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  • anatgonca
    Junior Member
    • Feb 2015
    • 6

    #1

    cd-hit-otu installation issue in Mac

    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 $

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