bcftools make 失败并在 win10 中出现大量 vcfmerge 错误

Question

I want to compile latest github bcftools but I get these errors below.

[Install instructions] https://raw.githubusercontent.com/samtools/bcftools/develop/INSTALL mentions:

git clone git://github.com/samtools/htslib.git
git clone git://github.com/samtools/bcftools.git
cd bcftools
make

Also, I did the following:

1. BCFTOOLS_PLUGINS=/path/to/bcftools/plugins (added to Makefile) and these 3rd party libraries (downloaded and added to path)
2. zlib, gsl and libperl

ERRORS when make command runs

C:\Users\Admin\bcftools>make
echo '#define BCFTOOLS_VERSION "1.10.2-122-gf09bac3-dirty"' > version.h
gcc -g -Wall -O2 -I. -I../htslib   -c -o main.o main.c
gcc -g -Wall -O2 -I. -I../htslib   -c -o vcfindex.o vcfindex.c
gcc -g -Wall -O2 -I. -I../htslib   -c -o tabix.o tabix.c
gcc -g -Wall -O2 -I. -I../htslib   -c -o vcfstats.o vcfstats.c
gcc -g -Wall -O2 -I. -I../htslib   -c -o vcfisec.o vcfisec.c
gcc -g -Wall -O2 -I. -I../htslib   -c -o vcfmerge.o vcfmerge.c
vcfmerge.c: In function 'merge_GT':
vcfmerge.c:1565:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !warned ) fprintf(stderr,"Warning: Too many genotypes at %s:%"PRId64", requires %zu 
bytes, skipping.\n", bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize);
         ^
vcfmerge.c:1565:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c:1572:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize);
         ^
vcfmerge.c:1572:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c: In function 'merge_format_string':
vcfmerge.c:1743:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at 
%s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out- 
>pos+1,msize);
         ^
vcfmerge.c:1743:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c:1750:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize);
         ^
vcfmerge.c:1750:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c: In function 'merge_localized_numberG_format_field':
vcfmerge.c:1777:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at 
%s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out- 
>pos+1,msize);
         ^
vcfmerge.c:1777:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c:1784:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", 
msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
         ^
vcfmerge.c:1784:9: warning: format '%s' expects argument of type 'char *', but argument 2 has type 
'size_t' [-Wformat=]
vcfmerge.c:1784:9: warning: format '%I64d' expects argument of type 'long long int', but argument 3 
has type 'const char *' [-Wformat=]
vcfmerge.c:1784:9: warning: format '%s' expects argument of type 'char *', but argument 4 has type 
'hts_pos_t' [-Wformat=]
vcfmerge.c:1784:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c: In function 'merge_localized_numberAR_format_field':
vcfmerge.c:1878:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at 
%s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out- 
>pos+1,msize);
         ^
vcfmerge.c:1878:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c:1885:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", 
msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
         ^
vcfmerge.c:1885:9: warning: format '%s' expects argument of type 'char *', but argument 2 has type 
'size_t' [-Wformat=]
vcfmerge.c:1885:9: warning: format '%I64d' expects argument of type 'long long int', but argument 3 
has type 'const char *' [-Wformat=]
vcfmerge.c:1885:9: warning: format '%s' expects argument of type 'char *', but argument 4 has type 
'hts_pos_t' [-Wformat=]
vcfmerge.c:1885:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c: In function 'merge_format_field':
vcfmerge.c:2015:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at 
%s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out- 
>pos+1,msize);
         ^
vcfmerge.c:2015:9: warning: too many arguments for format [-Wformat-extra-args]
vcfmerge.c:2022:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", 
msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
         ^
vcfmerge.c:2022:9: warning: format '%s' expects argument of type 'char *', but argument 2 has type 
'size_t' [-Wformat=]
vcfmerge.c:2022:9: warning: format '%I64d' expects argument of type 'long long int', but argument 3 
has type 'const char *' [-Wformat=]
vcfmerge.c:2022:9: warning: format '%s' expects argument of type 'char *', but argument 4 has type 
'hts_pos_t' [-Wformat=]
vcfmerge.c:2022:9: warning: too many arguments for format [-Wformat-extra-args]
gcc -g -Wall -O2 -I. -I../htslib   -c -o vcfquery.o vcfquery.c
gcc -g -Wall -O2 -I. -I../htslib   -c -o vcffilter.o vcffilter.c
gcc -g -Wall -O2 -I. -I../htslib    -c -o filter.o filter.c
filter.c:36:19: fatal error: regex.h: No such file or directory
 #include <regex.h>
                   ^
compilation terminated.
make: *** [Makefile:259: filter.o] Error 1

Answer 1

installed regex https://github.com/gskinner/regexr and it works

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