Hello. Latest samtools release removed legacy samtools API (libbam.a, bam_endian.h, sam.h and most of bam.h)

The legacy samtools API (libbam.a, bam_endian.h, sam.h and most of bam.h) has been removed. We recommend coding against the HTSlib API directly. The legacy API had not been actively maintained since 2015

Latest ROOT versions stopped working about year ago (at 6.22 approx). Do you have plans to support latest versions?

I'll post logs below:

All ok - samtools 1.13 & ROOT 6.20.08:


Step 12/19 : RUN cd "$SOFT"     && wget -q "https://github.com/abyzovlab/CNVnator/archive/v${CNVNATOR_VERSION}.tar.gz" -O "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz"     && tar -xzf "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz"     && mv "$SOFT/CNVnator-${CNVNATOR_VERSION}" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src"     && cd "$SOFT/CNVnator-${CNVNATOR_VERSION}-src"     && ln -s "$SOFT/samtools-$SAMTOOLS_VERSION-src" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/samtools"     && sed -i -e 's|-D_GLIBCXX_USE_CXX11_ABI=0 ||' "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/Makefile"     && LIBS="-L${LIBDEFLATE_ROOT}/lib -ldl -ldeflate" make -j"$(($(nproc)+1))"     && mkdir -p "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin"     && mv cnvnator ./*.py ./*.pl "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin"     && mv pytools /usr/local/lib/python*/dist-packages     && rm -rf "$SOFT/samtools-$SAMTOOLS_VERSION-src"     && rm -f "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz"
---> Running in 4bcb253cc49c
Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c cnvnator.cpp -o obj/cnvnator.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c EXOnator.cpp -o obj/EXOnator.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c IO.cpp -o obj/IO.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c Visualizer.cpp -o obj/Visualizer.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c HisMaker.cpp -o obj/HisMaker.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c AliParser.cpp -o obj/AliParser.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c FastaParser.cpp -o obj/FastaParser.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c VcfParser.cpp -o obj/VcfParser.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c Genotyper.cpp -o obj/Genotyper.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c Interval.cpp -o obj/Interval.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include      -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -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 samtools/htslib-1.13/libhts.a -L/soft/libdeflate-1.8/lib -ldl -ldeflate -lz -lbz2 -lcurl -llzma -lreadline -lcrypto -L/soft/root-v6.20.08/lib      -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
Removing intermediate container 4bcb253cc49c
---> 2fb915397b31
Step 13/19 : ENV CNVNATOR="$SOFT/CNVnator-${CNVNATOR_VERSION}/bin/cnvnator"     CNVNATOR2VCF="$SOFT/CNVnator-${CNVNATOR_VERSION}/bin/cnvnator2VCF.pl"     PATH="$SOFT/CNVnator-${CNVNATOR_VERSION}/bin:$PATH"
---> Running in d42f5f692790
Removing intermediate container d42f5f692790
---> 96fcc8b78aee

- samtools error - `samtools 1.14 & ROOT 6.20.08`:

Step 9/16 : RUN cd "$SOFT" && wget -q "https://github.com/abyzovlab/CNVnator/archive/v${CNVNATOR_VERSION}.tar.gz" -O "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && tar -xzf "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && mv "$SOFT/CNVnator-${CNVNATOR_VERSION}" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && cd "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && ln -s "$SOFT/samtools-$SAMTOOLS_VERSION-src" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/samtools" && sed -i -e 's|-D_GLIBCXX_USE_CXX11_ABI=0 ||' "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/Makefile" && LIBS="-L${LIBDEFLATE_ROOT}/lib -ldl -ldeflate" make -j"$(($(nproc)+1))" && mkdir -p "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv cnvnator ./.py ./.pl "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv pytools /usr/local/lib/python/dist-packages && rm -rf "$SOFT/samtools-$SAMTOOLS_VERSION-src" && rm -f "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" ---> Running in 90f899867ea9 Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c EXOnator.cpp -o obj/EXOnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c cnvnator.cpp -o obj/cnvnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c IO.cpp -o obj/IO.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c Visualizer.cpp -o obj/Visualizer.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c HisMaker.cpp -o obj/HisMaker.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c AliParser.cpp -o obj/AliParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c FastaParser.cpp -o obj/FastaParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c VcfParser.cpp -o obj/VcfParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c Genotyper.cpp -o obj/Genotyper.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c Genome.cpp -o obj/Genome.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.20.08/include -Isamtools -Isamtools/htslib-1.14 -Isamtools/htslib-1.14/htslib -c Interval.cpp -o obj/Interval.o [91mIn file included from AliParser.cpp:1:0: AliParser.hh:18:3: error: 'samfile_t' does not name a type; did you mean 'samFile'? samfile_t file; ^~~~~ samFile [0m[91mAliParser.hh:19:3: error: 'bam_index_t' does not name a type; did you mean 'bam_hdr_t'? bam_index_t *index; ^~~ bam_hdr_t [0m[91mAliParser.hh: In member function 'std::__cxx11::string AliParser::getQueryName()': AliParser.hh:98:52: error: 'bam1_qname' was not declared in this scope inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ [0m[91mAliParser.hh:98:52: note: suggested alternative: 'bam_set_qname' inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ bam_set_qname [0m[91mAliParser.cpp: In constructor 'AliParser::AliParser(std::__cxx11::string, bool)': AliParser.cpp:6:14: error: class 'AliParser' does not have any field named 'file' file(NULL), ^~~~ AliParser.cpp:7:14: error: class 'AliParser' does not have any field named 'index' index(NULL), ^~~~~ [0m[91mAliParser.cpp:23:5: error: 'file' was not declared in this scope file = samopen(fileName.c_str(),"rb",NULL); ^~~~ [0m[91mAliParser.cpp:23:5: note: suggested alternative: 'fin' file = samopen(fileName.c_str(),"rb",NULL); ^~~~ fin [0m[91mAliParser.cpp:23:12: error: 'samopen' was not declared in this scope file = samopen(fileName.c_str(),"rb",NULL); ^~~ [0m[91mAliParser.cpp:23:12: note: suggested alternative: 'sam_open' file = samopen(fileName.c_str(),"rb",NULL); ^~~ sam_open [0m[91mIn file included from AliParser.hh:10:0, from AliParser.cpp:1: samtools/htslib-1.14/htslib/sam.h:1143:58: error: overloaded function with no contextual type information

define bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI)

