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anuradhawick / LRBinner

LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.
https://doi.org/10.4230/LIPIcs.WABI.2021.11
GNU General Public License v2.0
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Build error: ISO C++ 2011 standard #6

Closed LynnLy closed 2 years ago

LynnLy commented 2 years ago

Hi there,

I am trying to build LRBinner within a linux/conda environment as you've described. After running sh build.sh, I run into this error: #error This file requires compiler and library support for the ISO C++ 2011 standard which can be fixed by adding "-std=c++11" to the g++ commands in build.sh, like so:

echo "BUILDING THE MetaBCC-LR 15 MER COMPUTATIONS"
g++ mbcclr_utils/search-15mers.cpp -fopenmp -lpthread -Wall -o mbcclr_utils/bin/search-15mers -lz -O3 -std=c++11
g++ mbcclr_utils/count-15mers.cpp -fopenmp -lpthread -Wall -o mbcclr_utils/bin/count-15mers -lz -O3 -std=c++11
echo "BUILDING THE MetaBCC-LR 3 MER COMPUTATIONS"
g++ mbcclr_utils/count-kmers.cpp -Wall -fopenmp -lpthread -o mbcclr_utils/bin/count-kmers -lz -O3 -std=c++11

I am also trying the contig mode, which required me to downgrade the joblib library, as described here: via conda install -c conda-forge joblib=0.17.0

It seems to build properly and run on my data after these changes!

anuradhawick commented 2 years ago

Thank you very much for the corrections. I will update the read me with this information.

The issue with joblib is due to conda version of hdbscan being outdated. It typically fixes itself when installed through GitHub repo right away.

I will update the descriptions soon.

Thanks.