[Dock-fans] execl: permission denied

[Teck Maan]

Hi Eric,
I decided to redo the installation again. So i unpack dms into my
desktop (home/Desktop/dms) and went from there. i did a shar then make
install. The GNUmakefile has LIBDIR  = /usr/local/lib and BINDIR
= /usr/local/bin. The following is what i have.

cd libpdb ; make OPT="-O"
make[1]: Entering directory `/home/tkmaan/Desktop/dms/libpdb'
cc -O    -c -o pdb_read.o pdb_read.c
cc -O    -c -o pdb_sprntf.o pdb_sprntf.c
cc -O    -c -o pdb_sscanf.o pdb_sscanf.c
cc -O    -c -o pdb_write.o pdb_write.c
cc -O    -c -o pdbrun.o pdbrun.c
cc -O    -c -o ms.o ms.c
ar cru libpdb.a pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
pdbrun.o ms.o
ranlib libpdb.a
make[1]: Leaving directory `/home/tkmaan/Desktop/dms/libpdb'
cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
\"/usr/local/lib/dms/dmsd\" -Ilibpdb -O   -c -o compute.o compute.c
cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
\"/usr/local/lib/dms/dmsd\" -Ilibpdb -O   -c -o fwritev.o fwritev.c
cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
\"/usr/local/lib/dms/dmsd\" -Ilibpdb -O   -c -o input.o input.c
cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
\"/usr/local/lib/dms/dmsd\" -Ilibpdb -O   -c -o ms.o ms.c
cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
\"/usr/local/lib/dms/dmsd\" -Ilibpdb -O   -c -o output.o output.c
cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
\"/usr/local/lib/dms/dmsd\" -Ilibpdb -O   -c -o emalloc.o emalloc.c
cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
\"/usr/local/lib/dms/dmsd\" -Ilibpdb -O   -c -o tokenize.o tokenize.c
cc -Llibpdb -o dms compute.o fwritev.o input.o ms.o output.o emalloc.o
tokenize.o -lpdb
rm -f /usr/local/man/man1/dms.1
cp dms.1 /usr/local/man/man1
cp: cannot create regular file `/usr/local/man/man1': No such file or
directory
make: *** [maninstall] Error 1

I have no idea why it cannot create /usr/local/man/man1.  So i compile
the rec_noH.pdb

[tkmaan at roam98-105 dms]$ ./dms rec_noH.pdb -n -w 1.4 -v -o rec.ms
2317 atoms
/usr/local/lib/dms/radii: No such file or directory

So i delete the "proto" in the radii.proto (in home/Desktop/dms) and
compile again.

[tkmaan at roam98-105 dms]$ ./dms rec_noH.pdb -n -w 1.4 -v -o rec.ms
2317 atoms
        S       11
        O       444
        N       389
        C       1473
execl: No such file or directory

and i got no such file or directory error instead of permission denied.
few things i do not get it is that, i unpack my shar files in my
home/Desktop/dms directory, and do a "make install". I
checked /usr/local/lib/ and usr/local/bin directory, i do not see any
file being created. In fact, files are compiled and put into my
home/Desktop/dms directory. I believe this usr/local/lib and
usr/local/bin must be pointing to the same directory. So i am just
wondering now how do to fix this "no such file or directory" error.
Thanks.

Teck Maan



On Wed, 2008-05-21 at 11:23 -0700, Eric Pettersen wrote:
> Hi Teck,
> 	You've duplicated the error described in this message:
> 
> http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2007-February/ 
> 000920.html
> 
> Basically, you can't edit the GNUmakefile to have the LIBDIR/BINDIR  
> variables point to the same place where the source is.  You need to  
> edit the GNUmakefile, change those variables, and recompile.
> 
> --Eric
> 
> On May 21, 2008, at 11:13 AM, Teck Maan wrote:
> 
> > Hi Eric,
> > I checked my dmsd folder. It is there. It contains 7 items.
> > 1. emalloc.c
> > 2. freadv.c
> > 3.GNUmakefile
> > 4. lookat.c
> > 5. server.c
> > 6. test.pdb
> > 7. viewat.c
> >
> > and the folder  /home/tkmaan/Desktop/dms, does exist. and i execute  
> > the
> > dms program using the following command: ./dms rec_noH.pdb -n -w  
> > 1.4 -v
> > -o rec.ms.  i am just stucked at execl line where the permission is
> > denied. I tried su, same error. Any thought?
> >
> > Teck Maan
> > On Tue, 2008-05-20 at 16:32 -0700, Eric Pettersen wrote:
> >>> cc -DDESTLIB=\"/home/tkmaan/Desktop/dms/\" -DSERVER_PATH=
> >>> \"/home/tkmaan/Desktop/dms/dmsd\" -Ilibpdb -O   -c -o tokenize.o
> >>> tokenize.c
> >>> cc -Llibpdb -o dms compute.o fwritev.o input.o ms.o output.o
> >>> emalloc.o
> >>> tokenize.o -lpdb
> >>> rm -f /home/tkmaan/Desktop/man/man1/dms.1
> >>> cp dms.1 /home/tkmaan/Desktop/man/man1
> >>> cp: cannot create regular file `/home/tkmaan/Desktop/man/man1': No
> >>> such
> >>> file or directory
> >>> make: *** [maninstall] Error 1
> >>> [root at localhost dms]# ./dms rec_noH.pdb -n -w 1.4 -v -o rec.ms
> >>> 2317 atoms
> >>>         S       11
> >>>         O       444
> >>>         N       389
> >>>         C       1473
> >>> execl: Permission denied
> >>
> >> Hi Teck,
> >> The error indicates that /home/tkmaan/Desktop/dms/dmsd cannot be
> >> executed.  Check that the folder /home/tkmaan/Desktop/dms exists.
> >>  Check that the file dmsd exists in that folder.  Check that the file
> >> is executable.
> >>
> >>
> >> --Eric
> >>
> >>
> >>                         Eric Pettersen
> >>
> >>                         UCSF Computer Graphics Lab
> >>
> >>                         http://www.cgl.ucsf.edu
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> Dock-fans mailing list
> >> Dock-fans at docking.org
> >> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
>