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bx3 / shannon_cpp

GNU General Public License v3.0
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Not able to install shannon_cpp #4

Open sunnyEV opened 4 years ago

sunnyEV commented 4 years ago

HI When i do make, showing error make g++ -o rcorrector -Wall -O3 -std=c++0x KmerCode.o ErrorCorrection.o main.o -I . -lpthread -lz /usr/bin/ld: KmerCode.o: relocation R_X86_64_32S against symbol nucToNum' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ErrorCorrection.o: relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: main.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: final link failed: Nonrepresentable section on output collect2: error: ld returned 1 exit status Makefile:9: recipe for target 'all' failed make: *** [all] Error 1

bx3 commented 4 years ago

Hi

Are you at the step of "cd Rcorrector & make"? I am thinking it is a Rcorrector installation issue, its repo locates at https://github.com/mourisl/Rcorrector. Can you first remove the existing Rcorrector directory by

  1. rm -rf Rcorrector
  2. git clone https://github.com/mourisl/Rcorrector.git
  3. cd Rcorrector
  4. make

I am working on a bioconda recipe now (hopefully it makes installation easier). what Operating system are you using? thanks, bowen

sunnyEV commented 4 years ago

Hi, ubuntu.

Thanks!

bx3 commented 4 years ago

Shannon is available on bioconda, currently only on linux, and MacOs is still developing. You can install by

conda install shannon_cpp

If you don't have bioconda, follow the wiki page.