The GRAB package can be installed in R or via docker.
Install GRAB package via docker
UK Biobank Research Analysis Platform (RAP) supports docker installation. For more details about the GRAB package build, installation, and usage, please check the section UK Biobank RAP.
Install GRAB package in R (current version: 0.0.3.9)
In Linux operation system
library(remotes)
install_github("GeneticAnalysisinBiobanks/GRAB")
library(GRAB)
In Windows operation system
library(remotes)
# options(download.file.method = "wininet")
install_github("GeneticAnalysisinBiobanks/GRAB", INSTALL_opts=c("--no-multiarch")) # The INSTALL_opts sometimes is required in Windows OS.
library(GRAB)
We note that package installation in Windows system is not as stable as in Linux system. Possible errors could be due to package dependency, network issue, et al.
The Linux environment of the maintainer
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /gdata01/user/wenjianb/software/miniconda3/envs/myEnvR4.0/lib/libopenblasp-r0.3.21.so
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] GRAB_0.1 Rcpp_1.0.10 igraph_1.4.3 dbplyr_2.3.2
[5] dplyr_1.1.2 tidyr_1.3.0 SKAT_2.2.5 RSpectra_0.16-1
[9] SPAtest_3.1.2 Matrix_1.5-3 ordinal_2022.11-16 survival_3.4-0
[13] remotes_2.4.2
loaded via a namespace (and not attached):
[1] compiler_4.0.5 pillar_1.9.0 prettyunits_1.1.1
[4] tools_4.0.5 pkgbuild_1.3.1 lifecycle_1.0.3
[7] tibble_3.2.1 nlme_3.1-159 lattice_0.20-45
[10] ucminf_1.2.0 pkgconfig_2.0.3 rlang_1.1.1
[13] DBI_1.1.3 cli_3.6.1 curl_5.0.0
[16] withr_2.5.0 generics_0.1.3 vctrs_0.6.2
[19] rprojroot_2.0.3 grid_4.0.5 tidyselect_1.2.0
[22] glue_1.6.2 R6_2.5.1 processx_3.8.1
[25] fansi_1.0.4 callr_3.7.3 purrr_1.0.1
[28] magrittr_2.0.3 ps_1.7.5 MASS_7.3-58.1
[31] splines_4.0.5 numDeriv_2016.8-1.1 utf8_1.2.3
[34] RcppParallel_5.1.7 crayon_1.5.2
The Windows environment of the maintainer
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
system code page: 936
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] GRAB_0.1 Rcpp_1.0.10 igraph_1.2.6
[4] dbplyr_2.3.2 dplyr_1.1.2 tidyr_1.3.0
[7] SKAT_2.2.5 RSpectra_0.16-1 SPAtest_3.1.2
[10] Matrix_1.3-3 ordinal_2022.11-16 survival_3.2-11
[13] remotes_2.4.2
loaded via a namespace (and not attached):
[1] compiler_4.1.0 pillar_1.9.0 prettyunits_1.1.1
[4] tools_4.1.0 pkgbuild_1.2.0 lifecycle_1.0.3
[7] tibble_3.2.1 nlme_3.1-152 lattice_0.20-44
[10] ucminf_1.2.0 pkgconfig_2.0.3 rlang_1.1.1
[13] DBI_1.1.3 cli_3.6.1 rstudioapi_0.13
[16] curl_4.3.2 withr_2.5.0 generics_0.1.3
[19] vctrs_0.6.2 rprojroot_2.0.2 grid_4.1.0
[22] tidyselect_1.2.0 glue_1.6.2 data.table_1.14.2
[25] R6_2.5.1 processx_3.5.2 fansi_1.0.4
[28] purrr_1.0.1 callr_3.7.0 magrittr_2.0.3
[31] ps_1.6.0 MASS_7.3-54 splines_4.1.0
[34] numDeriv_2016.8-1.1 utf8_1.2.3 RcppParallel_5.1.7
[37] crayon_1.5.1