I got errors when I run ./build_all.sh so I run step by step and finally found the error was caused by make in /polisher/external/install/htslib/. Here is the log:
cd external/install/htslib
autoreconf
./configure --prefix=$(pwd) --disable-bz2 --disable-lzma
make
/path/to/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /path/to/include -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /path/to/include -c -o bgzf.o bgzf.c
In file included from htslib/khash.h:131,
from bgzf.c:79:
/path/to/include/htslib/kstring.h:91:18: error: expected ';' before 'int'
91 | HTSLIB_EXPORT
| ^
| ;
92 | int kvsprintf(kstring_t *s, const char *fmt, va_list ap) KS_ATTR_PRINTF(2,0);
| ~~~
/path/to/include/htslib/kstring.h:94:18: error: expected ';' before 'int'
94 | HTSLIB_EXPORT
| ^
| ;
95 | int ksprintf(kstring_t *s, const char *fmt, ...) KS_ATTR_PRINTF(2,3);
| ~~~
/path/to/include/htslib/kstring.h:97:18: error: expected ';' before 'int'
97 | HTSLIB_EXPORT
| ^
| ;
98 | int kputd(double d, kstring_t *s); // custom %g only handler
| ~~~
/path/to/include/htslib/kstring.h:100:18: error: expected ';' before 'int'
100 | HTSLIB_EXPORT
| ^
| ;
101 | int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
| ~~~
/path/to/include/htslib/kstring.h:103:18: error: expected ';' before 'char'
103 | HTSLIB_EXPORT
| ^
| ;
104 | char *kstrstr(const char *str, const char *pat, int **_prep);
| ~~~~
/path/to/include/htslib/kstring.h:106:18: error: expected ';' before 'char'
106 | HTSLIB_EXPORT
| ^
| ;
107 | char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
| ~~~~
/path/to/include/htslib/kstring.h:109:18: error: expected ';' before 'void'
109 | HTSLIB_EXPORT
| ^
| ;
110 | void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);
| ~~~~
/path/to/include/htslib/kstring.h:116:18: error: expected ';' before 'char'
116 | HTSLIB_EXPORT
| ^
| ;
117 | char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);
| ~~~~
/path/to/include/htslib/kstring.h:124:18: error: expected ';' before 'int'
124 | HTSLIB_EXPORT
| ^
| ;
125 | int kgetline(kstring_t *s, kgets_func *fgets_fn, void *fp);
| ~~~
/path/to/include/htslib/kstring.h:132:18: error: expected ';' before 'int'
132 | HTSLIB_EXPORT
| ^
| ;
133 | int kgetline2(kstring_t *s, kgets_func2 *fgets_fn, void *fp);
| ~~~
make: *** [Makefile:132: bgzf.o] Error 1
The version of my gcc is 11.3.0 and cmake is 3.23.0. How can I fix this error?
Best wishes!
I got errors when I run
./build_all.sh
so I run step by step and finally found the error was caused bymake
in/polisher/external/install/htslib/
. Here is the log:The version of my gcc is 11.3.0 and cmake is 3.23.0. How can I fix this error? Best wishes!