AliParser.cpp:35:15: note: in expansion of macro 'bam_index_load' index = bam_index_load(fileName.c_str()); ^~~~~~ AliParser.cpp:36:12: error: cannot resolve overloaded function 'index' based on conversion to type 'bool' if (!index) cerr<<"Can't load index file for '"<<fileName<<"'."<<endl; ^~~~~ AliParser.cpp:36:12: error: in argument to unary ! [0m[91mAliParser.cpp:41:5: error: 'file' was not declared in this scope file = samopen(fileName.c_str(),"r",NULL); ^~~~ [0m[91mAliParser.cpp:41:5: note: suggested alternative: 'fin' file = samopen(fileName.c_str(),"r",NULL); ^~~~ fin AliParser.cpp:41:12: error: 'samopen' was not declared in this scope file = samopen(fileName.c_str(),"r",NULL); ^~~ [0m[91mAliParser.cpp:41:12: note: suggested alternative: 'sam_open' file = samopen(fileName.c_str(),"r",NULL); ^~~ sam_open [0m[91mAliParser.cpp:62:7: error: 'file' was not declared in this scope if (file) { // sam or bam ^~~~ [0m[91mAliParser.cpp:62:7: note: suggested alternative: 'fin' if (file) { // sam or bam ^~~~ fin [0m[91mAliParser.cpp: In destructor 'AliParser::~AliParser()': AliParser.cpp:77:7: error: 'file' was not declared in this scope if (file) samclose(file); ^~~~ [0m[91mAliParser.cpp:77:7: note: suggested alternative: 'fin' if (file) samclose(file); ^~~~ fin AliParser.cpp:77:16: error: 'samclose' was not declared in this scope if (file) samclose(file); ^~~~ [0m[91mAliParser.cpp:77:16: note: suggested alternative: 'sam_close' if (file) samclose(file); ^~~~ sam_close [0m[91mAliParser.cpp:79:12: error: cannot resolve overloaded function 'index' based on conversion to type 'bool' if (index) bam_index_destroy(index); ^ AliParser.cpp:79:16: error: 'bam_index_destroy' was not declared in this scope if (index) bam_index_destroy(index); ^~~~~ [0m[91mAliParser.cpp:79:16: note: suggested alternative: 'bam_hdr_destroy' if (index) bam_index_destroy(index); ^~~~~ bam_hdr_destroy [0m[91mAliParser.cpp: In member function 'bool AliParser::parseRecord()': AliParser.cpp:88:17: error: 'file' was not declared in this scope if (samread(file,record) < 0) return false; ^~~~ [0m[91mAliParser.cpp:88:17: note: suggested alternative: 'fin' if (samread(file,record) < 0) return false; ^~~~ fin AliParser.cpp:88:9: error: 'samread' was not declared in this scope if (samread(file,record) < 0) return false; ^~~ [0m[91mAliParser.cpp:88:9: note: suggested alternative: 'sam_read1' if (samread(file,record) < 0) return false; ^~~ sam_read1 [0m[91mAliParser.cpp:93:35: error: 'bam1cigar' was not declared in this scope end = bam_calend(&core,bam1_cigar(record)); ^~~~~~ [0m[91mAliParser.cpp:93:35: note: suggested alternative: 'bam_cigarop' end = bam_calend(&core,bam1_cigar(record)); ^~~~~~ bam_cigar_op AliParser.cpp:93:18: error: 'bamcalend' was not declared in this scope end = bam_calend(&core,bam1_cigar(record)); ^~~~~~ [0m[91mAliParser.cpp:93:18: note: suggested alternative: 'bamname2id' end = bam_calend(&core,bam1_cigar(record)); ^~~~~~ bam_name2id [0m[91mAliParser.cpp: In member function 'int AliParser::scrollTo(std::cxx11::string, int)': AliParser.cpp:196:13: error: 'file' was not declared in this scope bam_fetch(file->x.bam,index,chri,start - read_len,start - read_len + 1, ^~~~ [0m[91mAliParser.cpp:196:13: note: suggested alternative: 'fin' bam_fetch(file->x.bam,index,chri,start - read_len,start - read_len + 1, ^~~~ fin [0m[91mAliParser.cpp:196:3: error: 'bam_fetch' was not declared in this scope bam_fetch(file->x.bam,index,chri,start - read_len,start - read_len + 1, ^~~~~ [0m[91mAliParser.cpp:196:3: note: suggested alternative: 'bam_set1' bam_fetch(file->x.bam,index,chri,start - read_len,start - read_len + 1, ^~~~~ bam_set1 [0mMakefile:67: recipe for target 'obj/AliParser.o' failed [91mmake: [obj/AliParser.o] Error 1 make: Waiting for unfinished jobs.... [0m[91mIn file included from cnvnator.cpp:14:0: AliParser.hh:18:3: error: 'samfile_t' does not name a type; did you mean 'samFile'? samfile_t file; ^~~~~ samFile [0m[91mAliParser.hh:19:3: error: 'bam_index_t' does not name a type; did you mean 'bam_hdr_t'? bam_index_t index; ^~~ bam_hdr_t [0m[91mAliParser.hh: In member function 'std::__cxx11::string AliParser::getQueryName()': AliParser.hh:98:52: error: 'bam1_qname' was not declared in this scope inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ [0m[91mAliParser.hh:98:52: note: suggested alternative: 'bam_set_qname' inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ bam_set_qname [0m[91mIn file included from HisMaker.hh:37:0, from Genotyper.cpp:1: AliParser.hh:18:3: error: 'samfile_t' does not name a type; did you mean 'samFile'? samfile_t file; ^~~~~ samFile [0m[91mAliParser.hh:19:3: error: 'bam_index_t' does not name a type; did you mean 'bam_hdr_t'? bam_index_t index; ^~~ bam_hdr_t [0m[91mAliParser.hh: In member function 'std::cxx11::string AliParser::getQueryName()': AliParser.hh:98:52: error: 'bam1_qname' was not declared in this scope inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ [0m[91mAliParser.hh:98:52: note: suggested alternative: 'bam_set_qname' inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ bam_set_qname [0m[91mIn file included from HisMaker.hh:37:0, from HisMaker.cpp:2: AliParser.hh:18:3: error: 'samfile_t' does not name a type; did you mean 'samFile'? samfile_t file; ^~~~~ samFile [0m[91mAliParser.hh:19:3: error: 'bam_index_t' does not name a type; did you mean 'bam_hdr_t'? bam_index_t index; ^~~ bam_hdr_t [0m[91mAliParser.hh: In member function 'std::__cxx11::string AliParser::getQueryName()': AliParser.hh:98:52: error: 'bam1_qname' was not declared in this scope inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ [0m[91mAliParser.hh:98:52: note: suggested alternative: 'bam_set_qname' inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ bam_set_qname [0m[91mmake: [obj/Genotyper.o] Error 1 [0mMakefile:67: recipe for target 'obj/Genotyper.o' failed Makefile:67: recipe for target 'obj/cnvnator.o' failed [91mmake: [obj/cnvnator.o] Error 1 [0mMakefile:67: recipe for target 'obj/HisMaker.o' failed [91mmake: ** [obj/HisMaker.o] Error 1 [0mThe command '/bin/sh -c cd "$SOFT" && wget -q "https://github.com/abyzovlab/CNVnator/archive/v${CNVNATOR_VERSION}.tar.gz" -O "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && tar -xzf "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && mv "$SOFT/CNVnator-${CNVNATOR_VERSION}" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && cd "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && ln -s "$SOFT/samtools-$SAMTOOLS_VERSION-src" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/samtools" && sed -i -e 's|-D_GLIBCXX_USE_CXX11_ABI=0 ||' "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/Makefile" && LIBS="-L${LIBDEFLATE_ROOT}/lib -ldl -ldeflate" make -j"$(($(nproc)+1))" && mkdir -p "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv cnvnator ./.py ./.pl "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv pytools /usr/local/lib/python/dist-packages && rm -rf "$SOFT/samtools-$SAMTOOLS_VERSION-src" && rm -f "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz"' returned a non-zero code: 2 ERROR. Docker build command (/usr/bin/docker build -t nexus.cspmz.ru:8443/cnvnator:latest -t nexus.cspmz.ru:8443/cnvnator:v0.3.1 /var/jenkins/workspace/cnvnator_master/docker) has finished with non zero code (2).

