Re: [R] Difficulty with compiling R-2.4.1 on solaris 10

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Tue 30 Jan 2007 - 22:35:06 GMT

Andrew John Duba wrote:
> I am trying to compile R-2.4.1 in 64-bit on Solaris 10 running on AMD
> hardware. I am trying to do this with Sun Studio 11.
>
>
Oi!! We heard you the first three times. And you are still on the wrong list (this belongs on r-devel.)

Spamming the list will only annoy the people you are trying to get to help you....

Unfortunately, Solaris users are becoming scarce, and those with commercial compilers even more.
Some of the missing symbols, e.g. Rf_qt, are supposed to sit inside libnmath.a, so checking whether that looks OK (use the 'nm' command, I think) could be helpful.

> My config.site looks like this:
>
> #! /bin/sh
> AR="/usr/ccs/bin/ar"
>
> TEX="/usr/local/teTeX/bin/i386-pc-solaris2.10/tex"
> LATEX="/usr/local/teTeX/bin/i386-pc-solaris2.10/latex"
> PDFTEX="/usr/local/teTeX/bin/i386-pc-solaris2.10/pdftex"
> PDFLATEX="/usr/local/teTeX/bin/i386-pc-solaris2.10/pdflatex"
> DVIPS="/usr/local/teTeX/bin/i386-pc-solaris2.10/dvips"
> MAKEINFO="/usr/local/teTeX/bin/i386-pc-solaris2.10/makeinfo"
>
> UCOMPILER="-xarch=amd64"
> UFLAGS="-xO5 -xlibmil"
>
> CC="/opt/SUNWspro/bin/cc $UCOMPILER"
> CFLAGS="$UFLAGS -xc99=%all -xlibmieee"
> F77="/opt/SUNWspro/bin/f95 $UCOMPILER"
> FFLAGS="$UFLAGS -fsimple=0"
> CXX="/opt/SUNWspro/bin/CC $UCOMPILER"
> CXXFLAGS="$UFLAGS -xlibmieee"
> FC="/opt/SUNWspro/bin/f95 $UCOMPILER"
> FCFLAGS="$UFLAGS -fsimple=0 -xlang=c99"
> LD="/usr/ccs/bin/amd64/ld"
> LDFLAGS="-L/usr/local/lib/64 -L/usr/sfw/lib/64 -L/lib/amd64
> -R/usr/local/lib/64 -R/usr/sfw/lib/64 -R/lib/amd64"
>
> R_BROWSER="/usr/sfw/bin/mozilla"
>
> MAIN_LD="/opt/SUNWspro/bin/cc -xarch=amd64"
> LIBnn=amd64
>
>
> The ./configure runs without incident but make breaks down and the linker
> complains about undefined symbols. The symbols that the linker complains
> about are in Rmath.h. I have tried adding the folder with Rmath.h to the
> linkers path but that has not helped. Does anyone have any suggestions?
>
> If someone needs it below is an excript from the make session
>
> Thanks in advance for your help.
>
> /opt/SUNWspro/bin/f95 -xarch=amd64 -xO5 -xlibmil -fsimple=0 -c xxxpr.f
> -o xxxpr.o
> /opt/SUNWspro/bin/cc -xarch=amd64 -I../../src/extra/zlib
> -I../../src/extra/bzip2 -I../../src/extra/pcre -I. -I../../src/include
> -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H
> -D__NO_MATH_INLINES -xO5 -xlibmil -xc99=%all -xlibmieee -c mkdtemp.c -o
> mkdtemp.o
> /opt/SUNWspro/bin/cc -xarch=amd64 -L/usr/local/lib/64 -L/usr/sfw/lib/64
> -L/lib/amd64 -R/usr/local/lib/64 -R/usr/sfw/lib/64 -R/lib/amd64 -o R.bin
> Rmain.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o
> apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o
> character.o coerce.o colors.o complex.o connections.o context.o cov.o
> cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o
> dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o
> gevents.o gram.o gram-ex.o graphics.o identical.o internet.o iosupport.o
> lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o
> model.o names.o objects.o optim.o optimize.o options.o par.o paste.o
> pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o
> printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o
> rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o
> split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o
> sysutils.o unique.o util.o version.o vfonts.o xxxpr.o mkdtemp.o
> ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a -L../../lib
> -lRblas -R/usr/local/lib/64 -R/usr/sfw/lib/64 -R/lib/amd64
> -R/opt/SUNWspro/lib/amd64 -L/opt/SUNWspro/lib/amd64

