Problem with installing LRSIM

[aquaskyline]

Problem with installing LRSIM

[nicomy]

Hello,
I had the same problem and I resolve it by compiling samtools directly.
cd ../LRSIM/DWGSIMSrc/samtools/
make

[yoann-dufresne]

I had the same error.

Could you add a warning in the README and point the way to fix it ?

[hakonhagland]

Same problem but it does not help to go the specific folder either:

cd DWGSIMSrc/samtools/bcftools
make
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I..  call1.c -o call1.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I..  main.c -o main.o
gcc -g -Wall -O2  -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L.  -lbcf -lm -lz -lpthread
/bin/ld: ./libbcf.a(bcf.o): relocation R_X86_64_PC32 against symbol `strlen@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(vcf.o): relocation R_X86_64_PC32 against symbol `realloc@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(bcfutils.o): relocation R_X86_64_32S against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(prob1.o): relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(em.o): relocation R_X86_64_PC32 against symbol `log@@GLIBC_2.29' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(kfunc.o): relocation R_X86_64_PC32 against symbol `log@@GLIBC_2.29' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(kmin.o): relocation R_X86_64_PC32 against symbol `calloc@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(index.o): relocation R_X86_64_PC32 against symbol `free@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(fet.o): relocation R_X86_64_PC32 against symbol `exp@@GLIBC_2.29' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(mut.o): relocation R_X86_64_PC32 against symbol `calloc@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: ./libbcf.a(bcf2qcall.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/bin/ld: final link failed: nonrepresentable section on output
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:34: bcftools] Error 1

[aquaskyline]

I cannot repeat the problem in my servers. I was using Ubuntu 16.04. Please let me know what OS and version you were using.

…

On Fri, Jun 21, 2019 at 7:47 PM Håkon Hægland ***@***.***> wrote: Same problem but it does not help to go the specific folder either: cd DWGSIMSrc/samtools/bcftools make gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I.. call1.c -o call1.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I.. main.c -o main.o gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread /bin/ld: ./libbcf.a(bcf.o): relocation R_X86_64_PC32 against symbol `strlen@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(vcf.o): relocation R_X86_64_PC32 against symbol `realloc@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(bcfutils.o): relocation R_X86_64_32S against `.rodata' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(prob1.o): relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(em.o): relocation R_X86_64_PC32 against symbol `log@@GLIBC_2.29' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(kfunc.o): relocation R_X86_64_PC32 against symbol `log@@GLIBC_2.29' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(kmin.o): relocation R_X86_64_PC32 against symbol `calloc@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(index.o): relocation R_X86_64_PC32 against symbol `free@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(fet.o): relocation R_X86_64_PC32 against symbol `exp@@GLIBC_2.29' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(mut.o): relocation R_X86_64_PC32 against symbol `calloc@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIC /bin/ld: ./libbcf.a(bcf2qcall.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status make[1]: *** [Makefile:34: bcftools] Error 1 — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#22?email_source=notifications&email_token=AAG2SOO753GGFK7RYD3J62LP3S5VZA5CNFSM4FZT2C6KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYIH3XA#issuecomment-504397276>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAG2SOIHKTVMQLFNHJLH34LP3S5VZANCNFSM4FZT2C6A> .

-- Laurent