CD-HIT installation problem

[GoogleCodeExporter]

What steps will reproduce the problem?
1. download the cd-hit-v4.5.4-2011-03-07.tgz file from website
2. tar xvf cd-hit-v4.5.4-2011-03-07.tgz --gunzip
3. make openmp=yes

What is the expected output? What do you see instead?
expect the program executables to install properly

instead I get some error messages in log and executables have not been 
installed in cd-hit folder - at least, I do not see any of the 8 files with .o 
extension (cdhit.o, cdhit-div.o etc), nor any of the 6 executable files 
(cd-hit, cd-hit-2d, cd-hit-div etc)

here is the installation log

cdhit-common.c++: In constructor ‘TempFile::TempFile(const char*)’:
cdhit-common.c++:68:34: warning: format ‘%x’ expects argument of type 
‘unsigned int’, but argument 3 has type ‘TempFile*’ [-Wformat]
cdhit-common.c++: In member function ‘size_t SequenceDB::MinimalMemory(int, 
int, int, const Options&)’:
cdhit-common.c++:2258:47: warning: format ‘%i’ expects argument of type 
‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type 
‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++:2262:71: warning: format ‘%i’ expects argument of type 
‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type 
‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++:2266:78: warning: format ‘%i’ expects argument of type 
‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++:2271:52: warning: format ‘%i’ expects argument of type 
‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++:2274:51: warning: format ‘%i’ expects argument of type 
‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++:2279:30: warning: format ‘%i’ expects argument of type 
‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(int, 
const Options&)’:
cdhit-common.c++:2476:90: warning: format ‘%i’ expects argument of type 
‘int’, but argument 2 has type ‘std::vector<Sequence*, 
std::allocator<Sequence*> >::size_type {aka long unsigned int}’ [-Wformat]
cdhit-common.c++:2487:65: warning: format ‘%i’ expects argument of type 
‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
cdhit-common.c++: In member function ‘void SequenceDB::DoClustering(const 
Options&)’:
cdhit-common.c++:2994:65: warning: format ‘%i’ expects argument of type 
‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ 
[-Wformat]
In file included from cdhit-common.c++:28:0:
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) 
[with TYPE = NVector<long int>]’:
cdhit-common.c++:704:27:   required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and 
no declarations were found by argument-dependent lookup at the point of 
instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base 
‘std::vector<NVector<long int>, std::allocator<NVector<long int> > >’ are 
not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) 
[with TYPE = NVector<int>]’:
cdhit-common.c++:705:25:   required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and 
no declarations were found by argument-dependent lookup at the point of 
instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base 
‘std::vector<NVector<int>, std::allocator<NVector<int> > >’ are not found 
by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) 
[with TYPE = Sequence*]’:
cdhit-common.c++:1247:24:   required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and 
no declarations were found by argument-dependent lookup at the point of 
instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base 
‘std::vector<Sequence*, std::allocator<Sequence*> >’ are not found by 
unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
cdhit-common.h: In instantiation of ‘void Vector<TYPE>::Append(const TYPE&) 
[with TYPE = int]’:
cdhit-common.c++:1895:26:   required from here
cdhit-common.h:95:4: error: ‘push_back’ was not declared in this scope, and 
no declarations were found by argument-dependent lookup at the point of 
instantiation [-fpermissive]
cdhit-common.h:95:4: note: declarations in dependent base ‘std::vector<int, 
std::allocator<int> >’ are not found by unqualified lookup
cdhit-common.h:95:4: note: use ‘this->push_back’ instead
make: *** [cdhit-common.o] Error 1

What version of the product are you using? On what operating system?

cd-hit-v4.5.4-2011-03-07.tgz downloaded 19 March 2013

OS = Linux Mint 14 (Nadia)
64 bit

Please provide any additional information below.
The same command on a Linux Mint 12 machine installs the program correctly. So 
it is an issue of upgrade in gcc (Mint14 has gcc 4.7.2, Mint12 has 4.6.1), or 
any other component involved in the correct installation?

Original issue reported on code.google.com by hug...@ku.ac.th on 19 Mar 2013 at 3:46

[GoogleCodeExporter]

very first line of log was missing:

g++ -O2 -fopenmp cdhit-common.c++ -c

Original comment by hug...@ku.ac.th on 19 Mar 2013 at 3:50

[GoogleCodeExporter]

This was an issue of compiler compatibility, to avoid it, you need to use an 
older version of g++ compiler (maybe 4.2). Or you can simply use the latest 
release v4.6.1, which has solved this problem. Thanks.

Original comment by daoko...@gmail.com on 21 Mar 2013 at 10:53

• Changed state: Done

[GoogleCodeExporter]

OK... a problem of G++ compiler compatibility.
Since I have gcc compiler 4.7.2... which is apparently more "latest" than the 
latests release v4.6.1... whatever issue there was with earlier versions has 
resurfaced?
I am not a computer expert, but I don't agree that the problem has been solved 
and "Status: Done" is not warranted. Maybe time to look deeper into the 
compatibility problem?

Original comment by hug...@ku.ac.th on 22 Mar 2013 at 3:52

[GoogleCodeExporter]

Hi, I still am encountering this problem with gcc version 4.8.1 on ubuntu. Any 
solution?

Original comment by Shok...@gmail.com on 9 Jan 2014 at 10:22

[GoogleCodeExporter]

The latest CD-HIT version (4.6.1) does not have the problem.

Original comment by hug...@ku.ac.th on 9 Jan 2014 at 12:08

[GoogleCodeExporter]

Oh I see, sorry, this was a version that comes bundled with TransDecoder, I 
will submit an issue with them. Thank you for your response.

Original comment by Shok...@gmail.com on 9 Jan 2014 at 12:53