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styvon / TAPE

Test with Adjusted Phenotype and Empirical saddlepoint approximation in linear mixed model (TAPE) :radio:
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object 'setBGENobjInCPP' not found for TAPEtestM #1

Open qiyubio opened 3 years ago

qiyubio commented 3 years ago

Hi, I was testing on TAPE, and TAPEtest works fine, but TAPEtestM complains. The code I was running :

n_variants_tested = TAPEtestM(null_object=obj_null, genfile=file_geno_test, samplefile=file_idsingeno, outfile=file_output_s2M, genfile_format="bgen", bgibgi_suffix= .bgen.bgi

The error I got:

====== Matching IIDs ======
====== Loading genotype ======
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  object 'setBGENobjInCPP' not found

My sessionInfo():

sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: libmkl_rt.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] TAPE_0.3.0   SAIGE_0.29.6

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5         dbplyr_1.4.1       pillar_1.4.1       compiler_3.5.2
 [5] prettyunits_1.0.2  remotes_2.0.4      tools_3.5.2        SPAtest_3.0.0
 [9] testthat_2.1.1     digest_0.6.19      pkgbuild_1.0.3     pkgload_1.0.2
[13] bit_1.1-14         tibble_2.1.3       memoise_1.1.0      RSQLite_2.1.1
[17] lattice_0.20-38    pkgconfig_2.0.2    rlang_0.4.7        Matrix_1.2-17
[21] cli_1.1.0          DBI_1.0.0          curl_3.3           dplyr_0.8.1
[25] withr_2.1.2        desc_1.2.0         fs_1.3.1           devtools_2.0.2
[29] tidyselect_0.2.5   rprojroot_1.3-2    bit64_0.9-7        grid_3.5.2
[33] glue_1.3.1         data.table_1.12.2  R6_2.4.0           processx_3.3.1
[37] sessioninfo_1.1.1  purrr_0.3.2        blob_1.1.1         callr_3.2.0
[41] magrittr_1.5       backports_1.1.4    ps_1.3.0           usethis_1.5.0
[45] assertthat_0.2.1   RcppParallel_4.4.3 crayon_1.3.4

Any suggestion to fix it? Thanks, Qi

styvon commented 3 years ago

Hi Qi, There seems to be some compatibility issue when compiling the TAPEtestM() function. Please try cloning the repository locally and use devtools::load_all("TAPE/src") to load the function.