installation error CNVnator v0.4.1

[ubercomrade]

Hi, I'm trying to install CNVnator (v0.4.1). I got this error:

Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c EXOnator.cpp -o obj/EXOnator.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c IO.cpp -o obj/IO.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c Visualizer.cpp -o obj/Visualizer.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c HisMaker.cpp -o obj/HisMaker.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c AliParser.cpp -o obj/AliParser.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c FastaParser.cpp -o obj/FastaParser.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c VcfParser.cpp -o obj/VcfParser.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c Genotyper.cpp -o obj/Genotyper.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c Interval.cpp -o obj/Interval.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/home/anton/Programs/root/include      -Isamtools -c Genome.cpp -o obj/Genome.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -o cnvnator obj/cnvnator.o obj/EXOnator.o obj/IO.o obj/Visualizer.o obj/HisMaker.o obj/AliParser.o obj/FastaParser.o obj/VcfParser.o obj/Genotyper.o obj/Interval.o obj/Genome.o samtools/libbam.a -lz -lbz2 -lcurl -llzma -lreadline -L/home/anton/Programs/root/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
obj/AliParser.o: In function `AliParser::AliParser(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool)':
AliParser.cpp:(.text+0x573): undefined reference to `hts_idx_load'
obj/AliParser.o: In function `AliParser::~AliParser()':
AliParser.cpp:(.text+0x108b): undefined reference to `hts_idx_destroy'
obj/AliParser.o: In function `AliParser::parseRecord()':
AliParser.cpp:(.text+0x1b32): undefined reference to `sam_read1'
AliParser.cpp:(.text+0x1bd1): undefined reference to `bam_cigar2rlen'
obj/AliParser.o: In function `AliParser::scrollTo(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)':
AliParser.cpp:(.text+0x1d92): undefined reference to `sam_read1'
AliParser.cpp:(.text+0x1f39): undefined reference to `bam_cigar2rlen'
obj/VcfParser.o: In function `VcfParser::VcfParser(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
VcfParser.cpp:(.text+0x18e): undefined reference to `hts_open'
VcfParser.cpp:(.text+0x20f): undefined reference to `hts_open'
VcfParser.cpp:(.text+0x38c): undefined reference to `bcf_hdr_read'
VcfParser.cpp:(.text+0x45e): undefined reference to `bcf_init'
obj/VcfParser.o: In function `VcfParser::parseHeader()':
VcfParser.cpp:(.text+0x9b1): undefined reference to `bcf_hdr_read'
obj/VcfParser.o: In function `VcfParser::parseRecord(bool)':
VcfParser.cpp:(.text+0xb4d): undefined reference to `bcf_is_snp'
VcfParser.cpp:(.text+0xb62): undefined reference to `bcf_read'
VcfParser.cpp:(.text+0xb9c): undefined reference to `bcf_has_filter'
VcfParser.cpp:(.text+0xbc5): undefined reference to `bcf_get_format_values'
VcfParser.cpp:(.text+0xbec): undefined reference to `bcf_get_format_values'
samtools/libbam.a(bam.o): In function `bam_format1':
/home/anton/Programs/samtools/bam.c:39: undefined reference to `sam_format1'
samtools/libbam.a(bam.o): In function `bam_get_library':
/home/anton/Programs/samtools/bam.c:83: undefined reference to `bam_aux_get'
samtools/libbam.a(bam.o): In function `bam_fetch':
/home/anton/Programs/samtools/bam.c:141: undefined reference to `bam_init1'
samtools/libbam.a(bam.o): In function `bam_iter_query':
/home/anton/Programs/samtools/bam.h:481: undefined reference to `sam_itr_queryi'
samtools/libbam.a(bam.o): In function `bam_iter_read':
/home/anton/Programs/samtools/bam.h:482: undefined reference to `hts_itr_next'
/home/anton/Programs/samtools/bam.h:482: undefined reference to `bam_read1'
samtools/libbam.a(bam.o): In function `bam_iter_destroy':
/home/anton/Programs/samtools/bam.h:483: undefined reference to `hts_itr_destroy'
samtools/libbam.a(bam.o): In function `bam_fetch':
/home/anton/Programs/samtools/bam.c:145: undefined reference to `bam_destroy1'
