* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/corrcoverage.Rcheck’
* using R Under development (unstable) (2024-04-18 r86444)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)
    GNU Fortran (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)
* running under: Fedora Linux 38 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘corrcoverage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘corrcoverage’ version ‘1.2.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘corrcoverage’ can be installed ... [18s/18s] OK
* used C++ compiler: ‘g++ (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘corrcoverage-Ex.R’ failed
The error most likely occurred in:

> ### Name: corrcov_CI_bhat
> ### Title: Confidence interval for corrected coverage estimate using
> ###   estimated effect sizes and their standard errors
> ### Aliases: corrcov_CI_bhat
> 
> ### ** Examples
> 
> 
> ## No test: 
>  # this is a long running example
> set.seed(1)
> nsnps <- 100
> N0 <- 5000 # number of controls
> N1 <- 5000 # number of cases
> 
> ## generate example LD matrix
> library(mvtnorm)
> nsamples = 1000
> 
> simx <- function(nsnps, nsamples, S, maf=0.1) {
+     mu <- rep(0,nsnps)
+     rawvars <- rmvnorm(n=nsamples, mean=mu, sigma=S)
+     pvars <- pnorm(rawvars)
+     x <- qbinom(1-pvars, 1, maf)
+ }
> 
> S <- (1 - (abs(outer(1:nsnps,1:nsnps,`-`))/nsnps))^4
> X <- simx(nsnps,nsamples,S)
> LD <- cor2(X)
> maf <- colMeans(X)
> 
> varbeta <- Var.data.cc(f = maf, N = N0 + N1, s = N1/(N0+N1))
> 
> bhats = rnorm(nsnps,0,0.2) # log OR
> 
> corrcov_CI_bhat(bhat = bhats, V = varbeta, N0, N1, Sigma = LD)
Error in FUN(X[[i]], ...) : argument "thr" is missing, with no default
Calls: corrcov_CI_bhat ... corrected_cov -> lapply -> FUN -> credsetC -> credsetmat
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [13s/13s]
 [13s/13s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [20s/21s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/corrcoverage.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:24.33, 74.76 + 9.16