Installing A Program On Windows Using Cygwin

Question

[Diana]

Hello all!

I'm trying to install a Unix program through cygwin on windows. It was a tar.gz file. I've unwrapped it and then I move to the folder with the makefile but when I try to make the files, it gives me this error:

Diana@Diana-PC /cygdrive/C/Users/Diana/d2z.v01/code/iid
$ make
g++ -O5 -Wno-deprecated -c listop.cpp
In file included from listop.cpp:1:0:
listop.h:1:18: fatal error: list.h: No such file or directory
compilation terminated.
make: *** [listop.o] Error 1

I do not understand this error. Do I not have the proper packages or am I doing something wrong?

Thanks!

[Pierre Lindenbaum]

how is it related to bioinformatics ?

[Diana]

Its a bioinformatics program for enhancer prediction and I just cant get it to work. Maybe I should write in some programming blog.

[Whetting]

which program is it? The installer is looking for a file that it cannot find. You have all the required packages (like g++) installed?

Answer 1

[matted]

If you had told us the program, it would have been easier to help. I believe you're trying to install the D2Z suite found here.

I took a look at the package, and it looks like it was written in pretty old/bad C++. There are a lot of missing #include statements and namespace declarations that prevent it from compiling on modern systems. For instance, the list.h error you see is the old style STL header that is now just list.

To hack it to work, put the following includes in listop.h and wherever else is necessary to fix compile errors: #include <cstring>, #include <string>, #include <vector>, #include <list>, #include <algorithm>, and #include <cstdlib>. It's quickest to also add using namespace std; after the includes in those headers. You'll also have to run ./code/markov/matrix/matrixinstall, which isn't called by their makefiles.

There are probably better ways to make recent gcc toolkits act old (e.g. use old-style STL references), but I'm not enough of a C++ hacker to know them.

[Istvan Albert]

Whoa! Nice work!

[Diana]

Thank you so much for your reply. But I still can't get it to work. I am sorry I am not much of a programmer. Where should I put this: ./code/markov/matrix/matrixinstall? in the make files?

[matted]

That's a script that you should run before the rest of the makefiles (they're calling by the "install.sh" script). It updates some libraries that are already there in the package, but are out of date unless you run that command.