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

[Roland Schulz]

Hi,

you either need to use this patch: https://gerrit.gromacs.org/#/c/3764, or
the latest release-5-0 branch (which includes the patch), or
add -std=gnu++0x to the CXXFLAGS.

Roland


On Mon, Jul 21, 2014 at 6:51 PM, John Doe <helstreak at hotmail.com> wrote:

> 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
>
>
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