[R] pnmath compilation failure; dylib issue?

[Luke Tierney]

On Wed, 20 Aug 2008, Eric Rupley wrote:

>
>
>
> (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...

Using something like the snow package for explicitly parallelizing
your computations may give you the greatest improvement.

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

Looking at the error messages it seems you have a ppc version of the
libgomp dylib but are trying to build for i386.  How this came about
or how to fix your setup I do not know -- you might get more help on
the R-SIG-Mac list.

luke

> 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
>
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> and provide commented, minimal, self-contained, reproducible code.

-- 
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:      luke at stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu