Make error

[SuqinYang]

Thank you for the tool. When I install the tool, the error occurs. Would you please help me with the error?

Error:

/share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:46: undefined reference to H5Dget_space' /share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:47: undefined reference to H5Dget_type'
/share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:48: undefined reference to H5Dget_create_plist' /share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:49: undefined reference to H5Sget_simple_extent_ndims'
/share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:51: undefined reference to H5Sget_simple_extent_dims' /share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:63: undefined reference to H5open'
/share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:63: undefined reference to H5T_NATIVE_UINT64_g' /share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:63: undefined reference to H5Dread'
/share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:64: undefined reference to H5Aclose' /share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:65: undefined reference to H5Dclose'
/share/home//miniconda3/envs/rna_env/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data/home//software/ST_BarcodeMap/ST_BarcodeMap/src/chipMaskMerge.cpp:66: undefined reference to `H5Fclose'
collect2: error: ld returned 1 exit status
make: *** [Makefile:24: ST_BarcodeMap-0.0.1] Error 1

Package and version:
boost 1.85.0
zlib 1.2.13
hdf5 1.14.3

[wong-ziyi]

I used GitHub action to compile it, you can download the compiled binary file from my forked repository. Please check https://github.com/wong-ziyi/ST_BarcodeMap

[linxy29]

This is how I install it:

1. Modify the Makefile:
   change LIBS := -lz -lpthread to LIBS := -lz -lpthread -lboost_serialization -lhdf5_hl -lhdf5

2. Run the following:
   mamba create -n st_barcodemap boost=1.73 hdf5=1.12.0 zlib=1.2.11 -c conda-forge
conda activate st_barcodemap
mamba install -c conda-forge gcc_linux-64 gxx_linux-64
mamba install -c conda-forge boost=1.73
cd ST_BarcodeMap
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
make INCLUDE_DIRS=$CONDA_PREFIX/include LIBRARY_DIRS=$CONDA_PREFIX/lib