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Old 08-20-2012, 05:39 PM   #1
potatoo
Junior Member
 
Location: Vancouver

Join Date: Aug 2012
Posts: 1
Cool SPP -- ChIP-seq program installation 2??

Hi guys,
I've tried install spp (http://compbio.med.harvard.edu/Supplements/ChIP-seq/) to my macbook pro or my ubuntu, met the same error. Stcuking for ages!! hope anyone can help

Here is some detailed infor:
macbook pro 10.7.4 OSX Lion
ubuntu 12.04
I've successfully installed boost C++, and R( both are the most recent one).

below is the error message I got, every time, and on both machine :

----------------------
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fPIC -g -O2 -c bamread.cpp -o bamread.o
In file included from /usr/include/c++/4.2.1/backward/strstream:51,
from bamread.cpp:8:
/usr/include/c++/4.2.1/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
bamread.cpp:14:31: error: boost/tokenizer.hpp: No such file or directory
bamread.cpp: In function ‘SEXPREC* read_bam(SEXPREC*, SEXPREC*)’:
bamread.cpp:71: error: ‘boost’ has not been declared
bamread.cpp:71: error: expected initializer before ‘<’ token
bamread.cpp:72: error: ‘boost’ has not been declared
bamread.cpp:72: error: expected primary-expression before ‘char’
bamread.cpp:72: error: expected `;' before ‘char’
bamread.cpp:73: error: ‘boost’ has not been declared
bamread.cpp:73: error: expected primary-expression before ‘char’
bamread.cpp:73: error: expected `;' before ‘char’
make: *** [bamread.o] Error 1
ERROR: compilation failed for package ‘spp’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/spp’

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PS. I've looked up in the forum, a relative post (http://seqanswers.com/forums/showthr...&highlight=spp) has similar problem, but not quite same, and the link of patch is brocken.

Many thanks.
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