Error Installing HIBAG

[pbleic]

On R 4.1.2. Have tried to install using BiocManager, using the dev version, and from source. Each time have the same error:

LibHLA_ext_avx512vpopcnt.cpp: In function ‘int hamm_d(const TGenoStruct_512vpopcnt&, const HLA_LIB::THaplotype&, const HLA_LIB::THaplotype&)’: LibHLA_ext_avx512vpopcnt.cpp:173:15: error: ‘_mm_popcnt_epi64’ was not declared in this scope

Can anyone suggest how to install?

[zhengxw-ab]

Please show me sessionInfo() and your GCC version.

[pbleic]

gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] BiocManager_1.30.16

loaded via a namespace (and not attached): [1] compiler_4.1.2 tools_4.1.2

[zhengxw-ab]

The previous version (v1.28) of HIBAG does not contain LibHLA_ext_avx512vpopcnt.cpp. http://bioconductor.org/packages/3.13/bioc/src/contrib/HIBAG_1.28.0.tar.gz

I guess the previous version should work. Please use the previous version before I finally fix the issue.

[zhengxw-ab]

The new HIBAG_1.30.1.tar.gz is available at http://www.bioconductor.org/packages/release/bioc/html/HIBAG.html. avx512vpopcnt requires GCC >= v8.0 to compile.