[R] pnmath compilation failure; dylib issue?

[Eric Rupley]

(1) ...need to speed up a monte-carlo sampling...any suggestions about  
how I can get R to use all 8 cores of a mac pro would be most useful  
and very appreciated...

(2) spent the last few hours trying to get pnmath to compile under os- 
x 10.5.4...

using gcc version 4.2.1 (Apple Inc. build 5553) as downloaded from  
CRAN, xcode 3.0...

...xcode 3.1 installed over top of above after compilation  
failure...adverse effect, produced error on "-arch"

  any suggestion about how to get pnmath to compile would be most  
useful...I'm not sure it will even speed things up  but thought I  
would try...


pnmath failed:

...
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -dynamiclib -Wl,- 
headerpad_max_install_names -mmacosx-version-min=10.4 -undefined  
dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/ 
lib -o pnmath.so bd0.o beta.o chebyshev.o choose.o d1mach.o dbeta.o  
dbinom.o dcauchy.o dchisq.o dexp.o df.o dgamma.o dgeom.o dhyper.o  
dlnorm.o dlogis.o dnbeta.o dnbinom.o dnchisq.o dnf.o dnorm.o dnt.o  
dpois.o dt.o dunif.o dweibull.o fmax2.o fmin2.o ftrunc.o gamma.o  
gamma_cody.o i1mach.o imax2.o imin2.o lbeta.o lgamma.o lgammacor.o  
mlutils.o pbeta.o pbinom.o pcauchy.o pchisq.o pexp.o pf.o pgamma.o  
pgeom.o phyper.o plnorm.o plogis.o pnbeta.o pnbinom.o pnchisq.o pnf.o  
pnmath.o pnorm.o pnt.o polygamma.o ppois.o pt.o ptukey.o punif.o  
pweibull.o qbeta.o qbinom.o qcauchy.o qchisq.o qexp.o qf.o qgamma.o  
qgeom.o qhyper.o qlnorm.o qlogis.o qnbeta.o qnbinom.o qnchisq.o qnf.o  
qnorm.o qnt.o qpois.o qt.o qtukey.o qunif.o qweibull.o sign.o  
stirlerr.o toms708.o -lgomp  -F/Library/Frameworks/R.framework/.. - 
framework R -Wl,-framework -Wl,CoreFoundation
ld: warning, duplicate dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/local/ 
lib/libgcc_s.1.dylib
** arch - ppc
...
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -dynamiclib -Wl,- 
headerpad_max_install_names -mmacosx-version-min=10.4 -undefined  
dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/ 
lib -o pnmath.so bd0.o beta.o chebyshev.o choose.o d1mach.o dbeta.o  
dbinom.o dcauchy.o dchisq.o dexp.o df.o dgamma.o dgeom.o dhyper.o  
dlnorm.o dlogis.o dnbeta.o dnbinom.o dnchisq.o dnf.o dnorm.o dnt.o  
dpois.o dt.o dunif.o dweibull.o fmax2.o fmin2.o ftrunc.o gamma.o  
gamma_cody.o i1mach.o imax2.o imin2.o lbeta.o lgamma.o lgammacor.o  
mlutils.o pbeta.o pbinom.o pcauchy.o pchisq.o pexp.o pf.o pgamma.o  
pgeom.o phyper.o plnorm.o plogis.o pnbeta.o pnbinom.o pnchisq.o pnf.o  
pnmath.o pnorm.o pnt.o polygamma.o ppois.o pt.o ptukey.o punif.o  
pweibull.o qbeta.o qbinom.o qcauchy.o qchisq.o qexp.o qf.o qgamma.o  
qgeom.o qhyper.o qlnorm.o qlogis.o qnbeta.o qnbinom.o qnchisq.o qnf.o  
qnorm.o qnt.o qpois.o qt.o qtukey.o qunif.o qweibull.o sign.o  
stirlerr.o toms708.o -lgomp  -F/Library/Frameworks/R.framework/.. - 
framework R -Wl,-framework -Wl,CoreFoundation
ld: warning in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/ 
libgomp.dylib, file is not of required architecture
ld: warning, duplicate dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/local/ 
lib/libgcc_s.1.dylib
ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libstdc++. 
6.dylib, file is not of required architecture
collect2: ld returned 1 exit status
make: *** [pnmath.so] Error 1
chmod: /Library/Frameworks/R.framework/Resources/library/pnmath/libs/ 
ppc/*: No such file or directory
** Removing '/Library/Frameworks/R.framework/Resources/library/pnmath'
ERROR: compilation failed for package 'pnmath'
 >

pnmath0 failed with the same first error; the second error was:

...
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- 
version-min=10.4 -std=gnu99 -dynamiclib -Wl,- 
headerpad_max_install_names -mmacosx-version-min=10.4 -undefined  
dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/ 
lib -o pnmath0.so bd0.o beta.o chebyshev.o choose.o d1mach.o dbeta.o  
dbinom.o dcauchy.o dchisq.o dexp.o df.o dgamma.o dgeom.o dhyper.o  
dlnorm.o dlogis.o dnbeta.o dnbinom.o dnchisq.o dnf.o dnorm.o dnt.o  
dpois.o dt.o dunif.o dweibull.o fmax2.o fmin2.o ftrunc.o gamma.o  
gamma_cody.o i1mach.o imax2.o imin2.o lbeta.o lgamma.o lgammacor.o  
mlutils.o pbeta.o pbinom.o pcauchy.o pchisq.o pexp.o pf.o pgamma.o  
pgeom.o phyper.o plnorm.o plogis.o pnbeta.o pnbinom.o pnchisq.o pnf.o  
pnmath1.o pnorm.o pnt.o polygamma.o ppois.o pt.o ptukey.o punif.o  
pweibull.o qbeta.o qbinom.o qcauchy.o qchisq.o qexp.o qf.o qgamma.o  
qgeom.o qhyper.o qlnorm.o qlogis.o qnbeta.o qnbinom.o qnchisq.o qnf.o  
qnorm.o qnt.o qpois.o qt.o qtukey.o qunif.o qweibull.o sign.o  
stirlerr.o toms708.o workers1.o -lpthread  -F/Library/Frameworks/ 
R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning, duplicate dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/local/ 
lib/libgcc_s.1.dylib
ld: in /Developer/SDKs/MacOSX10.4u.sdk/usr/local/lib/libstdc++. 
6.dylib, file is not of required architecture
collect2: ld returned 1 exit status
make: *** [pnmath0.so] Error 1
** Removing '/Library/Frameworks/R.framework/Resources/library/pnmath0'
chmod: /Library/Frameworks/R.framework/Resources/library/pnmath0/libs/ 
ppc/*: No such file or directory
ERROR: compilation failed for package 'pnmath0'

--
  Eric Rupley
  University of Michigan, Museum of Anthropology
  1109 Geddes Ave, Rm. 4013
  Ann Arbor, MI 48109-1079

  erupley at umich.edu
  +1.734.276.8572