> -L/opt/SUNWspro/prod/lib/amd64 -L/usr/lib/amd64 -lfui -lfai -lfsu
> -lsunmath -lmtsk -lm ../extra/zlib/libz.a ../extra/bzip2/libbz2.a
> ../extra/pcre/libpcre.a ../extra/intl/libintl.a -lreadline -ltermcap
> -lnsl -lsocket -ldl -lm
> Undefined first referenced
> symbol in file
> cg_ registration.o
> ch_ registration.o
> rg_ registration.o
> rs_ registration.o
> bincount registration.o
> inflate connections.o
> Rf_df arithmetic.o
> Rf_dt arithmetic.o
> Rf_pf arithmetic.o
> Rf_pt arithmetic.o
> Rf_qf arithmetic.o
> Rf_qt arithmetic.o
> Rf_rf random.o
> Rf_rt random.o
> chol_ registration.o
> gzeof connections.o
> do_syssleep names.o
> R_EditFiles platform.o
> R_getProcTime memory.o
> R_ExpandFileName Renviron.o
> R_OpenInitFile main.o
> R_getClockIncrement eval.o
> R_ReadConsole connections.o
> Rf_initialize_R Rmain.o
> call_dqags registration.o
> call_dqagi registration.o
> deflateEnd connections.o
> ptr_R_EditFile ../unix/libunix.a(edit.o)
> inflateEnd connections.o
> Rf_lchoose arithmetic.o
> R_ChooseFile platform.o
> lminfl_ registration.o
> deflateInit2_ connections.o
> N01_kind RNG.o
> do_machine names.o
> libintl_dcigettext ../extra/intl/libintl.a(dcgettext.o)
> R_max_col registration.o
> R_ClearerrConsole connections.o
> pcre_maketables character.o
> spline_eval registration.o
> spline_coef registration.o
> R_Busy main.o
> R_approx registration.o
> Rf_dnf arithmetic.o
> Rf_dnt arithmetic.o
> Rf_pnf arithmetic.o
> Rf_pnt arithmetic.o
> Rf_qnf arithmetic.o
> Rf_qnt arithmetic.o
> BZ2_bzRead connections.o
> Rf_choose arithmetic.o
> Brent_fmin optimize.o
> Rf_dbinom arithmetic.o
> Rf_dchisq arithmetic.o
> R_cumsum registration.o
> Rf_dgamma arithmetic.o
> Rf_dhyper arithmetic.o
> Rf_dlogis arithmetic.o
> Rf_dlnorm arithmetic.o
> Rf_dnbeta arithmetic.o
> Rf_dnorm4 arithmetic.o
> fft_factor fourier.o
> Rf_fround arithmetic.o
> Rf_ftrunc arithmetic.o
> libintl_gettextparse ../extra/intl/libintl.a(plural-exp.o)
> Rf_pbinom arithmetic.o
> Rf_pchisq arithmetic.o
> Rf_pgamma arithmetic.o
> Rf_phyper arithmetic.o
> Rf_plogis arithmetic.o
> Rf_plnorm arithmetic.o
> Rf_pnbeta arithmetic.o
> Rf_pnorm5 arithmetic.o
> Rf_qbinom arithmetic.o
> R_pretty registration.o
> R_cpolyroot complex.o
> Rf_qchisq arithmetic.o
> Rf_ptukey arithmetic.o
> Rf_qgamma arithmetic.o
> Rf_qhyper arithmetic.o
> Rf_qlogis arithmetic.o
> Rf_qlnorm arithmetic.o
> Rf_qnbeta arithmetic.o
> Rf_qnorm5 arithmetic.o
> bakslv registration.o
> Rf_rbinom random.o
> Rf_rchisq random.o
> Rf_qtukey arithmetic.o
> Rf_rgamma random.o
> Rf_rhyper random.o
> Rf_rlogis random.o
> Rf_rlnorm random.o
> R_rowsum registration.o
> str_signif registration.o
> Rf_pcauchy arithmetic.o
> dchdc_ registration.o
> do_system names.o
> dpbfa_ registration.o
> dpbsl_ registration.o
> dpoco_ registration.o
> dpodi_ registration.o
> dpofa_ registration.o
> dposl_ registration.o
> dqrdc_ registration.o
> dqrls_ registration.o
> dqrsl_ registration.o
> dsvdc_ registration.o
> dtrco_ registration.o
> dtrsl_ registration.o
> wilcox_free registration.o
> fdhess optimize.o
> R_ShowFiles platform.o
> gzgetc connections.o
> gzopen connections.o
> gzread connections.o
> gzseek connections.o
> gztell connections.o
> BZ2_bzReadOpen connections.o
> R_zeroin optimize.o
> ptr_R_savehistory ../unix/libunix.a(stubs.o)
> loglin registration.o
> lowess registration.o
> machar platform.o
> ptr_R_loadhistory ../unix/libunix.a(stubs.o)
> Rf_pnchisq arithmetic.o
> Rf_pnbinom arithmetic.o
> optif9 optimize.o
> rcont2 random.o
> R_pretty0 engine.o
> setulb optim.o
