Failed installation in AWS Ubuntu 20 LTS #1379
Description
HI,
I downloaded the latest from the github ;
git clone https://github.com/alexdobin/STAR.git
and tired to compile STAR as suggested but it failed with a following error;
/usr/bin/ld: 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: htslib/libhts.a(hfile.o): relocation R_X86_64_32S against `.rodata' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: 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: htslib/libhts.a(sam.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: htslib/libhts.a(cram_decode.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: 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: 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: htslib/libhts.a(cram_io.o): relocation R_X86_64_32S against `.rodata' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: 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: htslib/libhts.a(cram_stats.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: htslib/libhts.a(mFILE.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: 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: 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: htslib/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: htslib/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: htslib/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: 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: 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: htslib/libhts.a(cram_codecs.o): relocation R_X86_64_32S against symbol `cram_external_decode_int' can not be used when making a PIE object; recompile with -fPIE
collect2: error: ld returned 1 exit status
make: *** [Makefile:145: STAR] Error 1
I'd really appreciate any pointers to fix this issue.
AWS Ubuntu server;
.-/+oossssoo+/-. ubuntu@ip-172-31-26-179
`:+ssssssssssssssssss+:` -----------------------
-+ssssssssssssssssssyyssss+- OS: Ubuntu 20.04.3 LTS x86_64
.ossssssssssssssssssdMMMNysssso. Host: z1d.xlarge
/ssssssssssshdmmNNmmyNMMMMhssssss/ Kernel: 5.11.0-1019-aws
+ssssssssshmydMMMMMMMNddddyssssssss+ Uptime: 1 hour, 5 mins
/sssssssshNMMMyhhyyyyhmNMMMNhssssssss/ Packages: 1681 (dpkg), 6 (snap)
.ssssssssdMMMNhsssssssssshNMMMdssssssss. Shell: zsh 5.8
+sssshhhyNMMNyssssssssssssyNMMMysssssss+ Terminal: /dev/pts/0
ossyNMMMNyMMhsssssssssssssshmmmhssssssso CPU: Intel Xeon Platinum 8151 (4) @ 3.399GHz
ossyNMMMNyMMhsssssssssssssshmmmhssssssso GPU: 00:03.0 Amazon.com, Inc. Device 1111
+sssshhhyNMMNyssssssssssssyNMMMysssssss+ Memory: 445MiB / 31649MiB
.ssssssssdMMMNhsssssssssshNMMMdssssssss.
/sssssssshNMMMyhhyyyyhdNMMMNhssssssss/
+sssssssssdmydMMMMMMMMddddyssssssss+
/ssssssssssshdmNNNNmyNMMMMhssssss/
.ossssssssssssssssssdMMMNysssso.
-+sssssssssssssssssyyyssss+-
`:+ssssssssssssssssss+:`
.-/+oossssoo+/-.
gcc;
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.3.0-17ubuntu1~20.04' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-HskZEa/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04)