[R] Problems Building R-2.3.1 on Alpha server ES40 running Tru64 V5.1B PK#5

[Prof Brian Ripley]

On Thu, 8 Jun 2006, Ravi, Narendra, INFOT wrote:

> R Listers,
>
> One of the list contributors suggested I abandon attempts to build
> R-1.9.1 and focus on building R-2.3.1. I believe the main set of
> packages have been built properly (with some changes to the code) -
> however, when building the Recommended packages, the build fails.
>
>
>
> CODE CHANGES:
> =============
>
> 1. My C compiler requires a ";" on line 589 of
> ..../src/main/printutils.c. Here is the diff:
> # diff src/main/printutils.c.orig src/main/printutils.c
> 589c589
> <  if (con_num>0) error("Internal error: this platform does not support
> split output")
> ---
>>  if (con_num>0) error("Internal error: this platform does not support
> split output");

That is already changed in R-devel and the most recent R-patched.  (Some 
platforms which do not have va_copy required more extensive changes.)

> Build Results:
> ==============
>
> The problem seems to be in building the Recommended packages. For MASS,
> The actual build seems to happen in /tmp, however, the next package
> expects the build somewhere else. Do I have to build the Recommended
> packages? If not, how do I avoid it? I suspect the unresolved symbols
> are OK, as they will get pulled in from shared libraries.

It looks like *warnings* are causing your linker to fail.  If so, you need 
to change the linker flags to allow this to complete.

You can configure and build without recommended packages, but likely the 
problem will arise when you try most additional packages.

>
> make[2]: Entering directory
> `/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/src/li
> brary/Recommended'
> begin installing recommended package VR
> * Installing *source* package 'MASS' ...
> ** libs
> make[3]: Entering directory
> `/cluster/members/member0/tmp/R.INSTALL.OVYGvZ/VR/MASS/src'
> cc
> -I/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/inclu
> de -I/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/buil
> d/include  -I/opt/gnu/include -I/opt/libjpeg/include
> -I/opt/libpng/include -I/opt/zlib/include -I/opt/ncurses/include
> -ieee_with_inexact    -st
> d1 -c MASS.c -o MASS.o
> cc
> -I/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/inclu
> de -I/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/buil
> d/include  -I/opt/gnu/include -I/opt/libjpeg/include
> -I/opt/libpng/include -I/opt/zlib/include -I/opt/ncurses/include
> -ieee_with_inexact    -st
> d1 -c lqs.c -o lqs.o
> cc -shared -L/opt/gnu/lib -L/opt/libjpeg/lib -L/opt/libpng/lib
> -L/opt/ncurses/lib -L/opt/zlib/lib -lncurses -ljpeg -lpng -lz -rpath
> /opt/libpng
> /lib:/opt/libjpeg/lib:/opt/ncurses/lib:/opt/gnu/lib:/usr/shlib:/opt/zlib
> /lib:/opt/R/lib -o MASS.so MASS.o lqs.o
> ld:
> Warning: Unresolved:
> exp
> fabs
> pow
> sqrt
> isnan
> Rf_error
> R_alloc
> Rprintf
> R_chk_calloc
> R_chk_free
> vmmin
> R_registerRoutines
> R_useDynamicSymbols
> log
> GetRNGstate
> PutRNGstate
> unif_rand
> R_rsort
> Rf_rPsort
> R_CheckUserInterrupt
> dqrsl_
> dqrdc2_
> make[3]: Leaving directory
> `/cluster/members/member0/tmp/R.INSTALL.OVYGvZ/VR/MASS/src'
> chmod: cannot access
> `/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/librar
> y/MASS/libs//*': No such file or directory
> ** R
> ** data
> chmod: cannot access
> `/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/librar
> y/MASS/data/*': No such file or directory
> **  moving datasets to lazyload DB
>
> *** caught segfault ***
> address 100000008, cause 'memory not mapped'
>
> Traceback:
> 1: print.default(f0)
> 2: print(f0)
> 3: tools:::data2LazyLoadDB("MASS",
> "/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/librar
> y")
> aborting ...
> /usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/bin/INS
> TALL: 367631 Memory fault - core dumped
> ERROR: lazydata failed for package 'MASS'
> ** Removing
> '/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/librar
> y/MASS'
> ** Removing
> '/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/librar
> y/class'
> ** Removing
> '/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/librar
> y/nnet'
> ** Removing
> '/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/librar
> y/spatial'
> make[2]: *** [VR.ts] Error 1
> make[2]: Leaving directory
> `/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/src/li
> brary/Recommended'
> make[1]: *** [recommended-packages] Error 2
> make[1]: Leaving directory
> `/usr/ruby-deploy/swkits/RUBY/SOFTWARE/3rdPartySW/R/R-2.3.1/build/src/li
> brary/Recommended'
> make: *** [stamp-recommended] Error 2
>
> Narendra Ravi
>
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>

-- 
Brian D. Ripley,                  ripley at 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