Hi,
I suspect that the issue here is the fact that for some reason you
have both yacc and yacc.exe. In cygwin, any binary you refer to will
get the .exe suffix automatically appended to it. So for example if I
type 'which ptraj' I get:
/home/droe/Amber/AmberTools-1.4/bin/ptraj
When in fact if you actually look at the directory in question there
is only ptraj.exe.
I assume you are using the Gnu compilers (4.3.4) that come with
cygwin. What options did you pass to the configure script? Also, have
you already looked at this page?
http://ambermd.org/mswindows.html
-Dan
On Tue, Jul 13, 2010 at 1:42 AM, Yan Gao <yan.gao.2001.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Tue Jul 13 2010 - 06:00:04 PDT