- ROOT error - `samtools 1.13 & ROOT 6.24.06`:

Step 12/19 : RUN cd "$SOFT" && wget -q "https://github.com/abyzovlab/CNVnator/archive/v${CNVNATOR_VERSION}.tar.gz" -O "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && tar -xzf "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && mv "$SOFT/CNVnator-${CNVNATOR_VERSION}" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && cd "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && ln -s "$SOFT/samtools-$SAMTOOLS_VERSION-src" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/samtools" && sed -i -e 's|-D_GLIBCXX_USE_CXX11_ABI=0 ||' "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/Makefile" && LIBS="-L${LIBDEFLATE_ROOT}/lib -ldl -ldeflate" make -j"$(($(nproc)+1))" && mkdir -p "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv cnvnator ./.py ./.pl "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv pytools /usr/local/lib/python/dist-packages && rm -rf "$SOFT/samtools-$SAMTOOLS_VERSION-src" && rm -f "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" ---> Running in 9b14ef2ebff4 Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c cnvnator.cpp -o obj/cnvnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c EXOnator.cpp -o obj/EXOnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c IO.cpp -o obj/IO.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c Visualizer.cpp -o obj/Visualizer.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c HisMaker.cpp -o obj/HisMaker.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c AliParser.cpp -o obj/AliParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c FastaParser.cpp -o obj/FastaParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c VcfParser.cpp -o obj/VcfParser.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c Genotyper.cpp -o obj/Genotyper.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c Interval.cpp -o obj/Interval.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/soft/root-v6.24.06/include -Isamtools -Isamtools/htslib-1.13 -Isamtools/htslib-1.13/htslib -c Genome.cpp -o obj/Genome.o [91mIn file included from /soft/root-v6.24.06/include/TString.h:29:0, from /soft/root-v6.24.06/include/TNamed.h:26, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TROOT.h:28, from IO.hh:20, from IO.cpp:1: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:32:37: error: 'experimental' in namespace 'std' does not name a type using basic_string_view = ::std::experimental::basic_string_view<_CharT,_Traits>; ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:35:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:36:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u16string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:37:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u32string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:38:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view wstring_view; ^~~~~ basic_streambuf /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: warning: inline variables are only available with -std=c++1z or -std=gnu++1z inline double stod(std::string_view str, size_t pos) ^~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: error: 'string_view' is not a member of 'std' [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: note: suggested alternative: 'stringstream' inline double stod(std::string_view str, size_t pos) ^~~ stringstream [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:52: error: expected primary-expression before '' token inline double stod(std::string_view str, size_t pos) ^ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: error: 'pos' was not declared in this scope inline double stod(std::string_view str, size_t pos) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: note: suggested alternative: 'pow' inline double stod(std::string_view str, size_t pos) ^~~ pow /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:56: error: expression list treated as compound expression in initializer [-fpermissive] inline double stod(std::string_view str, size_t pos) ^ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:65:56: error: 'std::string_view' has not been declared inline std::string &operator+=(std::string &left, std::string_view right) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: In function 'std::cxx11::string& std::ROOT::operator+=(std::__cxx11::string&, int)': /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:29: error: request for member 'data' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:43: error: request for member 'size' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: At global scope: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:84:17: error: expected type-specifier operator std::string_view() const { return std::string_view(fData,fLength); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TROOT.h:28, from IO.hh:20, from IO.cpp:1: /soft/root-v6.24.06/include/TString.h:115:13: error: expected type-specifier operator std::string_view() const { return std::string_view(Data(),fExtent); } ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:280:32: error: 'string_view' in namespace 'std' does not name a type explicit TString(const std::string_view &sub); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:317:37: error: 'string_view' in namespace 'std' does not name a type TString &operator=(const std::string_view &s); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:444:9: error: 'string_view' in namespace 'std' does not name a type std::string_view View() const { return std::string_view(GetPointer(),Length()); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TROOT.h:28, from IO.hh:20, from IO.cpp:1: /soft/root-v6.24.06/include/TString.h:839:53: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const char s1, const std::string_view &s2) ^~~ /soft/root-v6.24.06/include/TString.h:839:68: error: 'Bool_t operator==(const char, const int&)' must have an argument of class or enumerated type inline Bool_t operator==(const char s1, const std::string_view &s2) ^ /soft/root-v6.24.06/include/TString.h:844:37: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const std::string_view &s1, const char s2) ^~~ /soft/root-v6.24.06/include/TString.h:844:68: error: 'Bool_t operator==(const int&, const char)' must have an argument of class or enumerated type inline Bool_t operator==(const std::string_view &s1, const char s2) ^ /soft/root-v6.24.06/include/TString.h:857:37: error: 'string_view' in namespace 'std' does not name a type std::string printValue(const std::string_view val); ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TString.h:29:0, from /soft/root-v6.24.06/include/TNamed.h:26, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TROOT.h:28, from IO.hh:20, from Visualizer.hh:4, from Visualizer.cpp:1: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:32:37: error: 'experimental' in namespace 'std' does not name a type using basic_string_view = ::std::experimental::basic_string_view<_CharT,_Traits>; ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:35:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:36:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u16string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:37:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u32string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:38:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view wstring_view; ^~~~~ basic_streambuf /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: warning: inline variables are only available with -std=c++1z or -std=gnu++1z inline double stod(std::string_view str, size_t pos) ^~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: error: 'string_view' is not a member of 'std' [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: note: suggested alternative: 'stringstream' inline double stod(std::string_view str, size_t pos) ^~~ stringstream /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:52: error: expected primary-expression before '' token inline double stod(std::string_view str, size_t pos) ^ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: error: 'pos' was not declared in this scope inline double stod(std::string_view str, size_t pos) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: note: suggested alternative: 'pow' inline double stod(std::string_view str, size_t pos) ^~~ pow /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:56: error: expression list treated as compound expression in initializer [-fpermissive] inline double stod(std::string_view str, size_t pos) ^ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:65:56: error: 'std::string_view' has not been declared inline std::string &operator+=(std::string &left, std::string_view right) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: In function 'std::cxx11::string& std::ROOT::operator+=(std::cxx11::string&, int)': /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:29: error: request for member 'data' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:43: error: request for member 'size' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: At global scope: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:84:17: error: expected type-specifier operator std::string_view() const { return std::string_view(fData,fLength); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TString.h:29:0, from /soft/root-v6.24.06/include/TNamed.h:26, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TDirectoryFile.h:25, from /soft/root-v6.24.06/include/TFile.h:28, from EXOnator.hh:13, from EXOnator.cpp:2: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:32:37: error: 'experimental' in namespace 'std' does not name a type using basic_string_view = ::std::experimental::basic_string_view<_CharT,_Traits>; ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:35:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:36:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u16string_view; ^~~~~ basic_streambuf [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TROOT.h:28, from IO.hh:20, from Visualizer.hh:4, from Visualizer.cpp:1: /soft/root-v6.24.06/include/TString.h:115:13: error: expected type-specifier operator std::string_view() const { return std::string_view(Data(),fExtent); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TString.h:29:0, from /soft/root-v6.24.06/include/TNamed.h:26, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from Genotyper.cpp:1: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:32:37: error: 'experimental' in namespace 'std' does not name a type using basic_string_view = ::std::experimental::basic_string_view<_CharT,_Traits>; ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:37:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u32string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/TString.h:280:32: error: 'string_view' in namespace 'std' does not name a type explicit TString(const std::string_view &sub); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:317:37: error: 'string_view' in namespace 'std' does not name a type TString &operator=(const std::string_view &s); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:444:9: error: 'string_view' in namespace 'std' does not name a type std::string_view View() const { return std::string_view(GetPointer(),Length()); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TString.h:29:0, from /soft/root-v6.24.06/include/TNamed.h:26, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from cnvnator.cpp:15: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:32:37: error: 'experimental' in namespace 'std' does not name a type using basic_string_view = ::std::experimental::basic_string_view<_CharT,_Traits>; ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:38:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view wstring_view; ^~~~~ basic_streambuf /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: warning: inline variables are only available with -std=c++1z or -std=gnu++1z inline double stod(std::string_view str, size_t pos) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: error: 'string_view' is not a member of 'std' [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: note: suggested alternative: 'stringstream' inline double stod(std::string_view str, size_t pos) ^~~ stringstream /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:52: error: expected primary-expression before '' token inline double stod(std::string_view str, size_t pos) ^ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: error: 'pos' was not declared in this scope inline double stod(std::string_view str, size_t pos) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:35:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: note: suggested alternative: 'pow' inline double stod(std::string_view str, size_t pos) ^~~ pow /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:56: error: expression list treated as compound expression in initializer [-fpermissive] inline double stod(std::string_view str, size_t *pos) ^ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:65:56: error: 'std::string_view' has not been declared inline std::string &operator+=(std::string &left, std::string_view right) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: In function 'std::cxx11::string& std::ROOT::operator+=(std::cxx11::string&, int)': /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:29: error: request for member 'data' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:43: error: request for member 'size' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: At global scope: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:84:17: error: expected type-specifier operator std::string_view() const { return std::string_view(fData,fLength); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TROOT.h:28, from IO.hh:20, from Visualizer.hh:4, from Visualizer.cpp:1: /soft/root-v6.24.06/include/TString.h:839:53: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const char s1, const std::string_view &s2) ^~~ /soft/root-v6.24.06/include/TString.h:839:68: error: 'Bool_t operator==(const char, const int&)' must have an argument of class or enumerated type inline Bool_t operator==(const char s1, const std::string_view &s2) ^ [0m[91m/soft/root-v6.24.06/include/TString.h:844:37: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const std::string_view &s1, const char s2) ^~~ /soft/root-v6.24.06/include/TString.h:844:68: error: 'Bool_t operator==(const int&, const char)' must have an argument of class or enumerated type inline Bool_t operator==(const std::string_view &s1, const char s2) ^ [0m[91m/soft/root-v6.24.06/include/TString.h:857:37: error: 'string_view' in namespace 'std' does not name a type std::string printValue(const std::string_view val); ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:35:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:36:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u16string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:36:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u16string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:37:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u32string_view; ^~~~~ basic_streambuf [0m[91mIn file included from /soft/root-v6.24.06/include/TString.h:29:0, from /soft/root-v6.24.06/include/TNamed.h:26, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from HisMaker.cpp:2: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:32:37: error: 'experimental' in namespace 'std' does not name a type using basic_string_view = ::std::experimental::basic_string_view<_CharT,_Traits>; ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:37:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u32string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:38:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view wstring_view; ^~~~~ basic_streambuf /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: warning: inline variables are only available with -std=c++1z or -std=gnu++1z inline double stod(std::string_view str, size_t pos) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: error: 'string_view' is not a member of 'std' [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: note: suggested alternative: 'stringstream' inline double stod(std::string_view str, size_t pos) ^~~ stringstream /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:52: error: expected primary-expression before '' token inline double stod(std::string_view str, size_t pos) ^ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: error: 'pos' was not declared in this scope inline double stod(std::string_view str, size_t pos) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: note: suggested alternative: 'pow' inline double stod(std::string_view str, size_t pos) ^~~ pow /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:56: error: expression list treated as compound expression in initializer [-fpermissive] inline double stod(std::string_view str, size_t pos) ^ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:65:56: error: 'std::string_view' has not been declared inline std::string &operator+=(std::string &left, std::string_view right) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: In function 'std::cxx11::string& std::ROOT::operator+=(std::cxx11::string&, int)': /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:29: error: request for member 'data' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:43: error: request for member 'size' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: At global scope: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:84:17: error: expected type-specifier operator std::string_view() const { return std::string_view(fData,fLength); } ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:35:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view string_view; ^~~~~ basic_streambuf /soft/root-v6.24.06/include/ROOT/RStringView.hxx:38:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view wstring_view; ^~~~~ basic_streambuf /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: warning: inline variables are only available with -std=c++1z or -std=gnu++1z inline double stod(std::string_view str, size_t pos) ^~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: error: 'string_view' is not a member of 