Re: [R] pnmath compilation failure; dylib issue?

Thu, 21 Aug 2008 09:39:08 -0700 

On Thu, 21 Aug 2008, Luke Tierney wrote:


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.


You could also try pnmath0, which doesn't use OpenMP and so doesn't
need libgomp.

luke



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

[EMAIL PROTECTED]
+1.734.276.8572

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--
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:      [EMAIL PROTECTED]
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

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