Janet Young
2009-Nov-10 19:37 UTC
[Rd] compiling R-2.10.0 on solaris - lib_I_dbg_gen.so.1: version `DBG_GEN_5.1' not found
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/
Janet Young
2009-Nov-13 01:19 UTC
[Rd] compiling R-2.10.0 on solaris - lib_I_dbg_gen.so.1: version `DBG_GEN_5.1' not found
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/ > > ------------------------------------------------------------------- > > > > > >