Compile AV454 / ARACHNE error on MAC

[Peter Pham]

Hi,

I'm trying to compile and install AV454/ARACHNE on my iMAC (OS X, version 10.8.5).
I already upgrade g++ to 4.8.1 (by following the instruction from the link
http://solarianprogrammer.com/2013/06/11/compiling-gcc-mac-os-x/)
 and installed Xerces-C++.

I run configure, it looks like it's OK
./configure --with-xerces=/usr/local

However, when I run make, I got the following error messages:

Does AV454/ARACHNE only work on x86_64 Linux system (eg. CentOS Linux x86_64)?
Does anyone try it on Mac, OS X?

Thanks,

Peter

Making all in src
make  all-am
g++ -DHAVE_CONFIG_H -I.  -DRELEASE=3.0 -DMAKE_OS_RELEASE=12.5.0 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233  -I/usr/local/include -I/usr/local/include/xercesc -fopenmp -g -O2 -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG -MT ErrNo.o -MD -MP -MF .deps/ErrNo.Tpo -c -o ErrNo.o `test -f 'system/ErrNo.cc' || echo './'`system/ErrNo.cc
In file included from ./feudal/BinaryStream.h:26:0,
                 from ./feudal/FeudalString.h:21,
                 from ./feudal/CharString.h:19,
                 from ./string.h:13,
                 from /usr/gcc-4.8.1/include/c++/4.8.1/cstring:42,
                 from system/ErrNo.cc:17:
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:75:11: error: ‘::memchr’ has not been declared
   using ::memchr;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:76:11: error: ‘::memcmp’ has not been declared
   using ::memcmp;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:77:11: error: ‘::memcpy’ has not been declared
   using ::memcpy;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:78:11: error: ‘::memmove’ has not been declared
   using ::memmove;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:79:11: error: ‘::memset’ has not been declared
   using ::memset;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:80:11: error: ‘::strcat’ has not been declared
   using ::strcat;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:81:11: error: ‘::strcmp’ has not been declared
   using ::strcmp;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:82:11: error: ‘::strcoll’ has not been declared
   using ::strcoll;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:83:11: error: ‘::strcpy’ has not been declared
   using ::strcpy;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:84:11: error: ‘::strcspn’ has not been declared
   using ::strcspn;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:85:11: error: ‘::strerror’ has not been declared
   using ::strerror;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:86:11: error: ‘::strlen’ has not been declared
   using ::strlen;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:87:11: error: ‘::strncat’ has not been declared
   using ::strncat;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:88:11: error: ‘::strncmp’ has not been declared
   using ::strncmp;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:89:11: error: ‘::strncpy’ has not been declared
   using ::strncpy;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:90:11: error: ‘::strspn’ has not been declared
   using ::strspn;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:91:11: error: ‘::strtok’ has not been declared
   using ::strtok;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:92:11: error: ‘::strxfrm’ has not been declared
   using ::strxfrm;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:93:11: error: ‘::strchr’ has not been declared
   using ::strchr;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:94:11: error: ‘::strpbrk’ has not been declared
   using ::strpbrk;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:95:11: error: ‘::strrchr’ has not been declared
   using ::strrchr;
           ^
/usr/gcc-4.8.1/include/c++/4.8.1/cstring:96:11: error: ‘::strstr’ has not been declared
   using ::strstr;
           ^
In file included from ./feudal/FeudalString.h:21:0,
                 from ./feudal/CharString.h:19,
                 from ./string.h:13,
                 from /usr/gcc-4.8.1/include/c++/4.8.1/cstring:42,
                 from system/ErrNo.cc:17:
./feudal/BinaryStream.h: In constructor ‘MagicToken::MagicToken()’:
./feudal/BinaryStream.h:37:46: error: ‘memcpy’ was not declared in this scope
     { memcpy(mToken,"BINWRITE",sizeof(mToken)); }
                                              ^
./feudal/BinaryStream.h: In member function ‘bool MagicToken::isValid()’:
./feudal/BinaryStream.h:42:54: error: ‘memcmp’ was not declared in this scope
     { return !memcmp(mToken,"BINWRITE",sizeof(mToken)); }
                                                      ^
./feudal/BinaryStream.h: In member function ‘void BinaryWriter::writeBuf(const void*, size_t)’:
./feudal/BinaryStream.h:148:30: error: ‘memcpy’ was not declared in this scope
       { memcpy(mpBuf,data,len); mpBuf += len; }
                              ^
./feudal/BinaryStream.h:150:33: error: ‘memcpy’ was not declared in this scope
       { memcpy(mpBuf,data,remain);
                                 ^
./feudal/BinaryStream.h: In member function ‘void BinaryReader::read(void*, size_t)’:
./feudal/BinaryStream.h:272:30: error: ‘memcpy’ was not declared in this scope
       { memcpy(pVal,mpBuf,len); mpBuf += len; }
                              ^
./feudal/BinaryStream.h:275:35: error: ‘memcpy’ was not declared in this scope
         { memcpy(pVal,mpBuf,remain);
                                   ^
system/ErrNo.cc: In member function ‘std::string ErrNo::text() const’:
system/ErrNo.cc:30:55: error: ‘strerror_r’ was not declared in this scope
     long val = (long)strerror_r(mErrNo,buf,sizeof(buf));
                                                       ^
make[2]: *** [ErrNo.o] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

[Michael C. Zody]

I'm not 100% certain, but I believe Arachne just won't compile on OS X. I think it uses certain system calls that are not supported on BSD-derived unix.

Given the power of today's computers, if you want to run it on your mac, I might suggest installing virtual box and putting an Ubuntu instance in it to run AV454.

You could also try our newer assembler, Vicuna. It's mostly designed for Illumina, but should work for 454 with a little pre-processing.

Mike

[Peter Pham]

Thanks for your suggestion.  Mike.

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