Hi again,
My systems admin guy did come up with a fix after all:
setenv PATH /opt/gcc/bin:/usr/bin:/sbin:/usr/sbin:/usr/sfw/bin:/opt/
sfw/bin:/usr/xpg4/bin:/usr/ccs/bin:/usr/local/bin:/opt/torque/bin:/
home/mrg/bin
setenv LD_LIBRARY_PATH /home/mrg/apps/sparc-sun-solaris-2.10/lib:/usr/
sfw/lib:/opt/sfw/lib
unsetenv R_HOME
./configure R_PAPERSIZE='letter' --prefix='/home/btrask/traskdata'
make
(it doesn't work with the --enable-R-shlib option, but I can live
without that now)
Janet
On Nov 10, 2009, at 11:37 AM, Janet Young wrote:
Hi,
I'm having trouble compiling R-2.10.0 (R-patched_2009-11-02.tar.gz)
on solaris 10 and am hoping for some advice. I'm getting errors
about having the wrong version of lib_I_dbg_gen.so.1 ("version
`DBG_GEN_5.1' not found"), when it gets to the step of compiling
recommended packages (cluster).
I think we do have the right version of lib_I_dbg_gen.so.1 on the
system somewhere, but we also have older versions in other places. I
think it may be to do with our system having several versions of gcc
and lib_I_dbg_gen.so.1 in different places, including some old
versions, and me not managing to tell R where to find the right one
- perhaps some modifications to my setenv commands will fix this? I
also think we might have some non-standard library locations.
I'm not the sysadmin, and I'm a little out of my depth talking about
libraries etc. I asked our sysadmin for some advice, but for now we
are drawing a blank. If no-one has any ideas I may be able to ask
them to spend some more time trying to figure this out.
Here's what I'm doing to try to compile R: (my default path and
LD_LIBRARY_PATH have never worked for compiling R, hence the setenv
commands)
----------------------------
setenv LD_LIBRARY_PATH /opt/SUNW0scgfss/4.0.3/prod/lib:/opt/gcc/lib:/
opt/gcc/lib/gcc/sparc-sun-solaris2.10:/opt/SUNWspro/lib:/usr/lib:/
usr/openwin/lib
setenv PATH /opt/gcc/bin:/bin:/sbin:/usr/sbin:/etc:/opt/SUNWspro/
bin:/usr/ccs/bin:/usr/sfw/bin
unsetenv R_HOME
./configure --enable-R-shlib R_PAPERSIZE='letter' --prefix='/home/
btrask/traskdata'
make
----------------------------
Here's some information on compiler versions, etc, etc
----------------------------
[72] bedrock:/home/jayoung> uname -a
SunOS bedrock 5.10 Generic_139555-08 sun4v sparc SUNW,Sun-Fire-T200
[17] bedrock:/home/jayoung> which gcc
/opt/gcc/bin/gcc
[18] bedrock:/home/jayoung> gcc -v
Using built-in specs.
Target: sparc-sun-solaris2.10
Configured with: /net/tibia/export/bldmstr/nightly/
20060817_mars_gcc.s10.opt.tarbuild/src/configure --prefix=/opt/gcc --
enable-shared --with-system-zlib --enable-checking=release --disable-
libmudflap --enable-languages=c,c++ --enable-version-specific-
runtime-libs --with-gxx-include-dir=/opt/gcc/include/c++/4.0.3 --
with-cpu=v9
Thread model: posix
gcc version 4.0.3 (gccfss)
[21] bedrock:/home/jayoung> ldd /opt/gcc/libexec/gcc/sparc-sun-
solaris2.10/4.0.3/cc1
lib_I_dbg_gen.so.1 => /opt/SUNW0scgfss/4.0.3/prod/lib/
lib_I_dbg_gen.so.1
libsunir.so => /opt/gcc/bin/../../SUNW0scgfss/4.0.3/prod/
lib/sys/libsunir.so
libc.so.1 => /usr/lib/libc.so.1
libmd5.so.1 => /usr/lib/libmd5.so.1
libdl.so.1 => /usr/lib/libdl.so.1
libelf.so.1 => /usr/lib/libelf.so.1
liblni.so.1 => /opt/SUNW0scgfss/4.0.3/prod/lib/sys/
liblni.so.1
libm.so.2 => /usr/lib/libm.so.2
/platform/SUNW,Sun-Fire-T200/lib/libc_psr.so.1
libmd.so.1 => /usr/lib/libmd.so.1
/platform/SUNW,Sun-Fire-T200/lib/libmd_psr.so.1
[22] bedrock:/home/jayoung> version /opt/SUNW0scgfss/4.0.3/prod/lib/
lib_I_dbg_gen.so.1
version of "/opt/SUNW0scgfss/4.0.3/prod/lib/lib_I_dbg_gen.so.1": Sun
Debug Information DBG_GEN 5.1.17 gcc2ir_lang 2006/08/17
----------------------------
And here's the error I get during the make process:
begin installing recommended package cluster
* installing *source* package 'cluster' ...
