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make errors #8

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DCGenomics opened this issue Mar 6, 2024 · 1 comment
Open

make errors #8

DCGenomics opened this issue Mar 6, 2024 · 1 comment

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@DCGenomics
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/usr/bin/ld: libhts.a(rANS_static.o): relocation R_X86_64_32 against .rodata' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: libhts.a(thread_pool.o): relocation R_X86_64_32 against .text' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: libhts.a(vlen.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: libhts.a(zfio.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: libhts.a(knetfile.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: libhts.a(md5.o): relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: libhts.a(sam.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: libhts.a(files.o): relocation R_X86_64_PC32 against symbol __xstat@@GLIBC_2.2.5' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:294: bgzip] Error 1
make[1]: Leaving directory '/home/dnanexus/svaha/deps/htslib'
make: *** [Makefile:33: lib/libhts.a] Error 2

@DCGenomics
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Explicitly compiled htslib in the deps folder. Now this error: In file included from src/wrangler.hpp:8,
from src/svaha.cpp:13:
./include/gfakluge.hpp: In member function ‘std::string gfak::path_elem::to_string()’:
./include/gfakluge.hpp:83:9: warning: no return statement in function returning non-void [-Wreturn-type]
83 | }
| ^
In file included from src/svaha.cpp:17:
src/vcfparse.hpp: In function ‘std::vectorvcfparse::Variant vcfparse::parse_file(std::string)’:
src/vcfparse.hpp:103:5: warning: no return statement in function returning non-void [-Wreturn-type]
103 | };
| ^

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