[Dock-fans] Problem installing dock6.7 in mac

Debajyoti Dutta debajyoti_dutta47 at rediffmail.com
Fri Apr 17 13:55:47 PDT 2015



On Sat, 18 Apr 2015 02:00:56 +0530 Scott Brozell  wrote
>Hi,



What you show below does not indicate any problem.

Thus, i conclude that some critical parts of the outputs are missing;

please resend following the verbose and verbatim motto;

below i underscore where critical parts appear to be missing.

Hi Scott,

Thanks for the mail.


the lien you mentioned is not coming when i wanted to see the ver I am resending it ..


biochem30-198:install debajyoti$ gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.3.0
Thread model: posix
biochem30-198:install debajyoti$ 

Please let me know if anything

best

debajyoti









For general reference on Mac's see

http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#macosx





On Fri, Apr 17, 2015 at 05:08:15PM -0000, Debajyoti Dutta wrote:

> I am trying to install dock6 in mac which has "OS X Yosemite of version 10.10.3"

> an i updated the gcc using brew although it shows if I give the command "gcc -v"

> 

> biochem30-198:~ debajyoti$ gcc -v

> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1

> Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn)

> Target: x86_64-apple-darwin14.3.0

> Thread model: posix

> 



There should be a final line showing the gcc version, eg,

...

Thread model: posix

gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) 





> Then tried to build dock 6.7

> 

> 

> biochem30-198:install debajyoti$ ./configure gnu

> The requested configuration file was found.

> The DOCK configuration file has been created.

> 

> biochem30-198:install debajyoti$ make install

> Starting installation of 

> DOCK v6.7

> at Fri Apr 17 10:57:07 MDT 2015.

> 

> cd ../src && make install

> cd dock && make install

> g++ -c -O2 -o amber_typer.o amber_typer.cpp

> amber_typer.cpp:88:19: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]

>   while (branch = strtok(NULL, " ")) {

>      ~~~~~~~^~~~~~~~~~~~~~~~~~~

> amber_typer.cpp:88:19: note: place parentheses around the assignment to silence this warning

>   while (branch = strtok(NULL, " ")) {

>          ^

>      (             )

> amber_typer.cpp:88:19: note: use '==' to turn this assignment into an equality comparison

>   while (branch = strtok(NULL, " ")) {

>          ^

>          ==

> amber_typer.cpp:232:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]

>   if (match = check_type(mol.atom_types[current_atom].c_str(), node.type)) {

>     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> amber_typer.cpp:232:15: note: place parentheses around the assignment to silence this warning

>   if (match = check_type(mol.atom_types[current_atom].c_str(), node.type)) {

>        ^

>     (                                 )

> amber_typer.cpp:232:15: note: use '==' to turn this assignment into an equality comparison

>   if (match = check_type(mol.atom_types[current_atom].c_str(), node.type)) {

>        ^

>        ==

> amber_typer.cpp:607:23: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]

>       if (token = strtok(NULL, " "))

>         ~~~~~~^~~~~~~~~~~~~~~~~~~

> amber_typer.cpp:607:23: note: place parentheses around the assignment to silence this warning

>       if (token = strtok(NULL, " "))

>            ^

>         (            )

> amber_typer.cpp:607:23: note: use '==' to turn this assignment into an equality comparison

>       if (token = strtok(NULL, " "))

>            ^

>            ==

> amber_typer.cpp:626:23: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]

>       if (token = strtok(NULL, " "))

>         ~~~~~~^~~~~~~~~~~~~~~~~~~

> amber_typer.cpp:626:23: note: place parentheses around the assignment to silence this warning

>       if (token = strtok(NULL, " "))

>            ^

>         (            )

> amber_typer.cpp:626:23: note: use '==' to turn this assignment into an equality comparison

>       if (token = strtok(NULL, " "))

>            ^

>            ==

> amber_typer.cpp:645:27: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]

>         if (token = strtok(NULL, " ")) {

>           ~~~~~~^~~~~~~~~~~~~~~~~~~

> amber_typer.cpp:645:27: note: place parentheses around the assignment to silence this warning

>         if (token = strtok(NULL, " ")) {

>              ^

>           (            )

> amber_typer.cpp:645:27: note: use '==' to turn this assignment into an equality comparison

>         if (token = strtok(NULL, " ")) {

>              ^

>              ==

> 5 warnings generated.

> g++ -c -O2 -o base_grid.o base_grid.cpp

> g++ -c -O2 -o base_mpi.o base_mpi.cpp

> g++ -c -O2 -o base_score.o base_score.cpp

> g++ -c -O2 -o conf_gen.o conf_gen.cpp

> g++ -c -O2 -o dock.o dock.cpp

> g++ -c -O2 -o dockmol.o dockmol.cpp

> g++ -c -O2 -o filter.o filter.cpp

> g++ -c -O2 -o grid.o grid.cpp

> g++ -c -O2 -o hungarian.o hungarian.cpp

> g++ -c -O2 -o library_file.o library_file.cpp

> library_file.cpp:1962:1: warning: control may reach end of non-void function [-Wreturn-type]

> }

> ^

> 1 warning generated.

> g++ -c -O2 -o master_score.o master_score.cpp

> g++ -c -O2 -o orient.o orient.cpp

> g++ -c -O2 -o sasa.o sasa.cpp

> g++ -c -O2 -o score_amber.o score_amber.cpp

> g++ -c -O2 -o score.o score.cpp

> g++ -c -O2 -o score_descriptor.o score_descriptor.cpp

> g++ -c -O2 -o score_multigrid.o score_multigrid.cpp

> score_multigrid.cpp:500:1: warning: control may reach end of non-void function [-Wreturn-type]

> }

> ^

> 1 warning generated.

> g++ -c -O2 -o score_sasa.o score_sasa.cpp

> g++ -c -O2 -o score_solvent.o score_solvent.cpp

> g++ -c -O2 -o simplex.o simplex.cpp

> g++ -c -O2 -o sphere.o sphere.cpp

> g++ -c -O2 -o score_chemgrid.o score_chemgrid.cpp

> In file included from score_chemgrid.cpp:38:

> In file included from ./tnt/tnt.h:41:

> ./tnt/tnt_array1d.h:238:15: warning: '&&' within '||' [-Wlogical-op-parentheses]

>     if ((i0 > 0) && (i1 < n_) || (i0 0) && (i1 < n_) || (i0 0) && (i1 < n_) || (i0 0) && (i1 < n_) || (i0 

> _______________________________________________



All the compiler message to this point are merely warnings.



scott



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