* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/miWQS.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc3
    flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘miWQS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miWQS’ version ‘0.4.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘wqs’
* 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 ‘miWQS’ can be installed ... [24s/30s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/miWQS-00install.html' for details.
* 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 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 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 ... [39s/52s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘wqs’ in Rd xrefs
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/14s] ERROR
Running examples in ‘miWQS-Ex.R’ failed
The error most likely occurred in:

> ### Name: estimate.wqs
> ### Title: Weighted Quantile Sum (WQS) Regression
> ### Aliases: estimate.wqs
> ### Keywords: imputation wqs
> 
> ### ** Examples
> 
> # Example 1: Binary outcome using the example simulated dataset in this package.
> data(simdata87)
> set.seed(23456)
> W.bin4  <- estimate.wqs(
+   y = simdata87$y.scenario, X = simdata87$X.true[, 1:9],
+   B = 10, family = "binomial",
+   verbose = TRUE
+ )
## Outcome Summary 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.000   0.457   1.000   1.000 
## Classes: 
           y            X            Z 
   "integer" "data.frame"       "NULL" 
X 
 alpha.chlordane        dieldrin         gamma.chlordane     lindane      
 Min.   :0.000e+00   Min.   :    0.111   Min.   : 13.51   Min.   : 3.513  
 1st Qu.:1.110e+01   1st Qu.:   14.344   1st Qu.: 36.68   1st Qu.:11.163  
 Median :1.254e+02   Median :   52.536   Median : 46.35   Median :14.981  
 Mean   :4.410e+04   Mean   :  433.116   Mean   : 49.35   Mean   :17.174  
 3rd Qu.:1.682e+03   3rd Qu.:  218.957   3rd Qu.: 58.91   3rd Qu.:21.129  
 Max.   :1.735e+07   Max.   :48673.296   Max.   :139.34   Max.   :75.360  
  methoxychlor         dde                 ddt          pentachlorophenol
 Min.   : 17.30   Min.   :     0.02   Min.   :  1.382   Min.   :  1.615  
 1st Qu.: 55.83   1st Qu.:    13.69   1st Qu.:  7.307   1st Qu.:  8.390  
 Median : 75.17   Median :    84.22   Median : 12.290   Median : 14.651  
 Mean   : 83.29   Mean   :  2546.60   Mean   : 16.119   Mean   : 20.251  
 3rd Qu.:101.89   3rd Qu.:   529.84   3rd Qu.: 19.398   3rd Qu.: 23.942  
 Max.   :316.07   Max.   :383567.39   Max.   :178.854   Max.   :285.229  
    pcb_105       
 Min.   :  0.109  
 1st Qu.:  3.317  
 Median :  7.458  
 Mean   : 16.473  
 3rd Qu.: 17.779  
 Max.   :400.360  
y 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.000   0.000   0.000   0.457   1.000   1.000 
Z 
Length  Class   Mode 
     0   NULL   NULL 
## Place BDLs in Q1?  FALSE 
#> No missing values in matrix detected. Regular quantiles computed.
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 
  'partial' index 1001 outside bounds
Calls: estimate.wqs ... quantile.default -> sort -> sort.default -> sort.int
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘spelling.R’
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [29s/35s] OK
* checking PDF version of manual ... [8s/11s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... NOTE
Found the following files/directories:
  ‘par-7269706c6579’
* DONE
Status: 1 ERROR, 2 NOTEs