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Compilation fails with samtools 1.14 and root 6.22+ #255

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Stikus opened this issue Nov 26, 2021 · 1 comment
Open

Compilation fails with samtools 1.14 and root 6.22+ #255

Stikus opened this issue Nov 26, 2021 · 1 comment

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@Stikus
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Stikus commented Nov 26, 2021

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: 'bam1_cigar' was not declared in this scope
     end_       = bam_calend(&core,bam1_cigar(record));
                                   ^~~~~~~~~~
[0m[91mAliParser.cpp:93:35: note: suggested alternative: 'bam_cigar_op'
     end_       = bam_calend(&core,bam1_cigar(record));
                                   ^~~~~~~~~~
                                   bam_cigar_op
AliParser.cpp:93:18: error: 'bam_calend' was not declared in this scope
     end_       = bam_calend(&core,bam1_cigar(record));
                  ^~~~~~~~~~
[0m[91mAliParser.cpp:93:18: note: suggested alternative: 'bam_name2id'
     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<char> 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<char16_t> 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<char32_t> 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<wchar_t> 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<char> 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<char16_t> 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<char32_t> 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<wchar_t> 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<char> 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<char16_t> 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<char32_t> 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<wchar_t> 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<char> 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<char> 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<char16_t> 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<char16_t> 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<char32_t> 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<char32_t> 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<wchar_t> 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<char> 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<wchar_t> 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<char16_t> 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<char32_t> 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<wchar_t> 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<string> userchr;
   ^~~
[0m[91mIO.cpp:420:3: note: suggested alternative: 'gets'
   set<string> userchr;
   ^~~
   gets
IO.cpp:420:13: error: expected primary-expression before '>' token
   set<string> userchr;
             ^
IO.cpp:420:15: error: 'userchr' was not declared in this scope
   set<string> userchr;
               ^~~~~~~
[0m[91mIO.cpp:420:15: note: suggested alternative: 'strchr'
   set<string> 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
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abyzov commented Nov 28, 2021 via email

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