Unconfigured Ad

**dawe** · 08-03-2010, 01:51 AM

Hello Carl,
I've read your post just after Illumina released OLB 1.8.0... I've tried to install the latest version and I've succeeded with the following procedure:

Things I already had on my system

ImageMagick (Macports)

Things I had to install

fftw-3-single (Macports)
gnuplot (v 4.4, Macports)
boost ( v 1.43, Macports)
XML::Simple (CPAN)

I've skipped doxygen right now...

I've patched three files:

Code:

$ diff -u validate.sh validate.sh.1
--- validate.sh	2010-08-03 10:27:56.000000000 +0200
+++ validate.sh.1	2010-08-03 11:46:57.000000000 +0200
@@ -346,7 +346,7 @@
 
     log_msg "Wrote source to ${tmp_src_fn}."
 
-    cmd="g++ -o ${tmp_bin_fn} ${tmp_src_fn} -I/opt/local/include -L/opt/local/lib -l${lib_str}"
+    cmd="g++ -o ${tmp_bin_fn} ${tmp_src_fn} -l${lib_str}"
 
     cmd_out=`$cmd 2>&1`
     cmd_res=$?

To make it search fftw3f installed by macports

Code:

diff -u c++/CMakeLists.txt c++/CMakeLists.txt.1
--- c++/CMakeLists.txt	2010-08-03 10:42:17.000000000 +0200
+++ c++/CMakeLists.txt.1	2010-08-03 11:48:00.000000000 +0200
@@ -79,12 +79,12 @@
 macro(ga_find_library name header library)
 if    (NOT ${name}_INCLUDE_DIR)
     find_path(${name}_INCLUDE_DIR ${header} 
-              HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH /opt/local/include)
+              HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH)
 endif (NOT ${name}_INCLUDE_DIR)
 if    (${name}_INCLUDE_DIR AND NOT ${name}_LIBRARY)
     find_library(${name}_LIBRARY 
                  NAMES "${GA_LIBRARY_PREFIX}${library}${GA_LIBRARY_SUFFIX}"
-                 HINTS ENV LIBRARY_PATH /opt/local/lib)
+                 HINTS ENV LIBRARY_PATH)
 endif (${name}_INCLUDE_DIR AND NOT ${name}_LIBRARY)
 if(${name}_INCLUDE_DIR AND ${name}_LIBRARY)
     set (HAVE_${name} ${${name}_LIBRARY})

To be sure MacPorts path is searched at build time

Code:

$ diff -u c++/common/Sequence.hh c++/common/Sequence.hh.1
--- c++/common/Sequence.hh	2010-08-03 11:31:45.000000000 +0200
+++ c++/common/Sequence.hh.1	2010-08-03 11:47:23.000000000 +0200
@@ -22,7 +22,6 @@
 
 #include <string>
 #include <vector>
-#include <sys/types.h>
 
 #include "Spot.hh"
 #include "FilteringStreams.hh"

You already did this...

After that make && make install works fine (with some warnings, of course).

HTH

d

**Mercutio** · 08-03-2010, 06:07 AM

Hi!

Another solution is to compile fftw by hand using enable-single option.

Code:

./configure --enable-single
make
make install

And i've replace uint by unsigned int in
/c++/common/Alignment.hh, Alignment.cpp, Sequence.hh and Sequence.cpp
/c++/common/cppunit/testSequence.cpp

Jeremy

**dawe** · 08-03-2010, 11:00 AM

Originally posted by Mercutio View Post

Hi!
Another solution is to compile fftw by hand using enable-single option.

True but I personally prefer to use MacPorts so that everything is handled by a single application (port).

d

**cabroadb** · 08-04-2010, 11:10 AM

OLB v1.6 still gives me the errors after patching. I'm new on this project so I just registered with Illumina. In a couple days I should be able to download the newest source. I'll let you know if I run into any other issues.

Topics	Statistics	Last Post
New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2 Started by SEQadmin2, Yesterday, 10:04 AM	0 responses 8 views 0 reactions	Last Post by SEQadmin2 Yesterday, 10:04 AM
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, 07-08-2026, 10:08 AM	0 responses 7 views 0 reactions	Last Post by SEQadmin2 07-08-2026, 10:08 AM
Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2 Started by SEQadmin2, 07-07-2026, 11:05 AM	0 responses 10 views 0 reactions	Last Post by SEQadmin2 07-07-2026, 11:05 AM
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, 07-02-2026, 11:08 AM	0 responses 31 views 0 reactions	Last Post by SEQadmin2 07-02-2026, 11:08 AM

Unconfigured Ad

Building OLB for MacOS

Comment

Comment

Comment

Comment

Latest Articles

ad_right_rmr

News