Question: Platypus install errors when running ./buildPlatypus.sh
0
gravatar for PRIME_num
7 months ago by
PRIME_num0
PRIME_num0 wrote:

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!!!!!!

platypus build ubuntu • 258 views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 7 months ago by PRIME_num0

Have you tried installation with bioconda?

ADD REPLYlink written 7 months ago by WouterDeCoster39k
####Prerequisites

Platypus requires HTSlib 1.2.1 or greater. HTSlib can be downloaded from the HTSlib Web site.

To build and install HTSlib, cd into HTSlib source and type make install. This will install HTSlib under /usr/local/ (see note below). To install HTSlib in any other directory use make install prefix=/path/to/dir.

NOTE: HTSlib should be installed in a standard location (e.g. /usr/local/). If not installed in a standard location, you will need to set your library paths:

For GNU/Linux:

export C_INCLUDE_PATH=/path/to/dir/include
export LIBRARY_PATH=/path/to/dir/lib (only for making)
export LD_LIBRARY_PATH=/path/to/dir/lib

Did you do that?

ADD REPLYlink written 7 months ago by ATpoint18k
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