I wanted to install staden-2.0.0b2-src just for my account, since our sysadmins locked my workstation. I am using Fedora 8.
2) installed(? see below) io_lib, samtools and tklib in /my_home/soft/bin & /my_home/soft/lib
3) attempted to build Staden:
./configure -prefix=/my_home_dir/soft/molbio/ -with-tklib=/my_home_dir/soft/lib/tklib0.5/ -with-samtools=/my_home_dir/soft/molbio/samtools -enable-64bit
got one error:
samtools: ***NOT FOUND***
despite that I got in /my_home_dir/bin
blast2sam.pl bowtie2sam.pl export2sam.pl interpolate_sam.pl novo2sam.pl psl2sam.pl sam2vcf.pl samtools.pl soap2sam.pl wgsim_eval.pl zoom2sam.pl
gcc -g -O2 -m64 -I/include -I/include -DUSE_NON_CONST -I/my_home_dir/Desktop/staden-2.0.0b2-src/./tgap -I/my_home_dir/Desktop/staden-2.0.0b2-src/./Misc -I"/usr/include/tcl-private/generic" -I"/usr/include/tcl-private/unix" -I/my_home_dir/Desktop/staden-2.0.0b2-src/./tk_utils -I/my_home_dir/Desktop/staden-2.0.0b2-src/./seq_utils -I/my_home_dir/soft/include -I/my_home_dir/Desktop/staden-2.0.0b2-src -fPIC -o zfio.o -c zfio.c
zfio.c: In function 'zfopen':
zfio.c:69: error: 'R_OK' undeclared (first use in this function)
zfio.c:69: error: (Each undeclared identifier is reported only once
zfio.c:69: error: for each function it appears in.)
make: *** Error 1
make: Leaving directory `/my_home_dir/Desktop/staden-2.0.0b2-src/tgap'
make: *** Error 2
I will appreciate your ideas.
Samtools is rather messy at present, but perhaps the newer installs have fixed this. Specifically it had no way of installing header files and libraries - just the samtools program and manual. Hence it's easier to specify the build directory of samtools where we can ensure the complete package exists. In time I hope that samtools installs fix this problem; I believe some people are working on adding autoconf to it.
R_OK is defined in unistd.h. Maybe on my system I get this included by chance from some other route, but the fix will be to explicitly add:
to the start of zfio.c. I'll make this change in the SVN source tree. Thanks for the error report.
thanks for such quick fix. I checked out samtools source:
svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/samtools
compiledEdited zfio.c introducing #include <unistd.h>, it and run configure for staden again.
Samtools were found by ./configure, and compilation finished without error.
Installation also went OK, but somehow I can not setup env variables for this build. Can not find staden.profile even in source directory -> is this step no longer needed?
Running gap4 from the command line gives:
couldn't load file "/usr/lib/tk8.4/../libtk8.4.so": /usr/lib/tk8.4/../libtk8.4.so: wrong ELF class: ELFCLASS32
Well, I did recompiled staden without -enable-64bit but got exactly the same error message.
Is there any way (during configuration / compilation stage) that there is such mismatch ( ELFCLASS32 vs ELFCLASS64)?
Thank you very much for your help,
At one stage (ie when I built that release) I had concluded that staden.profile was no longer necessary as the wrapper scripts for gap4, gap5, pregap4, spin etc all handled the environment variables themselves.
However with hindsight it would be good to still have such a file for optional sourcing if people wanted to get access to the lower level tools, like makeSCF or getABISampleName, or to link against various run time libraries.
The tk8.4 problem is a new one to me. It seems to imply that you have a problem with your tk build, but possibly it's an autoconf problem too. Do you have both 32-bit and 64-bit tk libraries installed on the same system? If so maybe the contents of config.log will help us to work out whether autoconf chose the wrong version to link against.
WHat operating system are you using?