Dear all
I am trying to install cd-hit-otu to follow up in some results in metagenomics that received from 16S Miseq sequencing. The idea is to replicate a workflow so I can learn how to do and use it with future samples. I am using Macqiime and now I am in the stage of filtering reads and OTU cluster with cd-hit-otu but when I am installing in terminal I get errors when I do the "make" command. I believe this is a Mac issue but I only have macs to work with so no option for me. Plus I am a newbie with python or any language code for what is worth so I have been holding my own with google search and forums but now I got stuck. Is there anyone that can drop me a hand with this. I deeply appreciate it! Here is the terminal output I am receiving when I try to make the first file.
/Applications/Bioinformatics/cd-hit-otu-illumina-0.0.1/cd-hit-v4.5.5-2011-03-31
:cd-hit-v4.5.5-2011-03-31 $ make
g++ -O2 -DNO_OPENMP cdhit-common.c++ -c
cdhit-common.c++:68:29: warning: format specifies type 'unsigned int' but the
argument has type 'TempFile *' [-Wformat]
sprintf( buf + len, "%x", this );
~~ ^~~~
cdhit-common.c++:2260:38: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %iM\n", "Sequence", mem/mega );
~~ ^~~~~~~~
%lu
cdhit-common.c++:2264:50: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %i X %iM = %iM\n", "Buffer", T, mem/mega, T*mem/mega );
~~ ^~~~~~~~
%lu
cdhit-common.c++:2264:60: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %i X %iM = %iM\n", "Buffer", T, mem/mega, T*mem/mega );
~~ ^~~~~~~~~~
%lu
cdhit-common.c++:2268:53: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %i X %iM = %iM\n", "Table", table, mem/mega, tab...
~~ ^~~~~~~~
%lu
cdhit-common.c++:2268:63: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
..."%-16s: %i X %iM = %iM\n", "Table", table, mem/mega, table*mem/mega );
~~ ^~~~~~~~~~~~~~
%lu
cdhit-common.c++:2273:43: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %iM\n", "Miscellaneous", mem/mega );
~~ ^~~~~~~~
%lu
cdhit-common.c++:2276:37: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %iM\n\n", "Total", mem_need/mega );
~~ ^~~~~~~~~~~~~
%lu
cdhit-common.c++:2281:5: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
50*table + mem_need/mega );
^~~~~~~~~~~~~~~~~~~~~~~~
cdhit-common.c++:2478:62: warning: format specifies type 'int' but the argument
has type 'size_type' (aka 'unsigned long') [-Wformat]
...new table with %8i representatives\n", word_table.sequences.size() );
~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~
%8lu
cdhit-common.c++:2489:61: warning: format specifies type 'int' but the argument
has type 'size_t' (aka 'unsigned long') [-Wformat]
printf( "\nApprixmated maximum memory consumption: %iM\n", mem );
~~ ^~~
%lu
cdhit-common.c++:2996:61: warning: format specifies type 'int' but the argument
has type 'size_t' (aka 'unsigned long') [-Wformat]
printf( "\nApprixmated maximum memory consumption: %iM\n", mem );
~~ ^~~
%lu
In file included from cdhit-common.c++:28:
./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
push_back( item );
^
this->
cdhit-common.c++:704:14: note: in instantiation of member function
'Vector<NVector<long long> >::Append' requested here
score_mat.Append( row2 );
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
must qualify identifier to find this declaration in dependent base class
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from cdhit-common.c++:28:
./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
push_back( item );
^
this->
cdhit-common.c++:705:13: note: in instantiation of member function
'Vector<NVector<int> >::Append' requested here
back_mat.Append( row );
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
must qualify identifier to find this declaration in dependent base class
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from cdhit-common.c++:28:
./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
push_back( item );
^
this->
cdhit-common.c++:1249:12: note: in instantiation of member function
'Vector<Sequence *>::Append' requested here
sequences.Append( seq );
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
must qualify identifier to find this declaration in dependent base class
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from cdhit-common.c++:28:
./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
push_back( item );
^
this->
cdhit-common.c++:1897:16: note: in instantiation of member function
'Vector<int>::Append' requested here
clusters[id].Append( k );
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
must qualify identifier to find this declaration in dependent base class
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
12 warnings and 4 errors generated.
make: *** [cdhit-common.o] Error 1
:cd-hit-v4.5.5-2011-03-31 $
I am trying to install cd-hit-otu to follow up in some results in metagenomics that received from 16S Miseq sequencing. The idea is to replicate a workflow so I can learn how to do and use it with future samples. I am using Macqiime and now I am in the stage of filtering reads and OTU cluster with cd-hit-otu but when I am installing in terminal I get errors when I do the "make" command. I believe this is a Mac issue but I only have macs to work with so no option for me. Plus I am a newbie with python or any language code for what is worth so I have been holding my own with google search and forums but now I got stuck. Is there anyone that can drop me a hand with this. I deeply appreciate it! Here is the terminal output I am receiving when I try to make the first file.
