[Rd] compiling R-2.10.0 on solaris - lib_I_dbg_gen.so.1: version `DBG_GEN_5.1' not found

From: Janet Young <jayoung_at_fhcrc.org>
Date: Tue, 10 Nov 2009 11:37:38 -0800


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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