Error while compiling phlawd in a Mac Yosemite 10.10.4

[Diogo Borges Provete]

Hi All,

I'm trying to install phlawd in a mac following the instructions at http://phlawd.net/manual/installation . I got everything done, except for muscle installation. I went to the src folder inside muscle, which was inside the deps folder in phlawd and did:

make && sudo make install

But it returned an error

subfams.cpp:44:25: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]

        for (unsigned i = 0; i < uNodeCount; ++i)

                             ~ ^ ~~~~~~~~~~

1 warning generated.

In file included from treefrommsa.cpp:5:

In file included from ./clustsetmsa.h:8:

./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch]

                switch(m_Distance)

                       ^

1 warning generated.

-rwxr-xr-x  1 diogoborgesprovete  staff   362K 18 Ago 10:24 muscle

34707 363 muscle

make: *** No rule to make target `install'.  Stop.

I tried to do the homebrew and it didn't work either:

node.cpp:227: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available

node.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’:

node.cpp:227:   instantiated from here

node.cpp:227: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits<char>, _Alloc = std::allocator<char>]’ but no definition available

make: *** [node.o] Error 1

Warning: It appears you have MacPorts or Fink installed.

Software installed with other package managers causes known problems for

Homebrew. If a formula fails to build, uninstall MacPorts/Fink and try again.

READ THIS: https://git.io/brew-troubleshooting

If reporting this issue please do so at (not Homebrew/homebrew):

  https://github.com/homebrew/homebrew-science/issues

Any ideas of how to solve this?

Thank you very muchin advance,

Diogo 

[Stephen Smith]

Hm, I don't have that mac setup but I can try and track it down. Maybe Cody has a more similar setup and idea of a fix. 

[Cody Hinchliff]

I would try downloading the Mac executable directly from the muscle website:

http://www.drive5.com/muscle/downloads.htm

Then just put the program in your PATH somewhere so phlawd can access it. You may also need to rename it, I think phlawd just assumes it is called "muscle"

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