Instale o pacote R TwoSampleMR no Linux
Instale diretamente com devtools e relate um erro
library(devtools)
devtools::install_github("MRCIEU/TwoSampleMR")
#configure: error: Header file gmp.h not found; maybe use --with-gmp-include=INCLUDE_PATH
#ERROR: configuration failed for package ‘gmp’
#* removing ‘/public/home/wx2022/miniconda3/envs/MR_r4.1.2/lib/R/library/gmp’
#ERROR: dependency ‘gmp’ is not available for package ‘arrangements’
#* removing ‘/public/home/wx2022/miniconda3/envs/MR_r4.1.2/lib/R/library/arrangements’
#ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
#* removing ‘/public/home/wx2022/miniconda3/envs/MR_r4.1.2/lib/R/library/lme4’
#ERROR: dependencies ‘gmp’, ‘arrangements’ are not available for package ‘iterpc’
#* removing ‘/public/home/wx2022/miniconda3/envs/MR_r4.1.2/lib/R/library/iterpc’
#ERROR: dependency ‘lme4’ is not available for package ‘meta’
#* removing ‘/public/home/wx2022/miniconda3/envs/MR_r4.1.2/lib/R/library/meta’
#ERROR: dependency ‘iterpc’ is not available for package ‘MendelianRandomization’
#* removing ‘/public/home/wx2022/miniconda3/envs/MR_r4.1.2/lib/R/library/MendelianRandomization’
Solução
De acordo com o relatório de erros, instale os pacotes dependentes em ordem. Pacotes que não podem ser instalados diretamente no R (talvez porque a versão esteja incorreta) podem ser instalados com conda.
conda install -c conda-forge r-gmp
conda install -c conda-forge r-nloptr
install.packages("arrangements")
install.packages("lme4")
install.packages("iterpc")
install.packages("meta")
install.packages("MendelianRandomization")
Depois de instalar os pacotes de dependência, você pode instalar com êxito o pacote TwoSampleMR.
devtools::install_github("MRCIEU/TwoSampleMR")
library(TwoSampleMR)
#TwoSampleMR version 0.5.6
#[>] New: Option to use non-European LD reference panels for clumping etc
#[>] Some studies temporarily quarantined to verify effect allele
#[>] See news(package='TwoSampleMR') and https://gwas.mrcieu.ac.uk for further details
Se a biblioteca exibir as informações acima posteriormente, significa que a instalação foi bem-sucedida.