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tpook92 / HaploBlocker

R-package: Calculation of haplotype blocks and libraries
GNU General Public License v3.0
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installation error #6

Open SilvaPaula opened 4 years ago

SilvaPaula commented 4 years ago

Hi, I'm trying to install HaploBlocker but I get the following error. I tried also to install it directly using devtools::install_github('tpook92/HaploBlocker', subdir='pkg') but same error. Also when trying to load RandomFieldsUtils.

Any help will be much appreciated.

install.packages("~/Downloads/HaploBlocker_1.5.8.tar", repos = NULL, type='source')

  • installing source package ‘HaploBlocker’ ... using staged installation libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RandomFieldsUtils/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c chaploblocker.cc -o chaploblocker.o clang: error: unsupported option '-fopenmp' make: *** [chaploblocker.o] Error 1 ERROR: compilation failed for package ‘HaploBlocker’
  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/HaploBlocker’
tpook92 commented 4 years ago

I just checked and had no problems on all of my machines (Linux + Windows). I do not have a Mac to check sadly.

In case you are working on a windows machine it might be necessary to use the .zip-version of the package (https://github.com/tpook92/HaploBlocker/blob/master/HaploBlocker_1.5.8.zip) or prior to using install Rtools (https://cran.r-project.org/bin/windows/Rtools/).

It the issue is still occuring after this i would need more information on your system to check the issue more thoroughly.

SilvaPaula commented 4 years ago

Yeah, I am using Mac. For what I have been searching is a Mac issue with Rtools. Thanks for your reply.