/Applications/Bioinformatics/cd-hit-otu-illumina-0.0.1/cd-hit-v4.5.5-2011-03-31
:cd-hit-v4.5.5-2011-03-31 $ make
g++ -O2 -DNO_OPENMP cdhit-common.c++ -c
cdhit-common.c++:68:29: warning: format specifies type 'unsigned int' but the
argument has type 'TempFile *' [-Wformat]
sprintf( buf + len, "%x", this );
~~ ^~~~
cdhit-common.c++:2260:38: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %iM\n", "Sequence", mem/mega );
~~ ^~~~~~~~
%lu
cdhit-common.c++:2264:50: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %i X %iM = %iM\n", "Buffer", T, mem/mega, T*mem/mega );
~~ ^~~~~~~~
%lu
cdhit-common.c++:2264:60: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %i X %iM = %iM\n", "Buffer", T, mem/mega, T*mem/mega );
~~ ^~~~~~~~~~
%lu
cdhit-common.c++:2268:53: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %i X %iM = %iM\n", "Table", table, mem/mega, tab...
~~ ^~~~~~~~
%lu
cdhit-common.c++:2268:63: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
..."%-16s: %i X %iM = %iM\n", "Table", table, mem/mega, table*mem/mega );
~~ ^~~~~~~~~~~~~~
%lu
cdhit-common.c++:2273:43: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %iM\n", "Miscellaneous", mem/mega );
~~ ^~~~~~~~
%lu
cdhit-common.c++:2276:37: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
printf( "%-16s: %iM\n\n", "Total", mem_need/mega );
~~ ^~~~~~~~~~~~~
%lu
cdhit-common.c++:2281:5: warning: format specifies type 'int' but the argument
has type 'unsigned long' [-Wformat]
50*table + mem_need/mega );
^~~~~~~~~~~~~~~~~~~~~~~~
cdhit-common.c++:2478:62: warning: format specifies type 'int' but the argument
has type 'size_type' (aka 'unsigned long') [-Wformat]
...new table with %8i representatives\n", word_table.sequences.size() );
~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~
%8lu
cdhit-common.c++:2489:61: warning: format specifies type 'int' but the argument
has type 'size_t' (aka 'unsigned long') [-Wformat]
printf( "\nApprixmated maximum memory consumption: %iM\n", mem );
~~ ^~~
%lu
cdhit-common.c++:2996:61: warning: format specifies type 'int' but the argument
has type 'size_t' (aka 'unsigned long') [-Wformat]
printf( "\nApprixmated maximum memory consumption: %iM\n", mem );
~~ ^~~
%lu
In file included from cdhit-common.c++:28:
./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
push_back( item );
^
this->
cdhit-common.c++:704:14: note: in instantiation of member function
'Vector<NVector<long long> >::Append' requested here
score_mat.Append( row2 );
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
must qualify identifier to find this declaration in dependent base class
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from cdhit-common.c++:28:
./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
push_back( item );
^
this->
cdhit-common.c++:705:13: note: in instantiation of member function
'Vector<NVector<int> >::Append' requested here
back_mat.Append( row );
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
must qualify identifier to find this declaration in dependent base class
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from cdhit-common.c++:28:
./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
push_back( item );
^
this->
cdhit-common.c++:1249:12: note: in instantiation of member function
'Vector<Sequence *>::Append' requested here
sequences.Append( seq );
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
must qualify identifier to find this declaration in dependent base class
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
In file included from cdhit-common.c++:28:
./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
push_back( item );
^
this->
cdhit-common.c++:1897:16: note: in instantiation of member function
'Vector<int>::Append' requested here
clusters[id].Append( k );
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
must qualify identifier to find this declaration in dependent base class
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
12 warnings and 4 errors generated.
make: *** [cdhit-common.o] Error 1
:cd-hit-v4.5.5-2011-03-31 $