thr3ads.net - R help - [R] Problems Building R-2.3.1 on Alpha server ES40 running Tru64 V5.1B PK#5 [Jun 2006]

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Ravi, Narendra, INFOT

2006-Jun-08 11:59 UTC

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

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
supportsplit output");


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.


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

Prof Brian Ripley

2006-Jun-08 13:13 UTC

head link

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

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
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
-- 
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

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