Compiling error (tried using gcc version 5.1.1 and 5.4.0):

[gisleDK]

Hi tried updating the compiler to 5.4.0 but still same error. This link suggests that the problem could be that -lpthread is included several times although I fail to see where.

make
make -C bwt/
make[1]: Entering directory `/project/genomics/Gisle/Bin/Programs/kaiju-master/src/bwt'
gcc -O3 -g -Wno-unused-result   -c -o mkbwt.o mkbwt.c
gcc -O3 -g -Wno-unused-result   -c -o readFasta.o readFasta.c
gcc -O3 -g -Wno-unused-result   -c -o suffixArray.o suffixArray.c
gcc -O3 -g -Wno-unused-result   -c -o multikeyqsort.o multikeyqsort.c
gcc -O3 -g -Wno-unused-result   -c -o sequence.o sequence.c
gcc   mkbwt.o readFasta.o suffixArray.o multikeyqsort.o sequence.o  -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lm -o mkbwt
/usr/lib64/libpthread_nonshared.a(pthread_atfork.oS): In function `__pthread_atfork':
/usr/src/packages/BUILD/glibc-2.11.3/nptl/pthread_atfork.c:57: multiple definition of `__pthread_atfork'
/usr/lib64/libpthread_nonshared.a(pthread_atfork.oS):/usr/src/packages/BUILD/glibc-2.11.3/nptl/pthread_atfork.c:57: first defined here
/usr/lib64/libpthread_nonshared.a(pthread_atfork.oS): In function `__pthread_atfork':
/usr/src/packages/BUILD/glibc-2.11.3/nptl/pthread_atfork.c:57: multiple definition of `pthread_atfork'
/usr/lib64/libpthread_nonshared.a(pthread_atfork.oS):/usr/src/packages/BUILD/glibc-2.11.3/nptl/pthread_atfork.c:57: first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [mkbwt] Error 1
make[1]: Leaving directory `/project/genomics/Gisle/Bin/Programs/kaiju-master/src/bwt'
make: *** [bwt/mkbwt] Error 2

[gisleDK]

Problem solved by changing static: LDFLAGS = -static to LDFLAGS = -static in both makefile and bwt/Makefile

[pmenzel]

Great that it works now. Your change should be the same as just doing make static.

Maybe something isn't right in your glibc library setup, so that the normal build does not work and the static build works. I also have gcc 5.4.0 on Ubuntu here and it compiles fine.

[gisleDK]

Probably one of the joys of having several compilers installed locally. Thanks for the suggestion!