samtools/libbam.a(sam.o): In function `samthreads':
/home/anton/Programs/samtools/sam.c:35: undefined reference to `hts_get_format'
/home/anton/Programs/samtools/sam.c:36: undefined reference to `bgzf_mt'
samtools/libbam.a(sam.o): In function `samopen':
/home/anton/Programs/samtools/sam.c:43: undefined reference to `hts_open'
/home/anton/Programs/samtools/sam.c:55: undefined reference to `hts_set_fai_filename'
/home/anton/Programs/samtools/sam.c:61: undefined reference to `sam_hdr_read'
/home/anton/Programs/samtools/sam.c:68: undefined reference to `hts_verbose'
/home/anton/Programs/samtools/sam.c:72: undefined reference to `hts_get_format'
/home/anton/Programs/samtools/sam.c:76: undefined reference to `sam_hdr_write'
/home/anton/Programs/samtools/sam.c:77: undefined reference to `hts_verbose'
/home/anton/Programs/samtools/sam.c:79: undefined reference to `hts_close'
/home/anton/Programs/samtools/sam.c:48: undefined reference to `hts_close'
samtools/libbam.a(sam.o): In function `samclose':
/home/anton/Programs/samtools/sam.c:92: undefined reference to `bam_hdr_destroy'
/home/anton/Programs/samtools/sam.c:93: undefined reference to `hts_close'
samtools/libbam.a(sam.o): In function `samfetch':
/home/anton/Programs/samtools/sam.c:100: undefined reference to `bam_init1'
/home/anton/Programs/samtools/sam.c:101: undefined reference to `sam_itr_queryi'
/home/anton/Programs/samtools/sam.c:103: undefined reference to `hts_itr_next'
/home/anton/Programs/samtools/sam.c:104: undefined reference to `hts_itr_destroy'
/home/anton/Programs/samtools/sam.c:105: undefined reference to `bam_destroy1'
samtools/libbam.a(sam.o): In function `sampileup':
/home/anton/Programs/samtools/sam.c:114: undefined reference to `bam_init1'
samtools/libbam.a(sam.o): In function `samread':
/home/anton/Programs/samtools/sam.h:95: undefined reference to `sam_read1'
samtools/libbam.a(sam.o): In function `sampileup':
/home/anton/Programs/samtools/sam.c:125: undefined reference to `bam_destroy1'
samtools/libbam.a(sam.o): In function `samfaipath':
/home/anton/Programs/samtools/sam.c:139: undefined reference to `hts_verbose'
/home/anton/Programs/samtools/sam.c:140: undefined reference to `fai_build'
samtools/libbam.a(bam_plbuf.o): In function `bam_plbuf_init':
/home/anton/Programs/samtools/bam_plbuf.c:47: undefined reference to `bam_plp_init'
samtools/libbam.a(bam_plbuf.o): In function `bam_plbuf_destroy':
/home/anton/Programs/samtools/bam_plbuf.c:55: undefined reference to `bam_plp_destroy'
samtools/libbam.a(bam_plbuf.o): In function `bam_plbuf_push':
/home/anton/Programs/samtools/bam_plbuf.c:63: undefined reference to `bam_plp_push'
/home/anton/Programs/samtools/bam_plbuf.c:65: undefined reference to `bam_plp_next'
samtools/libbam.a(bam_plbuf.o): In function `bam_plbuf_reset':
/home/anton/Programs/samtools/bam_plbuf.c:40: undefined reference to `bam_plp_reset'
collect2: error: ld returned 1 exit status
Makefile:66: recipe for target 'cnvnator' failed
make: *** [cnvnator] Error 1

[suvakov]

It seems that something is wrong with samtools. Probably htslib is missing. You can try following: 1) Download newest samtools relaase from (do not clone): https://github.com/samtools/samtools/releases 2) Extracti files and compile with: ./configure make 3) replace "samtools" symbolic link in your CNVnator folder with new samtools folder. 4) Compile CNVnator with: make clean make

[moldach]

None of the install instructions in the README are working for me on Ubuntu 20.04 LTS.

Trying @suvakov suggestion I get the following error: make

Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/include      -Isamtools -Isamtools/htslib-1.10 -Isamtools/htslib-1.10/htslib -c cnvnator.cpp -o obj/cnvnator.o
In file included from cnvnator.cpp:15:
HisMaker.hh:15:10: fatal error: TFrame.h: No such file or directory
   15 | #include <TFrame.h>
      |          ^~~~~~~~~~
compilation terminated.
make: *** [Makefile:70: obj/cnvnator.o] Error 1