> stopifnot(All.eq(a, dbeta(0, 1, a, ncp=0)), >> + dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf >> + ) >> Error: dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf is not all TRUE >> In addition: Warning message: >> In dnbeta(x, shape1, shape2, ncp, log) : NaNs produced >> Execution halted >> >> Everything else passed, so I'm not sure how serious these failures >> are. >> >> I'd appreciate any suggestions about how to figure out what caused >> these >> failures (an inappropriate file somewhere in the path, a possible >> bug, improper compilation commands etc.) >> >> >> version information of compiled R (compilation information at end): >> >> >>> sessionInfo() >> R version 2.6.0 Patched (2007-10-29 r43302) >> powerpc64-apple-darwin8.10.0 >> >> locale: >> C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] lme4_0.99875-8 Matrix_0.999375-3 lattice_0.17-2 >> >> loaded via a namespace (and not attached): >> [1] grid_2.6.0 rcompgen_0.1-17 >>> R.Version() >> $platform >> [1] "powerpc64-apple-darwin8.10.0" >> >> $arch >> [1] "powerpc64" >> >> $os >> [1] "darwin8.10.0" >> >> $system >> [1] "powerpc64, darwin8.10.0" >> >> $status >> [1] "Patched" >> >> $major >> [1] "2" >> >> $minor >> [1] "6.0" >> >> $year >> [1] "2007" >> >> $month >> [1] "10" >> >> $day >> [1] "29" >> >> $`svn rev` >> [1] "43302" >> >> $language >> [1] "R" >> >> $version.string >> [1] "R version 2.6.0 Patched (2007-10-29 r43302)" >> >>> .Platform >> $OS.type >> [1] "unix" >> >> $file.sep >> [1] "/" >> >> $dynlib.ext >> [1] ".so" >> >> $GUI >> [1] "X11" >> >> $endian >> [1] "big" >> >> $pkgType >> [1] "source" >> >> $path.sep >> [1] ":" >> >> $r_arch >> [1] "" >> >>> >> >> I built 64-bit R on Mac OS X 10.4.10 with these commands: >> >> export PATH='/usr/local/lib64/X11/bin:/usr/local/lib64/X11/etc:/ >> usr/local/lib64/X11/include:/usr/local/lib64/X11/lib:/usr/lib:/usr/ >> bin:/usr/local/sbin:/usr/local/bin:/bin:/usr/sbin:/sbin:/usr/local/ >> teTeX/bin/powerpc-apple-darwin-current:~/perl:~/bin' >> >> ./configure --host=powerpc64-apple-darwin8.10.0 --build=powerpc64- >> apple-darwin8.10.0 \ >> --prefix=/usr/local/lib64 'CC=gcc-4.0 -arch ppc64' 'CXX=g++ -arch >> ppc64' \ >> 'FC=gfortran-4.0 -arch ppc64' 'F77=gfortran-4.0 -arch ppc64' \ >> 'CFLAGS=-g -O3 -mtune=G5 -mcpu=G5' 'FFLAGS=-g -O3 -mtune=G5 - >> mcpu=G5' \ >> 'LDFLAGS=-arch ppc64 -m64 -L/usr/local/lib' 'CXXFLAGS=-g -O3 - >> mtune=G5 -mcpu=G5' \ >> 'FCFLAGS=-g -O3 -mtune=G5 -mcpu=G5' --disable-R-framework --enable- >> R-shlib \ >> '--with-blas=-framework vecLib' --with-lapack 1> >> configure.R.ppc64.out.20071107.Run01.txt 2>&1 >> >> sudo make 1> make.R.ppc64.out.20071107.Run01.txt 2>&1 >> >> sudo make check 1> make.check.R.ppc64.out.20071107.Run01.txt 2>&1 >> >> >> >> >> Steve McKinney >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > -- > Brian D. Ripley, [EMAIL PROTECTED] > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
