[Dock-fans] DMS installation issues

Sebastian Fica smfica at uchicago.edu
Sat Dec 6 05:14:18 PST 2008


Hi,

I tried to install dms using Terminal on Mac Leopard and I ge the  
following message:

cd libpdb ; make OPT="-O"
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
cc -DDESTLIB=\"/users/sebastianfica/lib/dms/\" -DSERVER_PATH=\"/users/ 
sebastianfica/lib/dms/dmsd\" -Ilibpdb -O   -c -o compute.o compute.c
compute.c: In function ‘read_radii’:
compute.c:343: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c: In function ‘assign_radius’:
compute.c:393: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c: In function ‘start_servers’:
compute.c:474: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c:478: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c:489: warning: incompatible implicit declaration of built-in  
function ‘execl’
compute.c:491: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c:499: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c:514: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c: In function ‘get_server’:
compute.c:666: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c:680: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c:703: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c: In function ‘neighbors’:
compute.c:1071: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c: In function ‘probes’:
compute.c:1149: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c: In function ‘contact_surface’:
compute.c:1240: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c: In function ‘torus_surface’:
compute.c:1264: warning: incompatible implicit declaration of built-in  
function ‘exit’
compute.c: In function ‘probe_surface’:
compute.c:1289: warning: incompatible implicit declaration of built-in  
function ‘exit’
cc -DDESTLIB=\"/users/sebastianfica/lib/dms/\" -DSERVER_PATH=\"/users/ 
sebastianfica/lib/dms/dmsd\" -Ilibpdb -O   -c -o fwritev.o fwritev.c
cc -DDESTLIB=\"/users/sebastianfica/lib/dms/\" -DSERVER_PATH=\"/users/ 
sebastianfica/lib/dms/dmsd\" -Ilibpdb -O   -c -o input.o input.c
input.c: In function ‘read_pdb’:
input.c:151: warning: incompatible implicit declaration of built-in  
function ‘exit’
input.c: In function ‘read_wanted’:
input.c:270: warning: incompatible implicit declaration of built-in  
function ‘exit’
input.c:278: warning: incompatible implicit declaration of built-in  
function ‘exit’
input.c:297: warning: incompatible implicit declaration of built-in  
function ‘exit’
input.c:301: warning: incompatible implicit declaration of built-in  
function ‘exit’
input.c:306: warning: incompatible implicit declaration of built-in  
function ‘exit’
input.c:313: warning: incompatible implicit declaration of built-in  
function ‘exit’
cc -DDESTLIB=\"/users/sebastianfica/lib/dms/\" -DSERVER_PATH=\"/users/ 
sebastianfica/lib/dms/dmsd\" -Ilibpdb -O   -c -o ms.o ms.c
ms.c: In function ‘main’:
ms.c:106: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:123: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:130: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:138: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:150: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:159: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:172: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:184: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:208: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:229: warning: incompatible implicit declaration of built-in  
function ‘exit’
ms.c:248: warning: incompatible implicit declaration of built-in  
function ‘exit’
cc -DDESTLIB=\"/users/sebastianfica/lib/dms/\" -DSERVER_PATH=\"/users/ 
sebastianfica/lib/dms/dmsd\" -Ilibpdb -O   -c -o output.o output.c
cc -DDESTLIB=\"/users/sebastianfica/lib/dms/\" -DSERVER_PATH=\"/users/ 
sebastianfica/lib/dms/dmsd\" -Ilibpdb -O   -c -o emalloc.o emalloc.c
cc -DDESTLIB=\"/users/sebastianfica/lib/dms/\" -DSERVER_PATH=\"/users/ 
sebastianfica/lib/dms/dmsd\" -Ilibpdb -O   -c -o tokenize.o tokenize.c
tokenize.c: In function ‘tokenize’:
tokenize.c:58: warning: incompatible implicit declaration of built-in  
function ‘strcpy’
tokenize.c:95: warning: incompatible implicit declaration of built-in  
function ‘strcpy’
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: /usr/local/man/man1: No such file or directory
make: *** [maninstall] Error 1

I then corrected the man directory error and used make install again  
and got this message:

nsit-dhcp-205-208-124-215:dms sebastianfica$ make install
cd libpdb ; make OPT="-O"
make[1]: Nothing to be done for `all'.
cc -Llibpdb -o dms compute.o fwritev.o input.o ms.o output.o emalloc.o  
tokenize.o -lpdb
rm -f /users/sebastianfica/man/man1/dms.1
cp dms.1 /users/sebastianfica/man/man1
if [ -d /users/sebastianfica/lib/dms/ ]; then true ; else mkdir /users/ 
sebastianfica/lib/dms/; fi
cd dmsd ; make LIBDIR=/users/sebastianfica/lib install
cc -I.. -DDESTLIB=\"/users/sebastianfica/lib/dms\" -g   -c -o server.o  
server.c
server.c: In function ‘main’:
server.c:104: warning: incompatible implicit declaration of built-in  
function ‘exit’
server.c:134: warning: incompatible implicit declaration of built-in  
function ‘exit’
cc -I.. -DDESTLIB=\"/users/sebastianfica/lib/dms\" -g   -c -o viewat.o  
viewat.c
cc -I.. -DDESTLIB=\"/users/sebastianfica/lib/dms\" -g   -c -o lookat.o  
lookat.c
cc -I.. -DDESTLIB=\"/users/sebastianfica/lib/dms\" -g   -c -o freadv.o  
freadv.c
cc -I.. -DDESTLIB=\"/users/sebastianfica/lib/dms\" -g   -c -o  
emalloc.o emalloc.c
cc -o dmsd server.o viewat.o lookat.o freadv.o emalloc.o -lm
mkdir /users/sebastianfica/lib/dms
mkdir: /users/sebastianfica/lib/dms: File exists
make[1]: [beforeinstall] Error 1 (ignored)
cp dmsd /users/sebastianfica/lib/dms
strip /users/sebastianfica/lib/dms/dmsd
cp ../dms_servers.proto /users/sebastianfica/lib/dms/dms_servers.proto
cp dms /users/sebastianfica/bin
strip /users/sebastianfica/bin/dms
cp radii.proto /users/sebastianfica/lib/dms/radii

Then, when I tried to run dms, I always get command not found.

Does anyone have any idea on how to fix this?

Thanks,
Sebastian

Sebastian M. Fica
Graduate Student, Staley Laboratory
Department of Molecular Genetics and Cell Biology
The University of Chicago
920 E. 58th St., Chicago, IL 60637
Lab Phone: 773-834-5885











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