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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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Compiling error for homog... #27

Closed hmyh1202 closed 1 year ago

hmyh1202 commented 1 year ago

$python3 setup.py Compiling stdin2beta... SUCCESS Compiling stdin2pairs... SUCCESS Compiling pat_sampler... SUCCESS Compiling patter... SUCCESS Compiling bp_patter... SUCCESS Compiling snp_patter... SUCCESS Compiling match_maker... SUCCESS Compiling segmentor... SUCCESS Compiling cview... SUCCESS Compiling homog... FAIL Failed compilation. Command: g++ -std=c++11 -c -o src/homog/main.o src/homog/main.cpp; g++ -std=c++11 -c -o src/homog/homog.o src/homog/homog.cpp; g++ -std=c++11 -o src/homog/homog src/homog/main.o src/homog/homog.o -lz -lboost_iostreams return code: 1 stderr:

stdout: In file included from src/homog/main.cpp:5:0: src/homog/homog.h:8:48: fatal error: boost/algorithm/string/predicate.hpp: No such file or directory

include <boost/algorithm/string/predicate.hpp>

                                            ^

compilation terminated. In file included from src/homog/homog.cpp:2:0: src/homog/homog.h:8:48: fatal error: boost/algorithm/string/predicate.hpp: No such file or directory

include <boost/algorithm/string/predicate.hpp>

                                            ^

compilation terminated. g++: error: src/homog/main.o: No such file or directory g++: error: src/homog/homog.o: No such file or directory

Failed compiling homog Compiling add_cpg_counts... SUCCESS Compiling add_loci... SUCCESS

nloyfer commented 1 year ago

Hi, homog module uses the c++ boost library, and it seems like you don't have boost installed. I just changed homog.cpp such that it doesn't use boost, so if you clone the latest version of wgbstools, it should compile for you.

mHagiw commented 1 year ago

Hi, I am having trouble with a similar error. Have you already updated the tool? I cloned the latest version of wgbstools and still get the same error.

gat2010 commented 1 year ago

Hi, I am also getting the same error.

nloyfer commented 1 year ago

You guys are right, my fix didn't work as I expected. I forgot to remove the boost linkage from the setup.py file. And I had a couple of other compilation errors. But now I fixed all of that, please try again.

gat2010 commented 1 year ago

Thanks for the update. It's compiling now.

mHagiw commented 1 year ago

Thank you!! I have done.

hmyh1202 commented 1 year ago

Nice ! Good job