'std' [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: note: suggested alternative: 'stringstream' inline double stod(std::string_view str, size_t pos) ^~~ stringstream /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:52: error: expected primary-expression before '' token inline double stod(std::string_view str, size_t pos) ^ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: error: 'pos' was not declared in this scope inline double stod(std::string_view str, size_t pos) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: note: suggested alternative: 'pow' inline double stod(std::string_view str, size_t pos) ^~~ pow /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:56: error: expression list treated as compound expression in initializer [-fpermissive] inline double stod(std::string_view str, size_t *pos) ^ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:65:56: error: 'std::string_view' has not been declared inline std::string &operator+=(std::string &left, std::string_view right) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: In function 'std::cxx11::string& std::ROOT::operator+=(std::cxx11::string&, int)': /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:29: error: request for member 'data' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:43: error: request for member 'size' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: At global scope: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:84:17: error: expected type-specifier operator std::string_view() const { return std::string_view(fData,fLength); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TDirectoryFile.h:25, from /soft/root-v6.24.06/include/TFile.h:28, from EXOnator.hh:13, from EXOnator.cpp:2: /soft/root-v6.24.06/include/TString.h:115:13: error: expected type-specifier operator std::string_view() const { return std::string_view(Data(),fExtent); } ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:36:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u16string_view; ^~~~~ basic_streambuf [0m[91m/soft/root-v6.24.06/include/TString.h:280:32: error: 'string_view' in namespace 'std' does not name a type explicit TString(const std::string_view &sub); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:317:37: error: 'string_view' in namespace 'std' does not name a type TString &operator=(const std::string_view &s); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:444:9: error: 'string_view' in namespace 'std' does not name a type std::string_view View() const { return std::string_view(GetPointer(),Length()); } ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:37:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view u32string_view; ^~~~~ basic_streambuf [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TDirectory.h:24, from /soft/root-v6.24.06/include/TDirectoryFile.h:25, from /soft/root-v6.24.06/include/TFile.h:28, from EXOnator.hh:13, from EXOnator.cpp:2: /soft/root-v6.24.06/include/TString.h:839:53: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const char s1, const std::string_view &s2) ^~~ /soft/root-v6.24.06/include/TString.h:839:68: error: 'Bool_t operator==(const char, const int&)' must have an argument of class or enumerated type inline Bool_t operator==(const char s1, const std::string_view &s2) ^ /soft/root-v6.24.06/include/TString.h:844:37: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const std::string_view &s1, const char s2) ^~~ /soft/root-v6.24.06/include/TString.h:844:68: error: 'Bool_t operator==(const int&, const char)' must have an argument of class or enumerated type inline Bool_t operator==(const std::string_view &s1, const char s2) ^ /soft/root-v6.24.06/include/TString.h:857:37: error: 'string_view' in namespace 'std' does not name a type std::string printValue(const std::string_view val); ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:38:12: error: 'basic_string_view' does not name a type; did you mean 'basic_streambuf'? typedef basic_string_view wstring_view; ^~~~~ basic_streambuf /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: warning: inline variables are only available with -std=c++1z or -std=gnu++1z inline double stod(std::string_view str, size_t pos) ^~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: error: 'string_view' is not a member of 'std' [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:28: note: suggested alternative: 'stringstream' inline double stod(std::string_view str, size_t pos) ^~~ stringstream /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:52: error: expected primary-expression before '' token inline double stod(std::string_view str, size_t pos) ^ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: error: 'pos' was not declared in this scope inline double stod(std::string_view str, size_t pos) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:53: note: suggested alternative: 'pow' inline double stod(std::string_view str, size_t pos) ^~~ pow /soft/root-v6.24.06/include/ROOT/RStringView.hxx:48:56: error: expression list treated as compound expression in initializer [-fpermissive] inline double stod(std::string_view str, size_t pos) ^ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx:65:56: error: 'std::string_view' has not been declared inline std::string &operator+=(std::string &left, std::string_view right) ^~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: In function 'std::cxx11::string& std::ROOT::operator+=(std::__cxx11::string&, int)': /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:29: error: request for member 'data' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ /soft/root-v6.24.06/include/ROOT/RStringView.hxx:67:43: error: request for member 'size' in 'right', which is of non-class type 'int' return left.append(right.data(), right.size()); ^~~~ [0m[91m/soft/root-v6.24.06/include/ROOT/RStringView.hxx: At global scope: /soft/root-v6.24.06/include/ROOT/RStringView.hxx:84:17: error: expected type-specifier operator std::string_view() const { return std::string_view(fData,fLength); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from Genotyper.cpp:1: /soft/root-v6.24.06/include/TString.h:115:13: error: expected type-specifier operator std::string_view() const { return std::string_view(Data(),fExtent); } ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:280:32: error: 'string_view' in namespace 'std' does not name a type explicit TString(const std::string_view &sub); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:317:37: error: 'string_view' in namespace 'std' does not name a type TString &operator=(const std::string_view &s); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:444:9: error: 'string_view' in namespace 'std' does not name a type std::string_view View() const { return std::string_view(GetPointer(),Length()); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from cnvnator.cpp:15: /soft/root-v6.24.06/include/TString.h:115:13: error: expected type-specifier operator std::string_view() const { return std::string_view(Data(),fExtent); } ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:280:32: error: 'string_view' in namespace 'std' does not name a type explicit TString(const std::string_view &sub); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:317:37: error: 'string_view' in namespace 'std' does not name a type TString &operator=(const std::string_view &s); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:444:9: error: 'string_view' in namespace 'std' does not name a type std::string_view View() const { return std::string_view(GetPointer(),Length()); } ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from Genotyper.cpp:1: /soft/root-v6.24.06/include/TString.h:839:53: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const char s1, const std::string_view &s2) ^~~ /soft/root-v6.24.06/include/TString.h:839:68: error: 'Bool_t operator==(const char, const int&)' must have an argument of class or enumerated type inline Bool_t operator==(const char s1, const std::string_view &s2) ^ /soft/root-v6.24.06/include/TString.h:844:37: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const std::string_view &s1, const char s2) ^~~ /soft/root-v6.24.06/include/TString.h:844:68: error: 'Bool_t operator==(const int&, const char)' must have an argument of class or enumerated type inline Bool_t operator==(const std::string_view &s1, const char s2) ^ /soft/root-v6.24.06/include/TString.h:857:37: error: 'string_view' in namespace 'std' does not name a type std::string printValue(const std::string_view val); ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from cnvnator.cpp:15: /soft/root-v6.24.06/include/TString.h:839:53: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const char s1, const std::string_view &s2) ^~~ /soft/root-v6.24.06/include/TString.h:839:68: error: 'Bool_t operator==(const char, const int&)' must have an argument of class or enumerated type inline Bool_t operator==(const char s1, const std::string_view &s2) ^ /soft/root-v6.24.06/include/TString.h:844:37: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const std::string_view &s1, const char s2) ^~~ /soft/root-v6.24.06/include/TString.h:844:68: error: 'Bool_t operator==(const int&, const char)' must