This my install error, my root, samtools were installed successfully.
`Compiling with parallel (OpenMP) support
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c cnvnator.cpp -o obj/cnvnator.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c EXOnator.cpp -o obj/EXOnator.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c IO.cpp -o obj/IO.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c Visualizer.cpp -o obj/Visualizer.o
g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c HisMaker.cpp -o obj/HisMaker.o
In file included from VcfParser.hh:8:0,
from HisMaker.cpp:7:
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h: In function ‘void bcf_format_gt(bcf_fmt_t, int, kstring_t)’:
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:778:31: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_vector_end (INT8_MIN+1)
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:814:39: note: in definition of macro ‘BRANCH’
for (i=0; in && ptr[i]!=vector_end; i++) \
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:823:62: note: in expansion of macro ‘bcf_int8_vector_end’
case BCF_BT_INT8: BRANCH(int8_t, bcf_int8_missing, bcf_int8_vector_end); break;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:779:31: error: ‘INT16_MIN’ was not declared in this scope
define bcf_int16_vector_end (INT16_MIN+1)
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:814:39: note: in definition of macro ‘BRANCH’
for (i=0; in && ptr[i]!=vector_end; i++) \
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:824:63: note: in expansion of macro ‘bcf_int16_vector_end’
case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:780:31: error: ‘INT32_MIN’ was not declared in this scope
define bcf_int32_vector_end (INT32_MIN+1)
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:814:39: note: in definition of macro ‘BRANCH’
for (i=0; in && ptr[i]!=vector_end; i++) \
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:825:63: note: in expansion of macro ‘bcf_int32_vector_end’
case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h: In function ‘int bcf_enc_inttype(long int)’:
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:855:14: error: ‘INT8_MAX’ was not declared in this scope
if (x <= INT8_MAX && x > bcf_int8_missing) return BCF_BT_INT8;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:782:30: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_missing INT8_MIN
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:855:30: note: in expansion of macro ‘bcf_int8_missing’
if (x <= INT8_MAX && x > bcf_int8_missing) return BCF_BT_INT8;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:856:14: error: ‘INT16_MAX’ was not declared in this scope
if (x <= INT16_MAX && x > bcf_int16_missing) return BCF_BT_INT16;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:783:30: error: ‘INT16_MIN’ was not declared in this scope
define bcf_int16_missing INT16_MIN
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:856:31: note: in expansion of macro ‘bcf_int16_missing’
if (x <= INT16_MAX && x > bcf_int16_missing) return BCF_BT_INT16;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h: In function ‘void bcf_enc_int1(kstring_t*, int32_t)’:
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:780:31: error: ‘INT32_MIN’ was not declared in this scope
define bcf_int32_vector_end (INT32_MIN+1)
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:862:14: note: in expansion of macro ‘bcf_int32_vector_end’
if (x == bcf_int32_vector_end) {
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:778:31: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_vector_end (INT8_MIN+1)
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:864:15: note: in expansion of macro ‘bcf_int8_vector_end’
kputc(bcf_int8_vector_end, s);
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:782:30: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_missing INT8_MIN
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:867:15: note: in expansion of macro ‘bcf_int8_missing’
kputc(bcf_int8_missing, s);
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:868:21: error: ‘INT8_MAX’ was not declared in this scope
} else if (x <= INT8_MAX && x > bcf_int8_missing) {
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:782:30: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_missing INT8_MIN
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:868:37: note: in expansion of macro ‘bcf_int8_missing’
} else if (x <= INT8_MAX && x > bcf_int8_missing) {
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:871:21: error: ‘INT16_MAX’ was not declared in this scope
} else if (x <= INT16_MAX && x > bcf_int16_missing) {
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:783:30: error: ‘INT16_MIN’ was not declared in this scope
define bcf_int16_missing INT16_MIN
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:871:38: note: in expansion of macro ‘bcf_int16_missing’
} else if (x <= INT16_MAX && x > bcf_int16_missing) {
^
make: *** [obj/HisMaker.o] Error 1
`
This my install error, my root, samtools were installed successfully.
`Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c cnvnator.cpp -o obj/cnvnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c EXOnator.cpp -o obj/EXOnator.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c IO.cpp -o obj/IO.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c Visualizer.cpp -o obj/Visualizer.o g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/psd/biosoft/root/build/include -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1 -I/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib -c HisMaker.cpp -o obj/HisMaker.o In file included from VcfParser.hh:8:0, from HisMaker.cpp:7: /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h: In function ‘void bcf_format_gt(bcf_fmt_t, int, kstring_t)’: /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:778:31: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_vector_end (INT8_MIN+1)
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:814:39: note: in definition of macro ‘BRANCH’ for (i=0; in && ptr[i]!=vector_end; i++) \
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:823:62: note: in expansion of macro ‘bcf_int8_vector_end’
case BCF_BT_INT8: BRANCH(int8_t, bcf_int8_missing, bcf_int8_vector_end); break;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:779:31: error: ‘INT16_MIN’ was not declared in this scope
define bcf_int16_vector_end (INT16_MIN+1)
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:814:39: note: in definition of macro ‘BRANCH’ for (i=0; in && ptr[i]!=vector_end; i++) \
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:824:63: note: in expansion of macro ‘bcf_int16_vector_end’
case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:780:31: error: ‘INT32_MIN’ was not declared in this scope
define bcf_int32_vector_end (INT32_MIN+1)
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:814:39: note: in definition of macro ‘BRANCH’ for (i=0; in && ptr[i]!=vector_end; i++) \
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:825:63: note: in expansion of macro ‘bcf_int32_vector_end’
case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h: In function ‘int bcf_enc_inttype(long int)’:
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:855:14: error: ‘INT8_MAX’ was not declared in this scope
if (x <= INT8_MAX && x > bcf_int8_missing) return BCF_BT_INT8;
^
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:782:30: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_missing INT8_MIN
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:855:30: note: in expansion of macro ‘bcf_int8_missing’ if (x <= INT8_MAX && x > bcf_int8_missing) return BCF_BT_INT8; ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:856:14: error: ‘INT16_MAX’ was not declared in this scope if (x <= INT16_MAX && x > bcf_int16_missing) return BCF_BT_INT16; ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:783:30: error: ‘INT16_MIN’ was not declared in this scope
define bcf_int16_missing INT16_MIN
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:856:31: note: in expansion of macro ‘bcf_int16_missing’ if (x <= INT16_MAX && x > bcf_int16_missing) return BCF_BT_INT16; ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h: In function ‘void bcf_enc_int1(kstring_t*, int32_t)’: /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:780:31: error: ‘INT32_MIN’ was not declared in this scope
define bcf_int32_vector_end (INT32_MIN+1)
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:862:14: note: in expansion of macro ‘bcf_int32_vector_end’ if (x == bcf_int32_vector_end) { ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:778:31: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_vector_end (INT8_MIN+1)
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:864:15: note: in expansion of macro ‘bcf_int8_vector_end’ kputc(bcf_int8_vector_end, s); ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:782:30: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_missing INT8_MIN
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:867:15: note: in expansion of macro ‘bcf_int8_missing’ kputc(bcf_int8_missing, s); ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:868:21: error: ‘INT8_MAX’ was not declared in this scope } else if (x <= INT8_MAX && x > bcf_int8_missing) { ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:782:30: error: ‘INT8_MIN’ was not declared in this scope
define bcf_int8_missing INT8_MIN
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:868:37: note: in expansion of macro ‘bcf_int8_missing’ } else if (x <= INT8_MAX && x > bcf_int8_missing) { ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:871:21: error: ‘INT16_MAX’ was not declared in this scope } else if (x <= INT16_MAX && x > bcf_int16_missing) { ^ /psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:783:30: error: ‘INT16_MIN’ was not declared in this scope
define bcf_int16_missing INT16_MIN
/psd/biosoft/samtools_suit/samtools-1.3.1/samtools-1.3.1/htslib-1.3.1/htslib/vcf.h:871:38: note: in expansion of macro ‘bcf_int16_missing’ } else if (x <= INT16_MAX && x > bcf_int16_missing) { ^ make: *** [obj/HisMaker.o] Error 1 `