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bioinfomaticsCSU / BOSS

A new algorithm for scaffolding
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installation error #6

Open madhubioinfo opened 5 years ago

madhubioinfo commented 5 years ago

Hello I was trying to install BOSS scaffolder and i have the following error please help me in fixing this g++ -o boss main.o scaffoldgraph.o scaffolding.o ./lp/liblpsolve55.a -I /usr/local/include/bamtools/ /usr/local/lib/libbamtools.a -lm -ldl -std=gnu++98 -lz /usr/bin/ld: ./lp/liblpsolve55.a(lp_lib.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_wlp.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: ./lp/liblpsolve55.a(lp_matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_mipbb.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: ./lp/liblpsolve55.a(lp_MPS.o): relocation R_X86_64_32 against symbol MPSnameFIXED' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_params.o): relocation R_X86_64_32 against.rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_presolve.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: ./lp/liblpsolve55.a(lp_price.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_pricePSE.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_report.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: ./lp/liblpsolve55.a(lp_scale.o): relocation R_X86_64_32 against .text' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_simplex.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: ./lp/liblpsolve55.a(lp_SOS.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_utils.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: ./lp/liblpsolve55.a(lp_MDO.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(commonlib.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: ./lp/liblpsolve55.a(mmio.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: ./lp/liblpsolve55.a(myblas.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: ./lp/liblpsolve55.a(ini.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: ./lp/liblpsolve55.a(colamd.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: ./lp/liblpsolve55.a(lp_rlp.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_crash.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: ./lp/liblpsolve55.a(lp_LUSOL.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: ./lp/liblpsolve55.a(lusol.o): relocation R_X86_64_32S against.rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(lp_Hash.o): relocation R_X86_64_32 against .rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./lp/liblpsolve55.a(yacc_read.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:7: recipe for target 'boss' failed make: *** [boss] Error 1

pmoulos commented 3 years ago

Hi, I fixed this by editing the 1st line of makefile from

CC=g++

to

CC=g++ -no-pie
ardy20 commented 3 years ago

I also could not install tool. I get the following error:

make all

g++ -c main.cpp -I / -lz In file included from main.cpp:10:0: scaffoldgraph.h:13:32: fatal error: api/BamMultiReader.h: No such file or directory

include "api/BamMultiReader.h"

                            ^

compilation terminated. make: *** [main.o] Error 1