AMBER Archive (2006)

Subject: AMBER: Amber 9 Leap install error

From: A Box (boxtwin2_at_gmail.com)
Date: Sun Dec 17 2006 - 22:06:52 CST

I am trying to install Amber 9 on a 2.4 gig pentium running Fedora Coer 5
and using the intel fortran compiler (ia32). When I run the installation
command (make serial in /usr/local/amber9/src, or make in
/usr/local/amber9/src/leap/src/leap) i get the following erro to installing
leap:

/Xpm/libXpm.a ../Xmu/libXmu.a -L/usr/X11R6/lib -lXt -lXext -lSM -lICE -lX11
-lm -lpthread -ldl
gcc: ../Xraw/libXaw.a: No such file or directory
make: *** [xaLeap] Error 1

When i check, Xraw/libXaw.a does not exist, so i edited the Makefile, added
the -ldl tot the makefile and recompliled Leap. I still got the same error.

Any help would be greatly appreciated.

Andrew Box

The entire Leap install data is included below: when done from:
/usr/local/amber9/src/leap/src/leap.

Makefile:4: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o basics.o basics.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o sysdepend.o sysdepend.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o stringExtra.o stringExtra.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o varArray.o varArray.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o getline.o getline.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o avl.o avl.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o pdb_format.o pdb_format.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o pdb_read.o pdb_read.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o pdb_sprntf.o pdb_sprntf.c
pdb_sprntf.c: In function 'outstr':
pdb_sprntf.c:279: warning: incompatible implicit declaration of built-in
function 'strlen'
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o pdb_sscanf.o pdb_sscanf.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o pdb_write.o pdb_write.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o vector.o vector.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o zMatrix.o zMatrix.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o sort.o sort.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o bag.o bag.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o hash.o hash.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o dictionary.o dictionary.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o database.o database.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o nVector.o nVector.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o ring.o ring.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o matrix.o matrix.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o fortran.o fortran.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o displayer.o displayer.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o assoc.o assoc.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o atom.o atom.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o byteArray.o byteArray.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o collection.o collection.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o container.o container.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o internal.o internal.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o list.o list.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o loop.o loop.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o molecule.o molecule.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o oDouble.o oDouble.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o oInteger.o oInteger.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o oString.o oString.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o objekt.o objekt.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o parmSet.o parmSet.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o residue.o residue.c
residue.c: In function 'ResidueConnect':
residue.c:336: warning: passing argument 1 of 'AtomBondTo' from incompatible
pointer type
residue.c:336: warning: passing argument 2 of 'AtomBondTo' from incompatible
pointer type
residue.c: In function 'ResidueMutate':
residue.c:464: warning: passing argument 1 of 'BuildFixInternals' from
incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o unit.o unit.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o unitio.o unitio.c
unitio.c: In function 'zUnitIOSaveAmberParmFormat':
unitio.c:4047: warning: passing argument 1 of 'SortByInteger' from
incompatible pointer type
unitio.c:4047: warning: passing argument 4 of 'SortByInteger' from
incompatible pointer type
unitio.c: In function 'zUnitIOSaveAmberParmFormat_old':
unitio.c:6055: warning: passing argument 1 of 'SortByInteger' from
incompatible pointer type
unitio.c:6055: warning: passing argument 4 of 'SortByInteger' from
incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o tripos.o tripos.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o graphUtil.o graphUtil.c
graphUtil.c: In function 'GraphUtilFindAllSmallestRingsAndRingGroups':
graphUtil.c:675: warning: passing argument 1 of 'SortByInteger' from
incompatible pointer type
graphUtil.c:675: warning: passing argument 4 of 'SortByInteger' from
incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o select.o select.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o amber.o amber.c
amber.c: In function 'uAmberReadUnitFromPrep':
amber.c:986: warning: passing argument 1 of 'SortByInteger' from
incompatible pointer type
amber.c:986: warning: passing argument 4 of 'SortByInteger' from
incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o build.o build.c
build.c: In function 'bBuildFlipChiralityFor':
build.c:1901: warning: passing argument 1 of 'SortByInteger' from
incompatible pointer type
build.c:1901: warning: passing argument 4 of 'SortByInteger' from
