Dear All,

I want to use cufflinks to analyze RNA-seq Data. Therefore I first installed Boost148_0.tar.gz and built it with this code:

tar -zxf boost_1_48_0.tar.gz
cd boost_1_48_0
./bootstrap.sh
./b2
./bjam --prefix-/home/lisanne/Downloads/boost toolset=gcc link=static runtime-link=static stage install

It seems like the correct way for building. After the installation of boots, i installed cufflinks and buit it with this code:

tar -zxf cufflinks-0.7.0.tar.gz
cd cufflinks-0.7.0
./configure --with-boost=/home/lisanne/Downloads/boost
make

The last "make" command gives the following error:

make  all-recursive
make[1]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0'
Making all in src
make[2]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
g++ -DHAVE_CONFIG_H -I. -I..  -I../src    -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3  -DNDEBUG  -pthread -I/home/lisanne/Downloads/boost/include -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp
mv -f .deps/common.Tpo .deps/common.Po
g++ -DHAVE_CONFIG_H -I. -I..  -I../src    -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3  -DNDEBUG  -pthread -I/home/lisanne/Downloads/boost/include -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -c -o assemble.o assemble.cpp
assemble.cpp:37:41: fatal error: boost/vector_property_map.hpp: No such file or directory
compilation terminated.
make[2]: *** [assemble.o] Error 1
make[2]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0'
make: *** [all] Error 2

The file vectorpropertymap.hpp is not is the map boost, but in the map propertymap. I changed the file assemble.cpp on line 37 from the boost/vectorpropertymap.hpp to boost/propertymap.hpp. That solve this error, but by running the command again, there is another error in the file hits.cpp that i don't understand.

make  all-recursive
make[1]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0'
Making all in src
make[2]: Entering directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
g++ -DHAVE_CONFIG_H -I. -I..  -I../src    -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3  -DNDEBUG  -pthread -I/home/lisanne/Downloads/boost/include -MT hits.o -MD -MP -MF .deps/hits.Tpo -c -o hits.o hits.cpp
hits.cpp: In member function ‘virtual bool SAMHitFactory::get_hit_from_buf(const char*, ReadHit&, bool, char*, char*)’:
hits.cpp:262:32: error: invalid conversion from ‘const char*’ to ‘char*’
hits.cpp:270:33: error: invalid conversion from ‘const char*’ to ‘char*’
make[2]: *** [hits.o] Error 1
make[2]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/lisanne/Downloads/cufflinks-0.7.0'
make: *** [all] Error 2

and this is the code in the hits.cpp file where it is all about:

// Copy the tag out of the name field before we might wipe it out
char* pipe = strrchr(name, '|');
if (pipe)
{
    if (name_tags)
        strcpy(name_tags, pipe);
    *pipe = 0;
}
// Stripping the slash and number following it gives the insert name
char* slash = strrchr(name, '/');
if (strip_slash && slash)
    *slash = 0;

Can anyone help me with this kind of error? Many thanks! :)