install error

[yu-zhang-oYo]

Hi, when I am trying to install the SAIGE with 'R CMD INSTALL SAIGE', either with conda or source code, there is always such kind of error, I would like to know how to solve this problem. Please let me know if I need to provide more information. Thanks.

VCF.cpp:4:10: fatal error: savvy/reader.hpp: No such file or directory
    4 | #include "savvy/reader.hpp"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/N/u/yzh10/BigRed200/.conda/envs/RSAIGE/lib/R/etc/Makeconf:177: VCF.o] Error 1
ERROR: compilation failed for package ‘SAIGE’

[engwbc]

Hello,
Did you install savvy correctly? The error says it cannot find the C++ script reader.cpp within savvy/src

Building from source code, I first installed: pipx to avoid package compatibility issues then used pipx to install cget.
Finally, I installed savvy with the following command cget install statgen/savvy, or if you want to choose an install path use
cget install --prefix /path/to/install statgen/savvy.
You can then check if savvy has been installed by using cget list

Can't comment on conda as I have not worked with it, but there is also a command to install savvy there conda install -c conda-forge -c bioconda savvy

[yu-zhang-oYo]

thanks for this instruction.