[gmx-users] Installing 5.0 on Cygwin - Getting error

[John Doe]

Hello,

I'm attempting to install Gromacs-5.0 on Cygwin64.  I have a full install of Cygwin and I'm following the "Quick and dirty installation" instructions.  In the "make" step, I am getting the following error and have no clue what it means. Any help would be great.

[  8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.c.o
/home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/topshake.c: In function ‘count_hydrogens’:
/home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/topshake.c:98:9: warning: array subscript has type ‘char’ [-Wchar-subscripts]
         if (toupper(**(atomname[a[i]])) == 'H')
         ^
/home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/topshake.c: In function ‘make_shake’:
/home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/topshake.c:165:37: warning: array subscript has type ‘char’ [-Wchar-subscripts]
                                     (numhydrogens == 1 && toupper(**(info[ang->a[1]])) == 'O'))
                                     ^
[  8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.c.o
[  8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.c.o
[  8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.c.o
[  8%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.c.o
[  8%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o
/home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp: In function ‘int low_fflib_search_file_end(const char*, gmx_bool, const char*, gmx_bool, char***, char***)’:
/home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp:205:47: error: ‘strdup’ was not declared in this scope
                         fns[n] = strdup(fn_dir);
                                               ^
/home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp: In function ‘int fflib_search_file_in_dirend(const char*, const char*, char***)’:
/home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibutil.cpp:298:47: error: ‘strdup’ was not declared in this scope
                     dns[n] = strdup(f_short[i]);
                                               ^
src/gromacs/CMakeFiles/libgromacs.dir/build.make:1391: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o' failed
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o] Error 1
CMakeFiles/Makefile2:1924: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2