minia compile error in Max OS X v.10.7.5

Question

[gahunboo]

Hi, I have some error when I compile the program.

The error messages are below:

rm -rf *.o

g++ -o Pool.o -c Pool.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o Bank.o -c Bank.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o Bloom.o -c Bloom.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o Hash16.o -c Hash16.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o LargeInt.o -c LargeInt.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o Kmer.o -c Kmer.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o Terminator.o -c Terminator.cpp -O4 -D_FILE_OFFSET_BITS=64 
Terminator.cpp: In constructor 'BranchingTerminator::BranchingTerminator(BinaryBank*, uint64_t, Bloom*, Set*)':
Terminator.cpp:311: warning: format '%d' expects type 'int', but argument 4 has type 'long unsigned int'
Terminator.cpp:311: warning: format '%d' expects type 'int', but argument 5 has type 'long unsigned int'
Terminator.cpp:311: warning: format '%d' expects type 'int', but argument 4 has type 'long unsigned int'
Terminator.cpp:311: warning: format '%d' expects type 'int', but argument 5 has type 'long unsigned int'
Terminator.cpp:312: warning: format '%d' expects type 'int', but argument 3 has type 'long unsigned int'
Terminator.cpp:312: warning: format '%d' expects type 'int', but argument 4 has type 'long unsigned int'
Terminator.cpp:312: warning: format '%d' expects type 'int', but argument 3 has type 'long unsigned int'
Terminator.cpp:312: warning: format '%d' expects type 'int', but argument 4 has type 'long unsigned int'
Terminator.cpp: In constructor 'BranchingTerminator::BranchingTerminator(BinaryBank*, BinaryBank*, Bloom*, Set*)':
Terminator.cpp:337: warning: format '%d' expects type 'int', but argument 4 has type 'long unsigned int'
Terminator.cpp:337: warning: format '%d' expects type 'int', but argument 4 has type 'long unsigned int'
g++ -o Traversal.o -c Traversal.cpp -O4 -D_FILE_OFFSET_BITS=64 
Traversal.cpp: In member function 'bool MonumentTraversal::find_starting_kmer(kmer_type, kmer_type&)':
Traversal.cpp:344: warning: too few arguments for format
Traversal.cpp:344: warning: too few arguments for format
Traversal.cpp:358: warning: too few arguments for format
Traversal.cpp:358: warning: too few arguments for format
Traversal.cpp:396: warning: format '%d' expects type 'int', but argument 5 has type 'size_t'
Traversal.cpp:396: warning: format '%d' expects type 'int', but argument 5 has type 'size_t'
Traversal.cpp: In member function 'bool MonumentTraversal::validate_consensuses(std::set<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char*, int&)':
Traversal.cpp:835: warning: format '%d' expects type 'int', but argument 4 has type 'size_t'
Traversal.cpp:835: warning: format '%d' expects type 'int', but argument 4 has type 'size_t'
Traversal.cpp:856: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
Traversal.cpp:856: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
g++ -o LinearCounter.o -c LinearCounter.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o Set.o -c Set.cpp -O4 -D_FILE_OFFSET_BITS=64 
Set.cpp: In member function 'void AssocPairedSet::print()':
Set.cpp:242: warning: format '%i' expects type 'int', but argument 2 has type 'size_t'
Set.cpp:242: warning: format '%i' expects type 'int', but argument 2 has type 'size_t'
g++ -o Utils.o -c Utils.cpp -O4 -D_FILE_OFFSET_BITS=64 
Utils.cpp: In function 'uint64_t extrapolate_distinct_kmers_wrapped(long unsigned int, Bank*)':
Utils.cpp:434: warning: format '%d' expects type 'int', but argument 2 has type 'long unsigned int'
Utils.cpp:434: warning: format '%d' expects type 'int', but argument 2 has type 'long unsigned int'
g++ -o SortingCount.o -c SortingCount.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o Debloom.o -c Debloom.cpp -O4 -D_FILE_OFFSET_BITS=64 
Debloom.cpp: In function 'Set* load_false_positives_cascading4()':
Debloom.cpp:370: warning: format '%lld' expects type 'long long int', but argument 2 has type 'int'
Debloom.cpp:370: warning: format '%lld' expects type 'long long int', but argument 2 has type 'int'
Debloom.cpp:394: warning: format '%lld' expects type 'long long int', but argument 2 has type 'int'
Debloom.cpp:394: warning: format '%lld' expects type 'long long int', but argument 2 has type 'int'
Debloom.cpp:424: warning: format '%lld' expects type 'long long int', but argument 2 has type 'int'
Debloom.cpp:424: warning: format '%lld' expects type 'long long int', but argument 2 has type 'int'
g++ -o OAHash.o -c OAHash.cpp -O4 -D_FILE_OFFSET_BITS=64 
g++ -o minia Pool.o Bank.o Bloom.o Hash16.o LargeInt.o Kmer.o Terminator.o Traversal.o LinearCounter.o Set.o Utils.o SortingCount.o Debloom.o OAHash.o Minia.cpp -O4 -D_FILE_OFFSET_BITS=64  -lz
Minia.cpp: In function 'int main(int, char**)':
Minia.cpp:233: warning: format '%d' expects type 'int', but argument 2 has type 'long unsigned int'
Minia.cpp:233: warning: format '%d' expects type 'int', but argument 2 has type 'long unsigned int'
Minia.cpp:285: warning: format '%u' expects type 'unsigned int', but argument 3 has type 'long unsigned int'
Minia.cpp:285: warning: format '%u' expects type 'unsigned int', but argument 3 has type 'long unsigned int'
ld: lto: could not merge in Pool.o because Unknown instruction for architecture x86_64
collect2: ld returned 1 exit status
make: *** [minia] Error 1

How could I solve this error?

[Hugues]

Which version of Xcode do you use? If you haven't installed it, go to the App Store and install the latest Xcode.

Answer 1

[Michael]

I can't reproduce this error. It seems to be a linker error on your side, it compiles and links fine for me. You can ignore all warnings about format '%d'... for now. Downloaded latest version from http://minia.genouest.org/files/minia-1.6088.tar.gz

What is the output of g++ --version for you?

try:

make clean
make

$ g++ --version
i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)

[Hugues]

I cannot reproduce the error either. minia builds fine.