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i am new to stackflow and i previously i have no background in computer system and programming. However, now i need to run analysis under cygwin for my bioinformatics project. I encounter some error when i try to compile a file name 'zone_b.linux'using cygwin, to produce an executable program. The linux file is download from web https://github.com/haddocking/HADDOCK-binding-sites-tutorial/blob/master/ana_scripts/zone_b.linux. When i try to compile using the following command under cygwin it produce the following error:

$ gcc zone_b.linux
/usr/lib/gcc/i686-pc-cygwin/6.4.0/../../../libcygwin.a(libcmain.o): In 
function `main':
/usr/src/debug/cygwin-2.9.0-3/winsup/cygwin/lib/libcmain.c:37: undefined 
reference to `WinMain@16'
collect2: error: ld returned 1 exit status

Error description

I search the following error under stackoverflow, and i found two post with similar problem.

First is the post from undefined reference to `WinMain@16'. It stated that the problem is due the Microsoft'linker uses a runtime library entry point(winMainCRTStartup) that calls Microsoft's non-standard WinMain instead of standard main. So, i try the post's suggestion of including the entry by following command

$ gcc zone_b.linux /entry:winMainCRTStartup
gcc: error: /entry:winMainCRTStartup: No such file or directory

However i get the error no such file or directory. I think maybe it is because i am running under cygwin not mingW.

Second post is the Undefined reference to WinMain in Cygwin. From the post, it said use -c compile flag to only produce object file. However, for my case, i am not using any -c. Therefore, i think it is not relevant to my issue.

I would appreciate if anyone could kindly explain to me since i am new to this computing area. Thank you.

Shawn
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1 Answers1

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zone_b.linux is the compiled and linked executable program to run on a linux machine. It is a 32-bit ELF binary file. It will not work on a Windows machine, even using cygwin or mingw32, without re-compulation.

You probably have to compile zone_b.f, a FORTRAN source file, using the gfortran compiler to create a zone_b.exe that is usable in cygwin. I saw no instructions for this, but try something like gcc zone_b.f and cross fingers. Be sure gfortran is installed using cygwin setup.

You will also need to (re-)build the other executables (cluster_struc and contact) by performing make in the ana_scripts directory. Any supplied executables (from the git clone ... or a downloaded .zip file) will not work under cygwin.

You will need to have perl and python installed. I think perl is installed by default. You can install python2 using cygwin setup. The python script looked like it will work with python2 or python3, whichever is the default. On cygwin, today, python2 is the default python. I don't do perl, so cross your fingers.

Doug Henderson
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  • Thank you Doug Henderson for the reply. I already try to run the zone_b.linux on ubuntu. Here, I run the command source.csh and zone_b.exe is produced. However, even the executable zone_b produce error as well (zone_b command not found). Even after i have performed chmod a+x zone_b. The script is just not responding. I have also try to compile the zone_b.f, however it produce error as well. I have post the error under this post: https://stackoverflow.com/questions/47503002/syntax-error-in-open-statement-with-gfortran-at-carriagecontrol?noredirect=1#comment81986558_47503002 – Shawn Nov 28 '17 at 03:33