abyzov
commented
3 years ago Hi, looks like the error in assert.h file which is not part of CNVnator neither of ROOT. Not sure what causes this error.
Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic
Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745
When I try to run make I get the following error. I have the root package installed, but I'm still getting it. Any help is greatly appreciated. Thank you!
Compiling with parallel (OpenMP) support g++ -O3 -std=c++17 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/u/home/n/neharajk/miniconda3/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o In file included from /u/home/n/neharajk/miniconda3/include/assert.h:5, from /u/home/n/neharajk/miniconda3/include/TCollection.h:33, from /u/home/n/neharajk/miniconda3/include/TSeqCollection.h:25, from /u/home/n/neharajk/miniconda3/include/TObjArray.h:25, from /u/home/n/neharajk/miniconda3/include/TClass.h:29, from /u/home/n/neharajk/miniconda3/include/TKey.h:17, from HisMaker.hh:16, from cnvnator.cpp:15: /u/home/n/neharajk/miniconda3/include/except.h:15:32: error: conflicting declaration 'typedef struct Except_Frame_T Except_Frame_T' 15 | typedef struct Except_Frame_T Except_Frame_T; | ^
~~~~~ /u/home/n/neharajk/miniconda3/include/except.h:15:16: note: previous declaration as 'struct Except_Frame_T' 15 | typedef struct Except_Frame_T *Except_Frame_T; | ^~~~~~ /u/home/n/neharajk/miniconda3/include/except.h:17:18: error: field 'prev' has incomplete type 'Except_Frame_T' 17 | Except_Frame_T prev; | ^~~~ /u/home/n/neharajk/miniconda3/include/except.h:16:8: note: definition of 'struct Except_Frame_T' is not complete until the closing brace 16 | struct Except_Frame_T { | ^~~~~~ make: *** [obj/cnvnator.o] Error 1