Monday, July 4, 2016

Problem installing Cogent - COding GENome reconstruction Tool - SOLVED

I was trying to run the Cogent on data, and was using this tutorial for instructions.Everything was smooth, until i experienced this error:


$ make

gcc -o ssw_test ssw.o main.c -Wall -O3 -pipe  -lm -lz/usr/bin/ld: cannot find -lgcc_scollect2: error: ld returned 1 exit statusmake: *** [ssw_test] Error 1

I googled and tried different answers, but finally this one worked:

$ locate libgcc_s.so.1

/lib/x86_64-linux-gnu/libgcc_s.so.1

if you see directory and their paths listed, then make softlink in the same folder

$ ln -s 
/lib/x86_64-linux-gnu/libgcc_s.so.1 /lib/x86_64-linux-gnu/libgcc_s.so

This ran make command without any error

$ make

gcc -o ssw_test ssw.o main.c -Wall -O3 -pipe  -lm -lz
gcc -o example_c ssw.o example.c -Wall -O3 -pipe  -lm -lz
g++ -c -o ssw_cpp.o ssw_cpp.cpp -Wall -O3 -pipe 
g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -Wall -O3 -pipe  -lm -lz

gcc -Wall -O3 -pipe  -fPIC -shared -rdynamic -o libssw.so ssw.c

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