Compile Error - Githubissues

Hello, I'm getting a compile error. Any help would be greatly appreciated.

[rtaylor@Bio-DAP20 src]$ ./configure --prefix=$HOME/local --exec-prefix=$HOME/local --with-sparsehash=$HOME/local/ --with-bamtools=$HOME/local/bin/bamtools --with-jemalloc=$HOME/local/lib/ checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing clock_gettime... -lrt checking for OpenMP flag of C++ compiler... -fopenmp checking for host type... you are not using osx so multi-threading should work. checking for malloc in -ljemalloc... yes checking google/sparse_hash_set usability... yes checking google/sparse_hash_set presence... yes checking for google/sparse_hash_set... yes checking for google/sparse_hash_set... (cached) yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... no checking unordered_map presence... no checking for unordered_map... no checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking ext/hash_map usability... yes checking ext/hash_map presence... yes checking for ext/hash_map... yes checking unordered_set usability... no checking unordered_set presence... no checking for unordered_set... no checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking ext/hash_set usability... yes checking ext/hash_set presence... yes checking for ext/hash_set... yes checking api/BamReader.h usability... yes checking api/BamReader.h presence... yes checking for api/BamReader.h... yes configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating Thirdparty/Makefile config.status: creating Util/Makefile config.status: creating SQG/Makefile config.status: creating Bigraph/Makefile config.status: creating Algorithm/Makefile config.status: creating StringGraph/Makefile config.status: creating Concurrency/Makefile config.status: creating SuffixTools/Makefile config.status: creating GraphDiff/Makefile config.status: creating Scaffold/Makefile config.status: creating SGA/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands [rtaylor@Bio-DAP20 src]$ make

... ... No errors in previous directories ...

make[2]: Entering directory /home/rtaylor/local/src/sga/src/GraphDiff' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelUtil.o -MD -MP -MF .deps/libgraphdiff_a-DindelUtil.Tpo -c -o libgraphdiff_a-DindelUtil.otest -f 'DindelUtil.cpp' || echo './'DindelUtil.cpp mv -f .deps/libgraphdiff_a-DindelUtil.Tpo .deps/libgraphdiff_a-DindelUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelRealignWindow.o -MD -MP -MF .deps/libgraphdiff_a-DindelRealignWindow.Tpo -c -o libgraphdiff_a-DindelRealignWindow.otest -f 'DindelRealignWindow.cpp' || echo './'DindelRealignWindow.cpp mv -f .deps/libgraphdiff_a-DindelRealignWindow.Tpo .deps/libgraphdiff_a-DindelRealignWindow.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelHMM.o -MD -MP -MF .deps/libgraphdiff_a-DindelHMM.Tpo -c -o libgraphdiff_a-DindelHMM.otest -f 'DindelHMM.cpp' || echo './'DindelHMM.cpp mv -f .deps/libgraphdiff_a-DindelHMM.Tpo .deps/libgraphdiff_a-DindelHMM.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-OverlapHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Tpo -c -o libgraphdiff_a-OverlapHaplotypeBuilder.otest -f 'OverlapHaplotypeBuilder.cpp' || echo './'OverlapHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Tpo .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-StringHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-StringHaplotypeBuilder.Tpo -c -o libgraphdiff_a-StringHaplotypeBuilder.otest -f 'StringHaplotypeBuilder.cpp' || echo './'StringHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-StringHaplotypeBuilder.Tpo .deps/libgraphdiff_a-StringHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DeBruijnHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Tpo -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.otest -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'DeBruijnHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Tpo .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Tpo -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.otest -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'PairedDeBruijnHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Tpo .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-HapgenUtil.o -MD -MP -MF .deps/libgraphdiff_a-HapgenUtil.Tpo -c -o libgraphdiff_a-HapgenUtil.otest -f 'HapgenUtil.cpp' || echo './'HapgenUtil.cpp mv -f .deps/libgraphdiff_a-HapgenUtil.Tpo .deps/libgraphdiff_a-HapgenUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-VCFTester.o -MD -MP -MF .deps/libgraphdiff_a-VCFTester.Tpo -c -o libgraphdiff_a-VCFTester.otest -f 'VCFTester.cpp' || echo './'VCFTester.cpp mv -f .deps/libgraphdiff_a-VCFTester.Tpo .deps/libgraphdiff_a-VCFTester.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-GraphCompare.o -MD -MP -MF .deps/libgraphdiff_a-GraphCompare.Tpo -c -o libgraphdiff_a-GraphCompare.otest -f 'GraphCompare.cpp' || echo './'GraphCompare.cpp mv -f .deps/libgraphdiff_a-GraphCompare.Tpo .deps/libgraphdiff_a-GraphCompare.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-OverlapExtractorWithCorrection.o -MD -MP -MF .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo -c -o libgraphdiff_a-OverlapExtractorWithCorrection.otest -f 'OverlapExtractorWithCorrection.cpp' || echo './'OverlapExtractorWithCorrection.cpp mv -f .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DBGPathGuide.o -MD -MP -MF .deps/libgraphdiff_a-DBGPathGuide.Tpo -c -o libgraphdiff_a-DBGPathGuide.otest -f 'DBGPathGuide.cpp' || echo './'DBGPathGuide.cpp DBGPathGuide.cpp: In member function ‘void DBGPathGuide::printStats() const’: DBGPathGuide.cpp:40:132: error: ‘printf’ was not declared in this scope make[2]: *** [libgraphdiff_a-DBGPathGuide.o] Error 1 make[2]: Leaving directory/home/rtaylor/local/src/sga/src/GraphDiff' make[1]: * [all-recursive] Error 1 make[1]: Leaving directory `/home/rtaylor/local/src/sga/src' make: * [all] Error 2

[rtaylor@Bio-DAP20 src]$ gcc --version gcc (GCC) 4.6.3 20120306 (Red Hat 4.6.3-2) Copyright (C) 2011 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[rtaylor@Bio-DAP20 src]$ cat /proc/version Linux version 2.6.43.8-1.fc15.x86_64 (mockbuild@x86-02.phx2.fedoraproject.org) (gcc version 4.6.3 20120306 (Red Hat 4.6.3-2) (GCC) ) #1 SMP Mon Jun 4 20:33:44 UTC 2012

jts / sga

Compile Error #46