Re: [Rd] Install R-patched_2006-07-13 on i386-pc-solaris2.10 with Sun Studio 11

From: Latchezar Dimitrov <ldimitro_at_wfubmc.edu>
Date: Wed 26 Jul 2006 - 20:48:17 GMT


Dear Prof. Ripley and R-developers:

Thank you very much for the reply. Please see bellow

> -----Original Message-----
> From: Prof Brian Ripley [mailto:ripley@stats.ox.ac.uk]
> Sent: Wednesday, July 26, 2006 2:37 AM
> To: Latchezar Dimitrov
> Cc: r-devel@stat.math.ethz.ch
> Subject: Re: [Rd] Install R-patched_2006-07-13 on
> i386-pc-solaris2.10 with Sun Studio 11
>
> On Wed, 26 Jul 2006, Latchezar Dimitrov wrote:
>
> > Dear R-developers:
> >
> > I'm trying to build a 64-bit R-patched_2006-07-24 on
> SunFire V40z with
> > on Solaris OS 10 64-bit kernel and using Sun Studio 11 compilers.
> > Everything runs OK until it gets to building package tools (all.R)
> > where it fails. Bellow is how I tried it (I can provide any other
> > additional info if needed). Any help please?
>
> You seem to have gcc 4.1.1 in your paths, so can you try that instead.

True (that's why I gave the env) however that is c/c++ only. I cannot build gcc fortran right way and since R is on top of my list I switched to Sun Studio 11. I included the libraries and the path in order to use makeinfo and readline which I compiled with that gcc (I build most essential gnu utils with it too as well as some applications and everything seems ok). To avoid misuse of it I explicitly specified all the programs that I knew could be mistaken (CC,CXX,etc), gnu ld was renamed. I as sure as one can that there was not any (mis)use of /usr/local/ except for readline and makeinfo (I believe the build did not go that far though). One additional thing that I missed in my prev. e-mail is that R binary was build seemingly properly, i.e., it starts ok however with complaints about missing base parts (obviously).

Now to make it clear it has nothing to do with that gcc I removed all the paths from the environment and to make sure nothing leaks through I renamed /usr/local so it stays out of the way. Then I set --with-readline=no and started clean (as you may have already noticed I build in a separate from src dir (obj-R) completely empty at the beginning. It failed the very same way.

Further, I decided to give 32-bit build a try. To make things more interesting I restore /usr/local and the path to /usr/local/bin in order to be able to use makeinfo (since the only readline I had was a 64-bit one I gave it up). And voila, it built like a charm. The only tests that I noticed failed were those involving tcltk (I had only 64-bit ones installed).

The only problem still remaining is I cannot care less about 32-bit version.

Please find attached the log of 64-bit try and a little bit of 32 success in the end.

So would someone please help me find out what is wrong and build my favorite 64-bit R?

Thank you very much,
Latchezar Dimitrov

>
> This looks like a fairly fundamental problem with your
> current build, possibly a mis-compile.
>
> >
> > Thank you very much
> >
> > Latchezar Dimitrov
> > Wake Forest Univ. School of Medicine
> >
> >
> >
> > root@Huba # echo $PATH
> >
> /opt/SUNWspro/bin:/usr/sbin:/usr/bin:/usr/openwin/bin:/usr/ccs/bin:/us
> > r/
> >
> openwin/bin:/usr/dt/bin:/usr/platform/i86pc/sbin:/opt/SUNWvts/bin:/opt
> > /S
> > UNWexplo/bin:/usr/local/bin
> > root@Huba # echo $CC
> > cc
> > root@Huba # echo $CXX
> > CC
> > root@Huba # echo $CFLAGS
> > -xarch=amd64 -xmodel=medium
> > root@Huba # echo $CXXFLAGS
> > -xarch=amd64 -xmodel=medium
> > root@Huba # echo $FCFLAGS
> > -xarch=amd64 -xmodel=medium
> > root@Huba # echo $FFLAGS
> > -xarch=amd64 -xmodel=medium
> > root@Huba # echo $LDFLAGS
> > -xarch=amd64 -xmodel=medium
> > root@Huba # echo $R_BROWSER
> > /usr/sfw/bin/mozilla
> > root@Huba # echo $r_arch
> > amd64
> > root@Huba # echo $LD_LIBRARY_PATH
> >
> /usr/openwin/lib:/usr/local/gcc-4.1.1-x86-bootstrap/lib/gcc/i386-pc-so
> > la
> >
> ris2.10/4.1.1/amd64:/usr/local/lib:/usr/local/gcc-4.1.1-x86-bootstrap/
> > li
> >
> b/gcc/i386-pc-solaris2.10/4.1.1/amd64:/usr/local/lib:/usr/loca
> l/gcc-4.1.
> >
> 1-x86-bootstrap/lib/gcc/i386-pc-solaris2.10/4.1.1/amd64:/usr/local/lib
> > root@Huba #
> >
> >
> > ../src/R-patched_2006-07-24/configure
> > --prefix=/opt/R-2.3.1-patched_2006-07-24-Sun_Studio_11
> --with-readline
> > --disable-mbcs R_PAPERSIZE=letter --disable-rpath --with-bzlib
> > --with-zlib --with-spcre --with-tcltk --disable-R-profiling
> > --disable-nls
> >
> >
> >
> > Error in parseNamespaceFile(package, package.lib, mustExist
> = FALSE) :
> > subscript out of bounds
> > Execution halted
> > *** Error code 1
> > The following command caused the error:
> > (cat
> >
> ../../../../src/R-patched_2006-07-24/src/library/tools/R/makeLazyLoad.
> > R;
> > \
> > echo "makeLazyLoading(\"tools\")") | \
> > R_DEFAULT_PACKAGES=NULL LC_COLLATE=C ../../../bin/R --vanilla
> > --slave
> > > /dev/null
> > dmake: Fatal error: Command failed for target `all'
> > Current working directory /export/data/obj-R/src/library/tools
> > *** Error code 1
> > The following command caused the error:
> > for pkg in profile base tools utils grDevices graphics
> stats datasets
> > methods grid splines stats4 tcltk; do \
> > (cd ${pkg} && dmake) || exit 1; \
> > done
> > dmake: Fatal error: Command failed for target `R'
> > Current working directory /export/data/obj-R/src/library
> > *** Error code 1
> > The following command caused the error:
> > for d in scripts include extra appl nmath unix main modules
> library;
> > do \
> > (cd ${d} && dmake R) || exit 1; \
> > done
> > dmake: Fatal error: Command failed for target `R'
> > Current working directory /export/data/obj-R/src
> > *** Error code 1
> > The following command caused the error:
> > for d in m4 tools doc etc share src tests; do \
> > (cd ${d} && dmake R) || exit 1; \
> > done
> > dmake: Fatal error: Command failed for target `R'
> > root@Huba #
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>
> --
> Brian D. Ripley, ripley@stats.ox.ac.uk
> 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
>



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