SW.cpp:799:164: error: redeclaration of 'template<unsigned char banded,

[tseemann]

GCC 5.1 Linux gave this compilation error.
I "solved" it by putting -fpermissive into CPPFLAGS.

g++ -Wall -O3 -D COMPILE_USER_MODE -D BUILDNUM=83 -MMD -MP -c src/SW.cpp -o obj/SW.o
src/SW.cpp:799:164: error: redeclaration of 'template<unsigned char banded, unsigned char extension, unsigned char reverse, unsigned char XCutoff> int findAffineGapScore(QueryState_t*, char*, SUINT, char*, SUINT, EditOpList_t*, SUINT*, SUINT*)' may not have default arguments [-fpermissive]
 r * qStr, SUINT qLen, char * rStr, SUINT rLen, EditOpList_t * list, SUINT * addedQLen = NULL, SUINT * addedRLen = NULL)
                                                                                                                       ^
make: *** [obj/SW.o] Error 1

[SHuang-Broad]

Same issue here. I switched to gcc 4.9 and solved the issue.

[aallahyar]

gcc version 5.3.0 showed the same error. Using @tseemann approach fixed the problem. Just add "-fpermissive" flag to your Makefile file.

Before:
CPPFLAGS := $(CCFLAGS)

After:
CPPFLAGS := $(CCFLAGS) -fpermissive

Hope this fixes someones problem.

[V-Z]

Same here

gcc --version
gcc (SUSE Linux) 8.2.1 20181025 [gcc-8-branch revision 265488]

The suggested change "fixed" the issue.

[tseemann]

gcc -Wall -O3 -D COMPILE_USER_MODE -D BUILDNUM=83 -MMD -MP -std=gnu99 -c src/Math.c -o obj/Math.o
src/SW.cpp:799:164: error: redeclaration of 'template<unsigned char banded, unsigned char extension
, unsigned char reverse, unsigned char XCutoff> int findAffineGapScore(QueryState_t*, char*, SUINT,
 char*, SUINT, EditOpList_t*, SUINT*, SUINT*)' may not have default arguments [-fpermissive]
 int findAffineGapScore(QueryState_t * QS, char * qStr, SUINT qLen, char * rStr, SUINT rLen, EditOp
List_t * list, SUINT * addedQLen = NULL, SUINT * addedRLen = NULL)

just for the record, i encountered this again 4 years later :)