Question: minia compile error in Max OS X v.10.7.5
0
gravatar for gahunboo
2.9 years ago by
gahunboo0
Korea, Republic Of
gahunboo0 wrote:

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?

minia compile • 1.1k views
ADD COMMENTlink modified 2.9 years ago by Michael Dondrup41k • written 2.9 years ago by gahunboo0

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

ADD REPLYlink written 2.9 years ago by Hugues230
0
gravatar for Michael Dondrup
2.9 years ago by
Bergen, Norway
Michael Dondrup41k wrote:

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)

 

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Michael Dondrup41k

I cannot reproduce the error either. minia builds fine.

ADD REPLYlink written 2.9 years ago by Hugues230
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