Open firewater opened 6 years ago
Hello,
I am trying to install SpeedSeq in the following environment:
However, some error messages related to samtools/libbam.a are being returned which are preventing a successful installation.
I have included my installation notes below along with the first few error messages (there are many, all related to "undefined reference").
Thank you for any help you can provide.
Installation Notes:
/path/to/bin/root
/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
/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
... 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 tointel_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 tointel_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 functionsamopen': /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 tointel_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 tointel_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' ...
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:107: undefined reference to
bam_remove_B': /path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:235: 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' samtools/libbam.a(sam.o): In function
__intel_sse2_strchr' /path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:75: undefined reference to
samfaipath': /path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:133: undefined reference to
__intel_sse2_strcpy' /path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:134: undefined reference to
Hello,
I am trying to install SpeedSeq in the following environment:
However, some error messages related to samtools/libbam.a are being returned which are preventing a successful installation.
I have included my installation notes below along with the first few error messages (there are many, all related to "undefined reference").
Thank you for any help you can provide.
Installation Notes:
/path/to/bin/root/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/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/binsamtools/libbam.a(bam.o): In function
bam_get_library': /path/to/bin/speedseq/speedseq/src/samtools-1.3.1/bam.c:96: undefined reference tointel_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 tointel_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 functionbam_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 functionsamopen': /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 tointel_sse2_strchr' samtools/libbam.a(sam.o): In functionsamfaipath': /path/to/bin/speedseq/speedseq/src/samtools-1.3.1/sam.c:133: undefined reference tointel_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' ...