have an argument of class or enumerated type inline Bool_t operator==(const std::string_view &s1, const char s2) ^ /soft/root-v6.24.06/include/TString.h:857:37: error: 'string_view' in namespace 'std' does not name a type std::string printValue(const std::string_view val); ^~~ [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from HisMaker.cpp:2: /soft/root-v6.24.06/include/TString.h:115:13: error: expected type-specifier operator std::string_view() const { return std::string_view(Data(),fExtent); } ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:280:32: error: 'string_view' in namespace 'std' does not name a type explicit TString(const std::string_view &sub); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:317:37: error: 'string_view' in namespace 'std' does not name a type TString &operator=(const std::string_view &s); ^~~ [0m[91m/soft/root-v6.24.06/include/TString.h:444:9: error: 'string_view' in namespace 'std' does not name a type std::string_view View() const { return std::string_view(GetPointer(),Length()); } ^~~ [0m[91mIn file included from IO.hh:21:0, from IO.cpp:1: /soft/root-v6.24.06/include/TFile.h:327:45: error: 'std::string_view' has not been declared static Bool_t SetCacheFileDir(std::string_view cacheDir, Bool_t operateDisconnected = kTRUE, ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h: In static member function 'static Bool_t TFile::SetCacheFileDir(ROOT::Internal::TStringView, Bool_t, Bool_t)': /soft/root-v6.24.06/include/TFile.h:326:36: error: 'string_view' is not a member of 'std' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h:326:36: note: suggested alternative: 'stringstream' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ stringstream [0m[91mIn file included from /soft/root-v6.24.06/include/TNamed.h:26:0, from /soft/root-v6.24.06/include/TColor.h:15, from /soft/root-v6.24.06/include/TWbox.h:18, from /soft/root-v6.24.06/include/TFrame.h:16, from HisMaker.hh:15, from HisMaker.cpp:2: /soft/root-v6.24.06/include/TString.h:839:53: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const char s1, const std::string_view &s2) ^~~ /soft/root-v6.24.06/include/TString.h:839:68: error: 'Bool_t operator==(const char, const int&)' must have an argument of class or enumerated type inline Bool_t operator==(const char s1, const std::string_view &s2) ^ /soft/root-v6.24.06/include/TString.h:844:37: error: 'string_view' in namespace 'std' does not name a type inline Bool_t operator==(const std::string_view &s1, const char s2) ^~~ /soft/root-v6.24.06/include/TString.h:844:68: error: 'Bool_t operator==(const int&, const char)' must have an argument of class or enumerated type inline Bool_t operator==(const std::string_view &s1, const char s2) ^ /soft/root-v6.24.06/include/TString.h:857:37: error: 'string_view' in namespace 'std' does not name a type std::string printValue(const std::string_view val); ^~~ [0m[91mIn file included from IO.hh:21:0, from Visualizer.hh:4, from Visualizer.cpp:1: /soft/root-v6.24.06/include/TFile.h:327:45: error: 'std::string_view' has not been declared static Bool_t SetCacheFileDir(std::string_view cacheDir, Bool_t operateDisconnected = kTRUE, ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h: In static member function 'static Bool_t TFile::SetCacheFileDir(ROOT::Internal::TStringView, Bool_t, Bool_t)': /soft/root-v6.24.06/include/TFile.h:326:36: error: 'string_view' is not a member of 'std' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h:326:36: note: suggested alternative: 'stringstream' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ stringstream [0m[91mIO.cpp: In constructor 'IO::IO(std::__cxx11::string)': IO.cpp:41:23: error: invalid use of incomplete type 'class TKey' TObject obj = key->ReadObj(); ^~ In file included from /soft/root-v6.24.06/include/TROOT.h:28:0, from IO.hh:20, from IO.cpp:1: /soft/root-v6.24.06/include/TDirectory.h:38:7: note: forward declaration of 'class TKey' class TKey; ^~~~ [0m[91mIn file included from EXOnator.hh:13:0, from EXOnator.cpp:2: /soft/root-v6.24.06/include/TFile.h:327:45: error: 'std::string_view' has not been declared static Bool_t SetCacheFileDir(std::string_view cacheDir, Bool_t operateDisconnected = kTRUE, ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h: In static member function 'static Bool_t TFile::SetCacheFileDir(ROOT::Internal::TStringView, Bool_t, Bool_t)': /soft/root-v6.24.06/include/TFile.h:326:36: error: 'string_view' is not a member of 'std' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h:326:36: note: suggested alternative: 'stringstream' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ stringstream [0m[91mIO.cpp: In member function 'void IO::cptrees(std::cxx11::string, std::cxx11::string, int)': IO.cpp:420:3: error: 'set' was not declared in this scope set userchr; ^~~ [0m[91mIO.cpp:420:3: note: suggested alternative: 'gets' set userchr; ^~~ gets IO.cpp:420:13: error: expected primary-expression before '>' token set userchr; ^ IO.cpp:420:15: error: 'userchr' was not declared in this scope set userchr; ^~~ [0m[91mIO.cpp:420:15: note: suggested alternative: 'strchr' set userchr; ^~~ strchr [0m[91mIO.cpp:441:23: error: invalid use of incomplete type 'class TKey' TObject obj = key->ReadObj(); ^~ In file included from /soft/root-v6.24.06/include/TROOT.h:28:0, from IO.hh:20, from IO.cpp:1: /soft/root-v6.24.06/include/TDirectory.h:38:7: note: forward declaration of 'class TKey' class TKey; ^~~~ [0m[91mIn file included from HisMaker.hh:21:0, from cnvnator.cpp:15: /soft/root-v6.24.06/include/TFile.h:327:45: error: 'std::string_view' has not been declared static Bool_t SetCacheFileDir(std::string_view cacheDir, Bool_t operateDisconnected = kTRUE, ^~~ [0m[91mIn file included from HisMaker.hh:21:0, from Genotyper.cpp:1: /soft/root-v6.24.06/include/TFile.h:327:45: error: 'std::string_view' has not been declared static Bool_t SetCacheFileDir(std::string_view cacheDir, Bool_t operateDisconnected = kTRUE, ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h: In static member function 'static Bool_t TFile::SetCacheFileDir(ROOT::Internal::TStringView, Bool_t, Bool_t)': /soft/root-v6.24.06/include/TFile.h:326:36: error: 'string_view' is not a member of 'std' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h: In static member function 'static Bool_t TFile::SetCacheFileDir(ROOT::Internal::TStringView, Bool_t, Bool_t)': /soft/root-v6.24.06/include/TFile.h:326:36: error: 'string_view' is not a member of 'std' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h:326:36: note: suggested alternative: 'stringstream' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ stringstream [0m[91m/soft/root-v6.24.06/include/TFile.h:326:36: note: suggested alternative: 'stringstream' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ stringstream [0m[91mIn file included from HisMaker.hh:21:0, from HisMaker.cpp:2: /soft/root-v6.24.06/include/TFile.h:327:45: error: 'std::string_view' has not been declared static Bool_t SetCacheFileDir(std::string_view cacheDir, Bool_t operateDisconnected = kTRUE, ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h: In static member function 'static Bool_t TFile::SetCacheFileDir(ROOT::Internal::TStringView, Bool_t, Bool_t)': /soft/root-v6.24.06/include/TFile.h:326:36: error: 'string_view' is not a member of 'std' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ [0m[91m/soft/root-v6.24.06/include/TFile.h:326:36: note: suggested alternative: 'stringstream' { return SetCacheFileDir(std::string_view(cacheDir), operateDisconnected, forceCacheread); } ^~~ stringstream [0mMakefile:67: recipe for target 'obj/IO.o' failed [91mmake: [obj/IO.o] Error 1 make: Waiting for unfinished jobs.... [0mMakefile:67: recipe for target 'obj/cnvnator.o' failed [91mmake: [obj/cnvnator.o] Error 1 [0mMakefile:67: recipe for target 'obj/Genotyper.o' failed [91mmake: [obj/Genotyper.o] Error 1 [0mMakefile:67: recipe for target 'obj/EXOnator.o' failed [91mmake: [obj/EXOnator.o] Error 1 [0m[91mmake: [obj/Visualizer.o] Error 1 [0mMakefile:67: recipe for target 'obj/Visualizer.o' failed Makefile:67: recipe for target 'obj/HisMaker.o' failed [91mmake: ** [obj/HisMaker.o] Error 1 [0mThe command '/bin/sh -c cd "$SOFT" && wget -q "https://github.com/abyzovlab/CNVnator/archive/v${CNVNATOR_VERSION}.tar.gz" -O "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && tar -xzf "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && mv "$SOFT/CNVnator-${CNVNATOR_VERSION}" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && cd "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && ln -s "$SOFT/samtools-$SAMTOOLS_VERSION-src" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/samtools" && sed -i -e 's|-D_GLIBCXX_USE_CXX11_ABI=0 ||' "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/Makefile" && LIBS="-L${LIBDEFLATE_ROOT}/lib -ldl -ldeflate" make -j"$(($(nproc)+1))" && mkdir -p "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv cnvnator ./.py ./.pl "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv pytools /usr/local/lib/python/dist-packages && rm -rf "$SOFT/samtools-$SAMTOOLS_VERSION-src" && rm -f "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz"' returned a non-zero code: 2

