SAIGE install via Conda configuration failure (failed to build statgen/savvy)

[krishnaxamin]

Hi,

I've been trying to install SAIGE via Conda. The installation repeatedly fails at the R CMD INSTALL SAIGE step.

Could you please advise? Thank you in advance!

Here are the errors and warnings that come up: CMake Warning: Manually-specified variables were not used by the project:

BUILD_TESTING
CGET_CMAKE_DIR
CGET_CMAKE_ORIGINAL_SOURCE_FILE

-- Build files have been written to: /mnt/c/Users/krish/Documents/QMUL PhD/HPC/gwas_practice/SAIGE/thirdParty/cget/cget/build/tmp-6f7d5a19aed242d59296323b70f7e433/build [ 3%] Creating pkg-config file CMake Error: File /mnt/c/Users/.../SAIGE/thirdParty/cget/cget/build/tmp-79c4af0892624ffc85cb02c54ef89246/zstd-1.3.2/lib/libzstd.pc.in does not exist. CMake Error at /mnt/c/Users/.../SAIGE/thirdParty/cget/cget/build/tmp-79c4af0892624ffc85cb02c54ef89246/zstd-1.3.2/build/cmake/lib/pkgconfig.cmake:1 (CONFIGURE_FILE): CONFIGURE_FILE Problem configuring file

make[2]: [build/cmake/lib/CMakeFiles/libzstd.pc.dir/build.make:71: build/cmake/lib/CMakeFiles/libzstd.pc] Error 1 make[1]: [CMakeFiles/Makefile2:154: build/cmake/lib/CMakeFiles/libzstd.pc.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs....

Note: I can find this file (/mnt/c/Users/.../SAIGE/thirdParty/cget/cget/build/tmp-79c4af0892624ffc85cb02c54ef89246/zstd-1.3.2/lib/libzstd.pc.in) manually after the process exits.

then some time later

[ 96%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir///__/lib/deprecated/zbuff_decompress.c.o [100%] Built target libzstd_static gmake: *** [Makefile:136: all] Error 2 Command failed: ['/home/.../miniconda3/envs/RSAIGE/bin/cmake', '--build', '/mnt/c/Users/.../SAIGE/thirdParty/cget/cget/build/tmp-79c4af0892624ffc85cb02c54ef89246/build', '--config', 'Release', '--', '-j', '8'] Failed to build package statgen/savvy ERROR: configuration failed for package ‘SAIGE’

[jingydz]

Hello, have you solved your problem?

[krishnaxamin]

@jingydz I'm afraid not - I am using the Docker image instead.