compiler errors - Make fail during RSEM install -

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i following instruction install rsem on mac os x (el capitan).

below error get:

g++ -std=gnu++98 -wall -i. -i. -isamtools-1.3/htslib-1.3  -o3 -c -o extractref.o extractref.cpp in file included extractref.cpp:13: in file included ./utils.h:10: in file included /applications/xcode.app/contents/developer/toolchains/xcodedefault.xctoolchain/usr/bin/../include/c++/v1/cassert:21: in file included /usr/local/include/assert.h:5: /usr/local/include/except.h:15:32: error: typedef redefinition different       types ('struct except_frame_t *' vs 'except_frame_t') typedef struct except_frame_t *except_frame_t;                                ^ /usr/local/include/except.h:15:16: note: previous definition here typedef struct except_frame_t *except_frame_t;                ^ /usr/local/include/except.h:17:18: error: field has incomplete type       'except_frame_t'   except_frame_t prev;                  ^ /usr/local/include/except.h:16:8: note: definition of 'except_frame_t' not       complete until closing '}' struct except_frame_t {        ^ 2 errors generated. make: *** [extractref.o] error 1

i checked except.h , compared else's , looks doesn't have problem. i'm kind of lost next. i've tried make clean , starting over, still seems not work. there isn't configure file available either, making harder me figure things out. input appreciated.

thanks.

there weird /usr/local/include/assert.h . system header file meant /usr/include/assert.h . see evidence around web of other people having same problem, no clear diagnoses of cause. try:

ls -l /usr/local/include/assert.h

which should reveal homebrew package offending file -- symlink /usr/local/cellar/[packagename]. @ point may wish try uninstalling [packagename] see if helps.





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