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knausb / vcfR

Tools to work with variant call format files
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Don't install vcfR in Rstudio make: *** [gt_to_popsum.o] Error 1 #123

Closed zhenghy closed 5 years ago

zhenghy commented 5 years ago

R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.8 (Final)

Matrix products: default BLAS: /usr/local/lib64/R/lib/libRblas.so LAPACK: /usr/local/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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

loaded via a namespace (and not attached): [1] Rcpp_1.0.0 ps_1.3.0 prettyunits_1.0.2 rprojroot_1.3-2 withr_2.1.2 digest_0.6.18 crayon_1.3.4 assertthat_0.2.0 [9] R6_2.3.0 backports_1.1.3 magrittr_1.5 rlang_0.3.0.1 cli_1.0.1 curl_3.2 fs_1.2.6 remotes_2.0.2
[17] rstudioapi_0.8 callr_3.1.1 desc_1.2.0 devtools_2.0.1 tools_3.4.1 glue_1.3.0 pkgload_1.0.2 compiler_3.4.1
[25] processx_3.2.1 pkgbuild_1.0.2 sessioninfo_1.1.1 memoise_1.1.0 usethis_1.4.0

knausb commented 5 years ago

Hi @Haiyang, thanks for your post! You have not provided a minimal reproducible example, this make it very difficult to diagnose your issue. I've put some suggestions for how to do this here.

You appear to be having difficulties installing vcfR. Your session info reports that you are using R 3.4.1 where the current release is 3.5. I suggest you start by upgrading to the current version of R. Note that the upgrade from3.4 to 3.5 was substantial. I think I had to re-install all my packages. So good luck!

Your title includes RStudio. But I doubt this is part of the issue. You can circumvent RStudio by opening a terminal (i.e., bash) and using the following command.

Rscript -e "install.packages('vcfR')"

Also note that vcfR is currently building cleanly on CRAN. This seems to suggest that your issue may be specific to your system.

Please update your issue with a reproducible example and I'll try to help with it. Happy new year!