Error if trace = TRUE in ashci

[frederikziebell]

This

beta <-  c(rep(0,20),rnorm(20))
sebetahat <-  abs(rnorm(40,0,1))
betahat <-  rnorm(40,beta,sebetahat)
beta.ash <-  ash(betahat, sebetahat)
res <- ashci(beta.ash,betaindex = 1:10, trace = TRUE)

gives an error

Error in assign(".type", type, envir = baseenv()) : 
cannot add binding of '.type' to the base environment

which does not appear, if trace = FALSE is set

[pcarbo]

@frederikziebell I could not reproduce your error. Which version of the ashr package are you using? Maybe try with library(ashr) rather than, say, loading the package with devtools::load_all()?

[frederikziebell]

I'm using library(ashr), here's my session info:

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] ashr_2.2-54

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3    invgamma_1.1    lattice_0.20-45 digest_0.6.29   truncnorm_1.0-8 grid_4.2.0      evaluate_0.15   rlang_1.0.2     cli_3.3.0       irlba_2.3.5     Matrix_1.4-1    rmarkdown_2.14  tools_4.2.0    
[14] mixsqp_0.3-47   xfun_0.30       yaml_2.3.5      fastmap_1.1.0   compiler_4.2.0  SQUAREM_2021.1  htmltools_0.5.2 knitr_1.39     

[stephens999]

this appears to be due to a breaking change in R v 4.1.0 which had the following change:

The base environment and its namespace are now locked (so one can no longer add bindings to these or remove from these).

This lead to breaking of the ashr tic and toc functions. I've replaced these functions with the latest commit

[stephens999]

fixed with 9c5a495