> Rf_qcauchy arithmetic.o
> UsingReadline platform.o
> Rf_pwilcox arithmetic.o
> find_interv_vec registration.o
> Rf_qnchisq arithmetic.o
> Rf_qnbinom arithmetic.o
> Rf_rcauchy random.o
> Rf_trigamma arithmetic.o
> massdist registration.o
> pcre_info pcre.o
> pcre_exec character.o
> Rf_beta arithmetic.o
> Rf_dexp arithmetic.o
> Rf_pexp arithmetic.o
> Rf_qexp arithmetic.o
> Rf_rexp random.o
> Rf_sign arithmetic.o
> libintl_nl_domain_bindings ../extra/intl/libintl.a(bindtextdom.o)
> libintl_nl_current_default_domain ../extra/intl/libintl.a(textdomain.o)
> Rf_qwilcox arithmetic.o
> libintl_nl_default_default_domain ../extra/intl/libintl.a(textdomain.o)
> BZ2_bzWriteOpen connections.o
> bincode registration.o
> R_CleanTempDir main.o
> do_proctime names.o
> norm_rand optim.o
> Rf_rnchisq random.o
> Rf_rnbinom random.o
> R_running_as_main_program Rmain.o
> Rf_psigamma arithmetic.o
> ch2inv_ registration.o
> BZ2_bzWrite connections.o
> inflateInit2_ connections.o
> Rf_rwilcox random.o
> R_CleanUp errors.o
> _nl_find_msg ../extra/intl/libintl.a(loadmsgcat.o)
> Rf_dsignrank arithmetic.o
> Rf_psignrank arithmetic.o
> Rf_rsignrank random.o
> Rf_qsignrank arithmetic.o
> Rf_dcauchy arithmetic.o
> deflate connections.o
> R_Suicide Renviron.o
> stemleaf registration.o
> Rf_digamma arithmetic.o
> do_sysinfo names.o
> Rf_dnchisq arithmetic.o
> Rf_dnbinom arithmetic.o
> pcre_study character.o
> R_ShowMessage CommandLineArgs.o
> dqrdc2_ registration.o
> ptr_R_addhistory ../unix/libunix.a(stubs.o)
> Rf_InitFunctionHashing Rdynload.o
> R_FlushConsole errors.o
> Rf_gamma_cody arithmetic.o
> Rf_dwilcox arithmetic.o
> deflateInit_ ../extra/zlib/libz.a(compress.o)
> rmultinom random.o
> Rf_dbeta arithmetic.o
> Rf_dgeom arithmetic.o
> Rf_dpois arithmetic.o
> Rf_dunif arithmetic.o
> Rf_fmin2 engine.o
> Rf_fmax2 engine.o
> Rf_fprec arithmetic.o
> Rf_fsign complex.o
> Rf_imin2 scan.o
> Rf_imax2 bind.o
> Rf_lbeta arithmetic.o
> Rf_pbeta arithmetic.o
> Rf_pgeom arithmetic.o
> Rf_ppois arithmetic.o
> Rf_qbeta arithmetic.o
> Rf_punif arithmetic.o
> Rf_qgeom arithmetic.o
> Rf_qpois arithmetic.o
> Rf_rbeta random.o
> Rf_qunif arithmetic.o
> Rf_rgeom random.o
> Rf_rnorm random.o
> Rf_rpois random.o
> Rf_runif random.o
> Rf_bessel_i arithmetic.o
> Rf_bessel_j arithmetic.o
> Rf_bessel_k arithmetic.o
> Rf_bessel_y arithmetic.o
> Rf_lgammafn arithmetic.o
> BM_norm_keep RNG.o
> Rf_gammafn arithmetic.o
> inflateInit_ ../extra/zlib/libz.a(uncompr.o)
> fft_work fourier.o
> Rf_pweibull arithmetic.o
> Rf_qweibull arithmetic.o
> Rf_rweibull random.o
> Rf_dweibull arithmetic.o
> libintl_nl_default_dirname ../extra/intl/libintl.a(bindtextdom.o)
> R_WriteConsole printutils.o
> R_ResetConsole errors.o
> BZ2_bzWriteClose connections.o
> gzclose connections.o
> signrank_free registration.o
> gzwrite connections.o
> pcre_compile character.o
> BZ2_bzReadClose connections.o
> ld: fatal: Symbol referencing errors. No output written to R.bin
> make[3]: *** [R.bin] Error 1
> make[3]: Leaving directory `/home/aduba/source/R-2.4.1/src/main'
> make[2]: *** [R] Error 2
> make[2]: Leaving directory `/home/aduba/source/R-2.4.1/src/main'
> make[1]: *** [R] Error 1
> make[1]: Leaving directory `/home/aduba/source/R-2.4.1/src'
> make: *** [R] Error 1
>
> ______________________________________________
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>



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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. Received on Wed Jan 31 09:42:32 2007

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