Re: [Seqan-dev] RecordReader question

[Raymond Wan <rwan@cuhk.edu.hk>]

Hi Manuel,


On 2011-11-23 14:28, Raymond Wan wrote:
> > Apparently, you are using your own build/project files, i.e. not
> > generated with the SeqAn build system. Note that you have to add both
> > "core/include" and "extras/include" to the include path.
> Ah, yes. I'm adding SeqAn to my CMakeLists.txt rather than adding my
> project to SeqAn's CMakeLists.txt. I figured if I start off with an
> empty file, then I have an idea of what goes inside it. SeqAn's looks
> great but there are a lot of cmake directives I don't quite understand.


I'm starting to have doubts about what I'm doing is a good 
idea...  Perhaps you can tell me what I'm doing wrong?

If I'm not mistaken, SeqAn is a header-only library (like 
most of Boost).  And compiling is only needed if you want to 
look at the tutorials?  The 1.3 Release instructions says 
that I just have to move the include/ directory to the right 
place.

So, I created the subdirectories:
  ~/common/include/seqan-core
  ~/common/include/seqan-extras

Inside seqan-core, I have a symlink:
  seqan -> ../seqan/core/include/seqan

Likewise for seqan-extras.

In CMakeLists.txt, I did this:

INCLUDE_DIRECTORIES (~/common/include/seqan-core)
INCLUDE_DIRECTORIES (~/common/include/seqan-extras)

...I think this should work?

In my source, I did:

#include <seqan/basic.h>
#include <seqan/file/stream.h>

When I compile, I get this error:

In file included from 
/home/rwan/common/include/seqan-core/seqan/platform.h:43,
                 from 
/home/rwan/common/include/seqan-core/seqan/basic.h:39,
...
/home/rwan/common/include/seqan-core/seqan/platform/platform_gcc.h:82:56: 
error: seqan/platform/platform_generated_forwards.h: No such 
file or directory
/home/rwan/common/include/seqan-core/seqan/platform/platform_gcc.h:85:2: 
error: #error To use the SeqAn library you first have to 
execute 'make forwards' in the root directory
...

So, it found basic.h, platform.h, ... fine, but not 
platform_generated_forwards.h .  The error says I need to do 
a 'make forwards' but:

1)  I don't know what is the root directory; or, at least 
one with an obvious makefile.

2)  I could perform an out-of-source build and create a 
build/ directory and do "cmake | make" but that didn't copy 
the header files over -- moving the symlinks to this build/ 
directory doesn't seem to work.

I think I'm close :-) but I'm still stuck.  My only 
remaining idea is to do an in-source build -- such that the 
stuff that is created with "make" is in the same place where 
the .h files are.  Is that what I need to do?

Thank you and if I'm confusing myself and should just follow 
the instructions and work from SeqAn's CMakeLists.txt, 
please tell me.  :-)

Ray

PS:  This is the SVN release.  I'm not using 1.3 anymore.  ;-)