Hi There,
I am trying to install amberTools 1.4 in cygwin 1.7, and had below error:
********************************************************************************
make[2]: Entering directory
`/home/CEAM/amber11/AmberTools/src/gleap/leapsrc'
g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib
-I../plugins -I../freelib -I. -o strmain.o strmain.cpp
g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib
-I../plugins -I../freelib -I. -o strbuff.o strbuff.cpp
g++ -c -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib
-I../plugins -I../freelib -I. -o plugins.o plugins.cpp
g++ -static-libgcc -o sleap.exe strmain.o strbuff.o plugins.o
../freelib/readline/libreadline.a -lm ../plugins/libplugins.a
../mortsrc/libmort.a
mv sleap.exe /home/CEAM/amber11/bin
make[2]: Leaving directory `/home/CEAM/amber11/AmberTools/src/gleap/leapsrc'
make[1]: Leaving directory `/home/CEAM/amber11/AmberTools/src/gleap'
(cd cifparse && make install )
make[1]: Entering directory `/home/CEAM/amber11/AmberTools/src/cifparse'
flex -t cifparse.l | sed 's/yy/cifp/g' > lex.cif.c
*/home/CEAM/amber11/bin/yacc -v -d cifparse.y
/home/CEAM/amber11/bin/yacc: /home/CEAM/amber11/bin/yacc: cannot execute
binary file*
make[1]: Leaving directory `/home/CEAM/amber11/AmberTools/src/cifparse'
make[1]: *** [cifp.tab.c] Error 126
make[1]: Leaving directory `/home/CEAM/amber11/AmberTools/src/cifparse'
make: *** [serial] Error 2
********************************************************************************
After the install stopped, I manually ran the command:
*/home/CEAM/amber11/bin/yacc -v -d cifparse.y
*it gave the same error;*
*Then I ran:*
**/home/CEAM/amber11/bin/yacc.exe -v -d cifparse.y*
and there is no error report.
Also I found both *yacc* and *yacc.exe* in the bin folder.
So I thought it might be that the yacc file does not have the exec
permission,
so I ran:
*chmod a=rwx ~/amber11/bin/yacc*
and confirmed that the yacc file has the x permission with ls
but the red command still gave error
I tried another thing: go to the bin folder, and ran:
* yacc -v -d ~/amber11/AmberTools/src/cifparse/cifparse.y*
This time it gave no error...
So I do not understand why one work and another does not. Could you please
help me? Thanks.
I tried to link the yacc.exe to yacc with:
*ln -s yacc.exe yacc*
and it showed:
ln: creating symbolic link `yacc': File exists (it showed even I delete the
existing yacc file ...)
So I am stuck....
Any help is appreciated!
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Mon Jul 12 2010 - 23:00:03 PDT
