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unable to install #1082

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Heather1999 opened this issue Mar 13, 2024 · 1 comment
Open

unable to install #1082

Heather1999 opened this issue Mar 13, 2024 · 1 comment

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@Heather1999
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Hello, I was following the installation instruction but couldn't solve the following error:
make
Building BEDTools:

CXXFLAGS is [-g -Wall -O2 -I/home/sealight1999/miniconda3/envs/zlib/include -std=c++11 -fPIE]
DETECTED_VERSION = v2.29.1
CURRENT_VERSION = v2.29.1

  • Building main bedtools binary.
    /usr/bin/ld: src/utils/htslib/libhts.a(bgzf.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: src/utils/htslib/libhts.a(hfile.o): relocation R_X86_64_32 against .bss' can not be used when making a PIE object; recompile with -fPIE
    /usr/bin/ld: src/utils/htslib/libhts.a(hfile_net.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: src/utils/htslib/libhts.a(hts.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: src/utils/htslib/libhts.a(multipart.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: src/utils/htslib/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: src/utils/htslib/libhts.a(textutils.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: src/utils/htslib/libhts.a(thread_pool.o): relocation R_X86_64_32 against .rodata' can not be used when making a PIE object; recompile with -fPIE
    /usr/bin/ld: src/utils/htslib/libhts.a(cram_decode.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: src/utils/htslib/libhts.a(cram_encode.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: src/utils/htslib/libhts.a(cram_external.o): relocation R_X86_64_32S against symbol itf8_bytes' can not be used when making a PIE object; recompile with -fPIE /usr/bin/ld: src/utils/htslib/libhts.a(cram_index.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: src/utils/htslib/libhts.a(cram_io.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: src/utils/htslib/libhts.a(cram_samtools.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIE
    /usr/bin/ld: src/utils/htslib/libhts.a(cram_stats.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: src/utils/htslib/libhts.a(mFILE.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: src/utils/htslib/libhts.a(open_trace_file.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: src/utils/htslib/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: src/utils/htslib/libhts.a(sam_header.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: src/utils/htslib/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: src/utils/htslib/libhts.a(kstring.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: src/utils/htslib/libhts.a(faidx.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: src/utils/htslib/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: src/utils/htslib/libhts.a(cram_codecs.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIE
    collect2: error: ld returned 1 exit status

What could be the problem? Thank you!

@Elveera28
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Hello,
Even I'm encountering errors in the make command while trying to install bedtools version 2.25.0.

The Make command breaks with the following error:
/usr/include/c++/11/bits/stl_queue.h:480:67: error: static assertion failed: value_type must be the same as the underlying container
480 | static_assert(is_same<_Tp, typename _Sequence::value_type>::value,
| ^~~~~
/usr/include/c++/11/bits/stl_queue.h:480:67: note: ‘std::integral_constant<bool, false>::value’ evaluates to false
make[2]: *** [Makefile:39: ../../../../obj//StrandQueue.o] Error 1
make[1]: *** [Makefile:45: Records] Error 2
make: *** [Makefile:177: src/utils/FileRecordTools] Error 2

any help on how to resolve it and initiate the installation would be great!
Thank you!

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