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Old 10-02-2010, 09:13 AM   #1
chiendarret
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Registered: Mar 2007
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/usr/bin/ld cannot find -lXext


While gcc compiling a complex program (AmberTools of Amber suite, a molecular dynamics package) on amd64:

./configure_at gcc
make -f Makefile_at

After a lot of compiled packages, I am getting the error

******************
make[3]: Entering directory `/usr/local/amber10/src/leap/src/leap'
gcc -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o tLeap.o -lm
gcc -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o xTank.o xAction.o x3d.o xBasics.o xaLeapc.o xaUnitEditor.o xaTable.o xaAtomTable.o XrawRegistr.o xaCommand.o xaTools.o xaAtomParmTable.o xaBondParmTable.o xaAngleParmTable.o xaParmEditor.o xaTorsionParmTable.o xaImproperParmTable.o xaHBondParmTable.o ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a ../Xmu/libXmu.a -L/usr/X11R6/lib64 -L/usr/X11R6/lib -lXt -lXext -lSM -lICE -lX11 -lXau -lXdmcp -lm -lpthread
/usr/bin/ld: cannot find -lXext
collect2: ld returned 1 exit status
make[3]: *** [xaLeap] Error 1
make[3]: Leaving directory `/usr/local/amber10/src/leap/src/leap'
make[2]: *** [install_xleap] Error 2
make[2]: Leaving directory `/usr/local/amber10/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/usr/local/amber10/src/leap'
make: *** [install] Error 2
tya64:/usr/local/amber10/src#
****************

Info:

francesco@tya64:~$ apt-file search libXext
ia32-libs: /emul/ia32-linux/usr/lib/libXext.so
ia32-libs: /emul/ia32-linux/usr/lib/libXext.so.6
ia32-libs: /emul/ia32-linux/usr/lib/libXext.so.6.4.0
libxext-dev: /usr/lib/libXext.a
libxext-dev: /usr/lib/libXext.so
libxext6: /usr/lib/libXext.so.6
libxext6: /usr/lib/libXext.so.6.4.0
libxext6-dbg: /usr/lib/debug/usr/lib/libXext.so.6.4.0
lsb-build-base3: /usr/lib/lsb3/libXext.so
francesco@tya64:~$

tya64:/home/francesco# ldconfig -v | grep "libXext"
libXext.so.6 -> libXext.so.6.4.0
libXext.so.6 -> libXext.so.6.4.0
tya64:/home/francesco#

I am confused how to turnaround the problem. Thanks for help.
 
Old 10-02-2010, 12:36 PM   #2
mf93
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Registered: Jun 2009
Distribution: Debian Squeeze, centOS
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try upgrading ld, if its the newest, try downgrading it---I read somewhere that this problem occurs after a certain version. I think also uninstalling it might work provided you run ./configure again after you uninstall
 
Old 10-03-2010, 05:29 AM   #3
chiendarret
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Registered: Mar 2007
Posts: 208

Original Poster
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I noticed in my i386 squueze (Debian) installation that ld is linked to ld.bfd. Here in amd64 there is only ld and package binutils does not contain ld.bfd (package is in order, though I also tried reinstall).

In my amd64 lenny installation "ld" is not linked. Neither ld.bfd nor ld.gold exist in /usr/bin.

In contrast, in my i386 squeeze installation, ld is linked to ld.bfd and also ld.gold exist.
Also:
francesco@deb32:~$ apt-file search ld.bfd
binutils: /usr/bin/ld.bfd
binutils: /usr/share/man/man1/ld.bfd.1.gz
hardening-wrapper: /usr/bin/ld.bfd
francesco@deb32:~$

In contrast:
francesco@tya64:~$ apt-file search ld.bfd
francesco@tya64:~$

Neither binutils, nor hardening-wrapper contain ld.bfd. in either i386 or amd64.

So, I am puzzled how to make the symlink. Thanks for suggestions

francesco
 
Old 10-03-2010, 09:33 AM   #4
chiendarret
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Registered: Mar 2007
Posts: 208

Original Poster
Rep: Reputation: 15
SOLVED /usr/bin/ld cannot find -lXext

Solved by

(1) Reinstalling the nvidia driver (I had underlying remains from a nvidia-type installation in my "Debian way install".Uninstalled the nvidia-way and reinstalled the "debian way install"

(2) Installing packages libext-dev libext6-dbg.
 
  


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