* using log directory 'd:/Rcompile/CRANpkg/local/3.5/prewas.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'prewas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'prewas' version '1.1.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'prewas' can be installed ... OK
* checking installed package size ... OK
* 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 R 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 use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s] OK
* checking Rd files ... OK
* checking Rd metadata ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [3s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [37s] ERROR
  Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("prewas")
  Loading required package: prewas
  -- 1. Error: collapse_snps_into_genes_by_impact() behaves as expected when given
  subscript out of bounds
  Backtrace:
   1. testthat::expect_equal(...)
   4. base::unname(temp_gene_mat_list$gene_mat_moderate[2, , drop = TRUE])
  
  -- 2. Error: get_gene_mat_by_impact() behaves as expected when given valid input
  subscript out of bounds
  Backtrace:
   1. testthat::expect_equal(...)
   4. base::unname(gene_mat[2, , drop = TRUE])
  
  [1] "Start building tree"
  optimize edge weights:  -2420.974 --> -2415.557 
  optimize base frequencies:  -2415.557 --> -2415.352 
  optimize rate matrix:  -2415.352 --> -2413.979 
  optimize edge weights:  -2413.979 --> -2413.974 
  optimize topology:  -2413.974 --> -2413.974 
  0 
  [1] "Ratchet iteration  1 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  2 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  3 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  4 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  5 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  6 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  7 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  8 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  9 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  10 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  11 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  12 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  13 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  14 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  15 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  16 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  17 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  18 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  19 , best pscore so far: -2413.97385163831"
  [1] "Ratchet iteration  20 , best pscore so far: -2413.97385163831"
  optimize base frequencies:  -2413.974 --> -2413.742 
  optimize rate matrix:  -2413.742 --> -2413.699 
  optimize edge weights:  -2413.699 --> -2413.699 
  optimize topology:  -2413.699 --> -2413.699 
  0 
  optimize base frequencies:  -2413.699 --> -2413.692 
  optimize rate matrix:  -2413.692 --> -2413.691 
  optimize edge weights:  -2413.691 --> -2413.691 
  optimize base frequencies:  -2413.691 --> -2413.691 
  optimize rate matrix:  -2413.691 --> -2413.691 
  optimize edge weights:  -2413.691 --> -2413.691 
  optimize base frequencies:  -2413.691 --> -2413.691 
  optimize rate matrix:  -2413.691 --> -2413.691 
  optimize edge weights:  -2413.691 --> -2413.691 
  [1] "Finished building tree"
  == testthat results  ===========================================================
  [ OK: 314 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: collapse_snps_into_genes_by_impact() behaves as expected when given valid input (@test-collapse_snps_by_gene.R#115) 
  2. Error: get_gene_mat_by_impact() behaves as expected when given valid input (@test-collapse_snps_by_gene.R#263) 
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [27s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR