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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
268 stars 48 forks source link

Installation Issue #138

Open wshropshire opened 5 years ago

wshropshire commented 5 years ago

Hello,

I'm trying to install racon v1.4.5 on a MacBook Pro. I was able to download racon v1.3.1 a little over a year ago, but now I'm having a library linking issue which I wanted to know if there is an easy fix for this. Here is the output for my cmake command: 'wshropshire: build $cmake -DCMAKE_BUILD_TYPE=Release .. -- The C compiler identification is GNU 7.2.0 -- The CXX compiler identification is GNU 7.2.0 -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/local/bin/gcc-7 -- Check for working C compiler: /usr/local/bin/gcc-7 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/local/bin/gcc-7 -- Check for working CXX compiler: /usr/local/bin/gcc-7 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of off64_t -- Check size of off64_t - failed -- Looking for fseeko -- Looking for fseeko - found -- Looking for unistd.h -- Looking for unistd.h - found -- Renaming -- /Users/wshropshire/Documents/Programs/racon/racon/vendor/bioparser/vendor/zlib/zconf.h -- to 'zconf.h.included' because this file is included with zlib -- but CMake generates it automatically in the build directory. -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE Setting warning flags -- Configuring done CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

zlib

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done -- Build files have been written to: /Users/wshropshire/Documents/Programs/racon/racon/build'

I've figured that it might be a zlib issue so I've tried to link setting these flags: ' export LDFLAGS="-L/usr/local/opt/zlib/lib" export CPPFLAGS="-I/usr/local/opt/zlib/include"'

But it hasn't solved the issue. Any help would be appreciated!

rvaser commented 5 years ago

Hello, as I see there is only a warning and the Makefile should been generated. Can you verify that please? Nothing much changed with zlib inclusion so I guess there should not be any problems with compiling.

Sorry for the late response!

Best regards, Robert