** libs
gcc -std=gnu99 -I/home/jayoung/source_codes/R/R-2.10.0/solaris_6/R-
patched/include -I/usr/local/include -fPIC -g -O2 -c clara.c -o
clara.o
ld.so.1: cc1: fatal: lib_I_dbg_gen.so.1: version `DBG_GEN_5.1' not
found (required by file /opt/gcc/libexec/gcc/sparc-sun-
solaris2.10/4.0.3/cc1)
ld.so.1: cc1: fatal: lib_I_dbg_gen.so.1: open failed: No such file
or directory
gcc: Internal error: Killed (program cc1)
Please submit a full bug report to
<URL:http://forum.sun.com/jive/jorum.jspa?forumID=321>.
*** Error code 1
make: Fatal error: Command failed for target `clara.o'
Current working directory /tmp/RtmpJReZec/R.INSTALL2781446b/cluster/
src
ERROR: compilation failed for package 'cluster'
* removing '/home/jayoung/source_codes/R/R-2.10.0/solaris_6/R-
patched/library/cluster'
*** Error code 1
The following command caused the error:
MAKE="make" R_LIBS= ../../../bin/R CMD INSTALL --no-lock -l
"../../../library" cluster.tgz > cluster.ts.out 2>&1 || (cat
cluster.ts.out && exit 1)
make: Fatal error: Command failed for target `cluster.ts'
Current working directory /home/jayoung/source_codes/R/R-2.10.0/
solaris_6/R-patched/src/library/Recommended
*** Error code 1
The following command caused the error:
make stamp-recommended
make: Fatal error: Command failed for target `recommended-packages'
Current working directory /home/jayoung/source_codes/R/R-2.10.0/
solaris_6/R-patched/src/library/Recommended
*** Error code 1
The following command caused the error:
(cd src/library/Recommended && make)
make: Fatal error: Command failed for target `stamp-recommended'
-----------------------
On a suggestion from the sysadmin, I also tried doing the
compilation using a different LD_LIBRARY_PATH setting:
setenv LD_LIBRARY_PATH /opt/SUNWspro/prod/lib:/opt/SUNW0scgfss/4.0.3/
prod/lib:/opt/gcc/lib:/opt/gcc/lib/gcc/sparc-sun-solaris2.10:/opt/
SUNWspro/lib:/usr/lib:/usr/openwin/lib
With this setting, I get the same error (fatal: lib_I_dbg_gen.so.1:
version `DBG_GEN_5.1' not found (required by file /opt/gcc/libexec/
gcc/sparc-sun-solaris2.10/4.0.3/cc1) during the configure command,
instead of much later during the make of recommended packages. Here
is the relevant chunk of config.log:
configure:4685: checking for gcc
configure:4701: found /opt/gcc/bin/gcc
configure:4712: result: gcc
configure:4950: checking for C compiler version
configure:4957: gcc --version >&5
sparc-sun-solaris2.10-gcc (GCC) 4.0.3 (gccfss)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There
is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
configure:4960: $? = 0
configure:4967: gcc -v >&5
Using built-in specs.
Target: sparc-sun-solaris2.10
Configured with: /net/tibia/export/bldmstr/nightly/
20060817_mars_gcc.s10.opt.tarbuild/src/configure
--prefix=/opt/gcc --enable-shared --with-system-zlib --enable-
checking=release --disable-libmudfla
p --enable-languages=c,c++ --enable-version-specific-runtime-libs --
with-gxx-include-dir=/opt/gcc/i
nclude/c++/4.0.3 --with-cpu=v9
Thread model: posix
gcc version 4.0.3 (gccfss)
configure:4970: $? = 0
configure:4977: gcc -V >&5
gcc: '-V' option must have argument
configure:4980: $? = 1
configure:5003: checking for C compiler default output file name
configure:5030: gcc -I/usr/local/include -L/usr/local/lib
conftest.c >&5
ld.so.1: cc1: fatal: lib_I_dbg_gen.so.1: version `DBG_GEN_5.1' not
found (required by file /opt/gcc
/libexec/gcc/sparc-sun-solaris2.10/4.0.3/cc1)
ld.so.1: cc1: fatal: lib_I_dbg_gen.so.1: open failed: No such file
or directory
gcc: Internal error: Killed (program cc1)
Please submit a full bug report to
<URL:http://forum.sun.com/jive/jorum.jspa?forumID=321>.
configure:5033: $? = 1
-----------------------
This makes me think that when I use my first LD_LIBRARY_PATH setting
(with SUNW0scgfss first), configure manages to see the correct
version of lib_I_dbg_gen.so.1 but somehow when it gets to the make
for cluster package, it sees another, wrong version of
lib_I_dbg_gen.so.1. Does that make any sense? Is there a way to fix
it?
thanks in advance for any advice,
Janet Young
-------------------------------------------------------------------
Dr. Janet Young (Trask lab)
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168,
P.O. Box 19024, Seattle, WA 98109-1024, USA.
tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung ...at... fhcrc.org
http://www.fhcrc.org/labs/trask/
-------------------------------------------------------------------
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