[Dock-fans] execl: permission denied

[Eric Pettersen]

Hi Teck,
	You need to point LIBDIR and BINDIR to directories that actually  
exist.  /usr/local does not exist by default on a Mac, much less /usr/ 
local/lib and /usr/local/bin.  Either you can create these  
directories or you can make some additional directories on your  
Desktop and point LIBDIR and BINDIR to those.  If you decide to  
create the /usr/local directories, you will probably have to have  
admin privileges to do so, and you would want to ensure that the  
directories were writable by you (e.g. "sudo chown -R tkmaan /usr/ 
local").

--Eric

On May 21, 2008, at 12:37 PM, Teck Maan wrote:

> 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
>>>
>>
>