Hello,
I am trying to install a package named SpeedSeq which depends on SAMtools.
However, some error messages related to samtools/libbam.a are being
returned which are preventing a successful installation. I have also posted
this to the SpeedSeq forum but am still awaiting a reply.
Computing environment:
- OS: Redhat Enterprise Linux 7.4
- Kernel: Linux 3.10.0-693.2.2.el7.x86_64
- gcc: 4.8.5
- icc: 17.0.1 (gcc version 4.8.5 compatibility)
- openmpi: 2.0.1
- cmake: 3.8.2
I have included my installation notes below along with the first few error
messages (there are many, all related to "undefined reference").
Installation Notes:
- load root: cd /path/to/bin/root/ && . bin/thisroot.sh
- echo $ROOTSYS: /path/to/bin/root
- echo $LD_LIBRARY_PATH:
/path/to/bin/root/lib:/usr/local/intel-17/cmake/3.8.2/lib:/usr/local/intel-17/openmpi/2.0.1/lib:/usr/local/intel/17/tbb/lib/intel64/gcc4.7:/usr/local/intel/17/compilers_and_libraries_2017/linux/mkl/lib/intel64:/usr/local/intel/17/compilers_and_libraries_2017/linux/lib/intel64::/usr/local/lib
- echo $PATH:
/path/to/bin/root/bin:/usr/local/intel-17/cmake/3.8.2/bin:/usr/local/intel-17/openmpi/2.0.1/bin:/usr/local/intel/17/compilers_and_libraries_2017/linux/bin/intel64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/dell/srvadmin/bin
- Install speedseq:
- cd /path/to/bin
- mkdir speedseq && cd speedseq
- git clone --recursive https://github.com/hall-lab/speedseq
- cd speedseq && make
- Result:
...
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.3.3\" -fopenmp -o cnvnator
obj/cnvnator.o obj/EXOnator.o obj/HisMaker.o obj/AliParser.o
obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a
samtools/htslib-1.3.1/libhts.a -lz -L/path/to/bin/root/lib -lCore
-lRIO -lHist -lGraf -lGpad -lTree -lMathCore
samtools/libbam.a(bam.o): In function `bam_get_library':
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:96: undefined
reference to `__intel_sse2_strncmp'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:119: undefined
reference to `__intel_sse2_strlen'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:119: undefined
reference to `__intel_sse2_strncmp'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:107: undefined
reference to `__intel_sse2_strncmp'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:109: undefined
reference to `__intel_sse2_strncmp'
samtools/libbam.a(bam.o): In function `bam_remove_B':
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:235: undefined
reference to `_intel_fast_memcpy'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:237: undefined
reference to `_intel_fast_memmove'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:238: undefined
reference to `_intel_fast_memmove'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:239: undefined
reference to `_intel_fast_memmove'
samtools/libbam.a(sam.o): In function `samopen':
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:53: undefined
reference to `__intel_sse2_strchr'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:75: undefined
reference to `__intel_sse2_strchr'
samtools/libbam.a(sam.o): In function `samfaipath':
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:133: undefined
reference to `__intel_sse2_strlen'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:134: undefined
reference to `__intel_sse2_strcpy'
/path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:134: undefined
reference to `__intel_sse2_strcat'
...
Thank you for any help you can provide.
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