incompatible pointer type
build.c:1907: warning: passing argument 1 of 'GraphUtilFindAllSmallestRings'
from incompatible pointer type
build.c: In function 'BuildInternalsForSimpleRings':
build.c:2185: warning: passing argument 1 of
'GraphUtilFindAllSmallestRingsAndRingGroups' from incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o elements.o elements.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o library.o library.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o chirality.o chirality.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o minimizer.o minimizer.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o model.o model.c
model.c: In function 'zModelOrderAtoms':
model.c:497: warning: passing argument 1 of 'Sift' from incompatible pointer
type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o parmLib.o parmLib.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o pdbFile.o pdbFile.c
pdbFile.c: In function 'zPdbBuildCoordinatesForContainer':
pdbFile.c:1088: warning: passing argument 1 of 'BuildFixInternals' from
incompatible pointer type
pdbFile.c: In function 'zPdbAddAtom':
pdbFile.c:1207: warning: passing argument 1 of 'BuildInternalsForContainer'
from incompatible pointer type
pdbFile.c: In function 'writeTER':
pdbFile.c:1761: warning: initialization from incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o tools.o tools.c
tools.c: In function 'iToolDistanceSearch':
tools.c:1643: warning: passing argument 1 of 'SortByDouble' from
incompatible pointer type
tools.c:1643: warning: passing argument 4 of 'SortByDouble' from
incompatible pointer type
tools.c: In function 'ToolOrientPrincipleAxisAlongCoordinateAxis':
tools.c:1714: warning: passing argument 2 of 'MathOpDiagonalize' from
incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o variables.o variables.c
yacc parser.y
yacc: 6 shift/reduce conflicts
(The warning 'conflicts: 6 shift/reduce' is normal)
/bin/rm parser.c
/bin/rm: cannot remove `parser.c': No such file or directory
make: [parser.c] Error 1 (ignored)
mv y.tab.c parser.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o parser.o parser.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o help.o help.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o utilMakeHelp.o utilMakeHelp.c
gcc -m32 -o utilMakeHelp 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 utilMakeHelp.o -lm
./utilMakeHelp helptext.text helptext.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o helptext.o helptext.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o octree.o octree.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o commands.o commands.c
commands.c: In function 'oCmd_impose':
commands.c:3835: warning: passing argument 1 of 'bBuildChangeInternalBond'
from incompatible pointer type
commands.c:3859: warning: passing argument 1 of 'bBuildChangeInternalAngle'
from incompatible pointer type
commands.c:3885: warning: passing argument 1 of
'bBuildChangeInternalTorsion' from incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o mathop.o mathop.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o block.o block.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o restraint.o restraint.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o hybrid.o hybrid.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o tLeap.o tLeap.c
gcc -m32 -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 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 -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xTank.o xTank.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xAction.o xAction.c
xAction.c: In function 'zActionTwistTorsions':
xAction.c:1112: warning: passing argument 1 of 'BuildRotateAroundBondFromTo'
from incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o x3d.o x3d.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xBasics.o xBasics.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaLeapc.o xaLeapc.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaUnitEditor.o xaUnitEditor.c
xaUnitEditor.c: In function 'XAUEAddHydrogensAndBuildExternals':
xaUnitEditor.c:888: warning: passing argument 1 of
'BuildInternalsForSimpleRings' from incompatible pointer type
xaUnitEditor.c: In function 'XAUESelectedAtomsFlipChirality':
xaUnitEditor.c:1335: warning: passing argument 1 of 'bBuildFlipChiralityFor'
from incompatible pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaTable.o xaTable.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaAtomTable.o xaAtomTable.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o XrawRegistr.o XrawRegistr.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaCommand.o xaCommand.c
xaCommand.c: In function 'xtcpXACInitializeDirectoryList':
xaCommand.c:840: warning: passing argument 4 of 'qsort' from incompatible
pointer type
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaTools.o xaTools.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaAtomParmTable.o xaAtomParmTable.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaBondParmTable.o xaBondParmTable.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaAngleParmTable.o xaAngleParmTable.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaParmEditor.o xaParmEditor.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaTorsionParmTable.o xaTorsionParmTable.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaImproperParmTable.o xaImproperParmTable.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o xaHBondParmTable.o xaHBondParmTable.c
gcc -m32 -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 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/lib -lXt -lXext -lSM -lICE -lX11 -lm -lpthread
-ldl
gcc: ../Xraw/libXaw.a: No such file or directory
make: *** [xaLeap] Error 1

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