Hi Konstantin, we recommend switching to CNVpytor (https://github.com/abyzovlab/cnvpytor). Though we may support CNVnator for some time.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978

On Nov 26, 2021, at 4:39 AM, Grammatikati Konstantin @.**@.>> wrote:

Hello. Latest samtools releasehttps://github.com/samtools/samtools/releases/tag/1.14 removed legacy samtools API (libbam.a, bam_endian.h, sam.h and most of bam.h)

The legacy samtools API (libbam.a, bam_endian.h, sam.h and most of bam.h) has been removed. We recommend coding against the HTSlib API directly. The legacy API had not been actively maintained since 2015

Latest ROOT versions stopped working about year ago (at 6.22 approx). Do you have plans to support latest versions?

I'll post logs below:

All ok - samtools 1.13 & ROOT 6.20.08:

samtools error - samtools 1.14 & ROOT 6.20.08:

define bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI)

AliParser.cpp:35:15: note: in expansion of macro 'bam_index_load' index = bam_index_load(fileName.c_str()); ^~~~~~ AliParser.cpp:36:12: error: cannot resolve overloaded function 'index' based on conversion to type 'bool' if (!index) cerr<<"Can't load index file for '"<<fileName<<"'."<<endl; ^~~~~ AliParser.cpp:36:12: error: in argument to unary ! [0m[91mAliParser.cpp:41:5: error: 'file' was not declared in this scope file = samopen(fileName.c_str(),"r",NULL); ^~~~ [0m[91mAliParser.cpp:41:5: note: suggested alternative: 'fin' file = samopen(fileName.c_str(),"r",NULL); ^~~~ fin AliParser.cpp:41:12: error: 'samopen' was not declared in this scope file = samopen(fileName.c_str(),"r",NULL); ^~~ [0m[91mAliParser.cpp:41:12: note: suggested alternative: 'sam_open' file = samopen(fileName.c_str(),"r",NULL); ^~~ sam_open [0m[91mAliParser.cpp:62:7: error: 'file' was not declared in this scope if (file) { // sam or bam ^~~~ [0m[91mAliParser.cpp:62:7: note: suggested alternative: 'fin' if (file) { // sam or bam ^~~~ fin [0m[91mAliParser.cpp: In destructor 'AliParser::~AliParser()': AliParser.cpp:77:7: error: 'file' was not declared in this scope if (file) samclose(file); ^~~~ [0m[91mAliParser.cpp:77:7: note: suggested alternative: 'fin' if (file) samclose(file); ^~~~ fin AliParser.cpp:77:16: error: 'samclose' was not declared in this scope if (file) samclose(file); ^~~~ [0m[91mAliParser.cpp:77:16: note: suggested alternative: 'sam_close' if (file) samclose(file); ^~~~ sam_close [0m[91mAliParser.cpp:79:12: error: cannot resolve overloaded function 'index' based on conversion to type 'bool' if (index) bam_index_destroy(index); ^ AliParser.cpp:79:16: error: 'bam_index_destroy' was not declared in this scope if (index) bam_index_destroy(index); ^~~~~ [0m[91mAliParser.cpp:79:16: note: suggested alternative: 'bam_hdr_destroy' if (index) bam_index_destroy(index); ^~~~~ bam_hdr_destroy [0m[91mAliParser.cpp: In member function 'bool AliParser::parseRecord()': AliParser.cpp:88:17: error: 'file' was not declared in this scope if (samread(file,record) < 0) return false; ^~~~ [0m[91mAliParser.cpp:88:17: note: suggested alternative: 'fin' if (samread(file,record) < 0) return false; ^~~~ fin AliParser.cpp:88:9: error: 'samread' was not declared in this scope if (samread(file,record) < 0) return false; ^~~ [0m[91mAliParser.cpp:88:9: note: suggested alternative: 'sam_read1' if (samread(file,record) < 0) return false; ^~~ sam_read1 [0m[91mAliParser.cpp:93:35: error: 'bam1cigar' was not declared in this scope end = bam_calend(&core,bam1_cigar(record)); ^~~~~~ [0m[91mAliParser.cpp:93:35: note: suggested alternative: 'bam_cigarop' end = bam_calend(&core,bam1_cigar(record)); ^~~~~~ bam_cigar_op AliParser.cpp:93:18: error: 'bamcalend' was not declared in this scope end = bam_calend(&core,bam1_cigar(record)); ^~~~~~ [0m[91mAliParser.cpp:93:18: note: suggested alternative: 'bamname2id' end = bam_calend(&core,bam1_cigar(record)); ^~~~~~ bam_name2id [0m[91mAliParser.cpp: In member function 'int AliParser::scrollTo(std::cxx11::string, int)': AliParser.cpp:196:13: error: 'file' was not declared in this scope bam_fetch(file->x.bam,index,chri,start - read_len,start - read_len + 1, ^~~~ [0m[91mAliParser.cpp:196:13: note: suggested alternative: 'fin' bam_fetch(file->x.bam,index,chri,start - read_len,start - read_len + 1, ^~~~ fin [0m[91mAliParser.cpp:196:3: