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I'm trying to compile a program called PEAR enter link description here and seems there is something wrong at this step.

I have Xcode installed.

Thanks for your help, Bernardo

Bernardos-MacBook-Pro:pear-0.9.0-src bernardo$ make
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C src all
gcc -c -Wall -fomit-frame-pointer -O3 -lm pear-pt.c -o pear-pt.o
clang: warning: -lm: 'linker' input unused
gcc -c -Wall -fomit-frame-pointer -O3 -lm reader.c -o reader.o
clang: warning: -lm: 'linker' input unused
reader.c:670:1: warning: unused function 'do_cpuid' [-Wunused-function]
do_cpuid(uint32_t selector, uint32_t *data)
^
1 warning generated.
gcc -Wall -fomit-frame-pointer -O3 -lm pear-pt.o args.o statistics.o reader.o -lm -lpthread -o pear
ld: warning: ignoring file args.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x01 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): args.o
ld: warning: ignoring file statistics.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x01 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): statistics.o
Undefined symbols for architecture x86_64:
  "_decode_switches", referenced from:
      _main in pear-pt.o
  "_stat_test2", referenced from:
      _assembly_FORWARD_LONGER in pear-pt.o
      _assembly_READS_EQUAL in pear-pt.o
      _assembly_REVERSE_LONGER in pear-pt.o
      _assembly in pear-pt.o
  "_usage", referenced from:
      _main in pear-pt.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [pear] Error 1
make: *** [all] Error 2
  • 1
    Don't ask the same question on different sites in Stack Exchange stackoverflow.com/questions/24286559/… – user151019 Jun 18 '14 at 19:13
  • Cross-posting is not permitted. If you do not get the desired response on the original site, request a moderator migrate your question. – grg Jun 18 '14 at 20:12
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Try building PEAR from the latest source. The output in your question suggests you are using an older version: 0.9.0.

At the time of answering, PEAR's version has climbed to 0.9.3.

Building PEAR from the source

git clone https://github.com/xflouris/PEAR.git
cd PEAR
make
make install

The build instructions mention using python 2.4 to run the tests. You may need to install additional versions of python.

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