Two compile errors - FIXED

[guyleonard]

Not really sure these are issues but might be useful for future reference.

[ 61%] Linking CXX executable TestTools
/usr/lib/R/lib/libR.so: undefined reference to `GOMP_parallel@GOMP_4.0'

Fixed this by editing line 7 of CMakeLists.txt to include '-fopenmp':

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -m64 -DBOOST_LOG_DYN_LINK -std=c++11 -Wno-attributes -Wno-deprecated -Wno-deprecated-declarations")

Also, when having previously installed the software GMAP/GSNAP it seems to add two files in /usr/local/include/ - except.h and assert.h which causes the below errors, until they are removed .

                 from /home/transcriptomics/software/dropEst/Tools/ReadParameters.cpp:1:
/usr/local/include/except.h:15:32: error: conflicting declaration ‘typedef struct Except_Frame_T* Except_Frame_T’
 typedef struct Except_Frame_T *Except_Frame_T;
                                ^
/usr/local/include/except.h:15:16: note: previous declaration as ‘struct Except_Frame_T’
 typedef struct Except_Frame_T *Except_Frame_T;
                ^
/usr/local/include/except.h:17:18: error: field ‘prev’ has incomplete type ‘Except_Frame_T’
   Except_Frame_T prev;
                  ^
/usr/local/include/except.h:16:8: note: definition of ‘struct Except_Frame_T’ is not complete until the closing brace
 struct Except_Frame_T {
        ^
CMakeFiles/DropTools.dir/build.make:62: recipe for target 'CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o' failed
make[2]: *** [CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o] Error 1
CMakeFiles/Makefile2:179: recipe for target 'CMakeFiles/DropTools.dir/all' failed
make[1]: *** [CMakeFiles/DropTools.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2
master@transcriptomics:/ho

and

/usr/local/include/assert.h:5:20: fatal error: except.h: No such file or directory
compilation terminated.
CMakeFiles/DropTools.dir/build.make:62: recipe for target 'CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o' failed
make[2]: *** [CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o] Error 1
CMakeFiles/Makefile2:179: recipe for target 'CMakeFiles/DropTools.dir/all' failed
make[1]: *** [CMakeFiles/DropTools.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2

[VPetukhov]

Thank you for the information! I'll check it.