error: 'bam_fetch' was not declared in this scope bam_fetch(file->x.bam,index,chri,start - read_len,start - read_len + 1, ^~~~~ [0m[91mAliParser.cpp:196:3: note: suggested alternative: 'bam_set1' bam_fetch(file->x.bam,index,chri,start - read_len,start - read_len + 1, ^~~~~ bam_set1 [0mMakefile:67: recipe for target 'obj/AliParser.o' failed [91mmake: [obj/AliParser.o] Error 1 make: Waiting for unfinished jobs.... [0m[91mIn file included from cnvnator.cpp:14:0: AliParser.hh:18:3: error: 'samfile_t' does not name a type; did you mean 'samFile'? samfile_t file; ^~~~~ samFile [0m[91mAliParser.hh:19:3: error: 'bam_index_t' does not name a type; did you mean 'bam_hdr_t'? bam_index_t index; ^~~ bam_hdr_t [0m[91mAliParser.hh: In member function 'std::__cxx11::string AliParser::getQueryName()': AliParser.hh:98:52: error: 'bam1_qname' was not declared in this scope inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ [0m[91mAliParser.hh:98:52: note: suggested alternative: 'bam_set_qname' inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ bam_set_qname [0m[91mIn file included from HisMaker.hh:37:0, from Genotyper.cpp:1: AliParser.hh:18:3: error: 'samfile_t' does not name a type; did you mean 'samFile'? samfile_t file; ^~~~~ samFile [0m[91mAliParser.hh:19:3: error: 'bam_index_t' does not name a type; did you mean 'bam_hdr_t'? bam_index_t index; ^~~ bam_hdr_t [0m[91mAliParser.hh: In member function 'std::cxx11::string AliParser::getQueryName()': AliParser.hh:98:52: error: 'bam1_qname' was not declared in this scope inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ [0m[91mAliParser.hh:98:52: note: suggested alternative: 'bam_set_qname' inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ bam_set_qname [0m[91mIn file included from HisMaker.hh:37:0, from HisMaker.cpp:2: AliParser.hh:18:3: error: 'samfile_t' does not name a type; did you mean 'samFile'? samfile_t file; ^~~~~ samFile [0m[91mAliParser.hh:19:3: error: 'bam_index_t' does not name a type; did you mean 'bam_hdr_t'? bam_index_t index; ^~~ bam_hdr_t [0m[91mAliParser.hh: In member function 'std::__cxx11::string AliParser::getQueryName()': AliParser.hh:98:52: error: 'bam1_qname' was not declared in this scope inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ [0m[91mAliParser.hh:98:52: note: suggested alternative: 'bam_set_qname' inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^~~~~~ bam_set_qname [0m[91mmake: [obj/Genotyper.o] Error 1 [0mMakefile:67: recipe for target 'obj/Genotyper.o' failed Makefile:67: recipe for target 'obj/cnvnator.o' failed [91mmake: [obj/cnvnator.o] Error 1 [0mMakefile:67: recipe for target 'obj/HisMaker.o' failed [91mmake: ** [obj/HisMaker.o] Error 1 [0mThe command '/bin/sh -c cd "$SOFT" && wget -q "https://github.com/abyzovlab/CNVnator/archive/v${CNVNATOR_VERSION}.tar.gz" -O "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && tar -xzf "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz" && mv "$SOFT/CNVnator-${CNVNATOR_VERSION}" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && cd "$SOFT/CNVnator-${CNVNATOR_VERSION}-src" && ln -s "$SOFT/samtools-$SAMTOOLS_VERSION-src" "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/samtools" && sed -i -e 's|-D_GLIBCXX_USE_CXX11_ABI=0 ||' "$SOFT/CNVnator-${CNVNATOR_VERSION}-src/Makefile" && LIBS="-L${LIBDEFLATE_ROOT}/lib -ldl -ldeflate" make -j"$(($(nproc)+1))" && mkdir -p "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv cnvnator ./.py ./.pl "$SOFT/CNVnator-${CNVNATOR_VERSION}/bin" && mv pytools /usr/local/lib/python/dist-packages && rm -rf "$SOFT/samtools-$SAMTOOLS_VERSION-src" && rm -f "$SOFT/CNVnator-${CNVNATOR_VERSION}.tar.gz"' returned a non-zero code: 2 ERROR. Docker build command (/usr/bin/docker build -t nexus.cspmz.ru:8443/cnvnator:latesthttp://nexus.cspmz.ru:8443/cnvnator:latest -t nexus.cspmz.ru:8443/cnvnator:v0.3.1http://nexus.cspmz.ru:8443/cnvnator:v0.3.1 /var/jenkins/workspace/cnvnator_master/docker) has finished with non zero code (2).

ROOT error - samtools 1.13 & ROOT 6.24.06:

abyzovlab / CNVnator

Compilation fails with samtools 1.14 and root 6.22+ #255

define bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI)

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

define bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI)