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Hi, I'm trying to build Platypus and having issues with the build step.
$ ./buildPlatypus.sh
Building Platypus
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_py
running build
running build_ext
building 'ctabix' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-nbjU53/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Itabix -Ipysam -I/usr/include/python2.7 -c ctabix.c -o build/temp.linux-x86_64-2.7/ctabix.o
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:58:3: error: conflicting types for ‘BGZF’
} BGZF;
^~~~
In file included from ctabix.c:358:0:
bgzf.h:77:21: note: previous declaration of ‘BGZF’ was here
typedef struct BGZF BGZF;
^~~~
bgzf.h:111:46: error: expected declaration specifiers or ‘...’ before ‘(’ token
#define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
^
tabix/bgzf.h:70:7: note: in expansion of macro ‘bgzf_fdopen’
BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
^~~~~~~~~~~
bgzf.h:111:52: error: expected declaration specifiers or ‘...’ before ‘(’ token
#define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
^
tabix/bgzf.h:70:7: note: in expansion of macro ‘bgzf_fdopen’
BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
^~~~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:77:7: error: conflicting types for ‘bgzf_open’
BGZF* bgzf_open(const char* path, const char* __restrict mode);
^~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:116:11: note: previous declaration of ‘bgzf_open’ was here
BGZF* bgzf_open(const char* path, const char *mode);
^~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:84:5: error: conflicting types for ‘bgzf_close’
int bgzf_close(BGZF* fp);
^~~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:129:9: note: previous declaration of ‘bgzf_close’ was here
int bgzf_close(BGZF *fp);
^~~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:92:5: error: conflicting types for ‘bgzf_read’
int bgzf_read(BGZF* fp, void* data, int length);
^~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:139:13: note: previous declaration of ‘bgzf_read’ was here
ssize_t bgzf_read(BGZF *fp, void *data, size_t length) HTS_RESULT_USED;
^~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:99:5: error: conflicting types for ‘bgzf_write’
int bgzf_write(BGZF* fp, const void* data, int length);
^~~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:150:13: note: previous declaration of ‘bgzf_write’ was here
ssize_t bgzf_write(BGZF *fp, const void *data, size_t length) HTS_RESULT_USED;
^~~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:108:0: warning: "bgzf_tell" redefined
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
In file included from ctabix.c:358:0:
bgzf.h:202:0: note: this is the location of the previous definition
#define bgzf_tell(fp) (((fp)->block_address << 16) | ((fp)->block_offset & 0xFFFF))
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:118:9: error: conflicting types for ‘bgzf_seek’
int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
^~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:212:13: note: previous declaration of ‘bgzf_seek’ was here
int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence) HTS_RESULT_USED;
^~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:125:6: error: conflicting types for ‘bgzf_set_cache_size’
void bgzf_set_cache_size(BGZF *fp, int cache_size);
^~~~~~~~~~~~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:255:10: note: previous declaration of ‘bgzf_set_cache_size’ was here
void bgzf_set_cache_size(BGZF *fp, int size);
^~~~~~~~~~~~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:127:5: error: conflicting types for ‘bgzf_check_EOF’
int bgzf_check_EOF(BGZF *fp);
^~~~~~~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:223:9: note: previous declaration of ‘bgzf_check_EOF’ was here
int bgzf_check_EOF(BGZF *fp);
^~~~~~~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:128:5: error: conflicting types for ‘bgzf_read_block’
int bgzf_read_block(BGZF* fp);
^~~~~~~~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:283:9: note: previous declaration of ‘bgzf_read_block’ was here
int bgzf_read_block(BGZF *fp) HTS_RESULT_USED;
^~~~~~~~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:129:5: error: conflicting types for ‘bgzf_flush’
int bgzf_flush(BGZF* fp);
^~~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:194:9: note: previous declaration of ‘bgzf_flush’ was here
int bgzf_flush(BGZF *fp) HTS_RESULT_USED;
^~~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:130:5: error: conflicting types for ‘bgzf_flush_try’
int bgzf_flush_try(BGZF *fp, int size);
^~~~~~~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:261:9: note: previous declaration of ‘bgzf_flush_try’ was here
int bgzf_flush_try(BGZF *fp, ssize_t size) HTS_RESULT_USED;
^~~~~~~~~~~~~~
In file included from tabix/tabix.h:33:0,
from ctabix.c:359:
tabix/bgzf.h:137:19: error: conflicting types for ‘bgzf_getc’
static inline int bgzf_getc(BGZF *fp)
^~~~~~~~~
In file included from ctabix.c:358:0:
bgzf.h:268:9: note: previous declaration of ‘bgzf_getc’ was here
int bgzf_getc(BGZF *fp);
^~~~~~~~~
ctabix.c: In function ‘__pyx_pf_6ctabix_9Tabixfile_7contigs___get__’:
ctabix.c:3304:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
__pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nsequences));
^
ctabix.c: In function ‘__pyx_pf_6ctabix_13TabixIterator_4__next__’:
ctabix.c:3858:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
^
ctabix.c: In function ‘__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__’:
ctabix.c:4239:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
^
ctabix.c: In function ‘__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__’:
ctabix.c:5249:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
^
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
Setup failed. Check previous lines for errors
there're so many errors i met. please help me!!!! thanks a lot!!!!!!
Have you tried installation with bioconda?
Did you do that?