* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miWQS.Rcheck’ * using R Under development (unstable) (2025-02-25 r87824) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-16) 14.2.0 GNU Fortran (Debian 14.2.0-16) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * 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 ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/miWQS-00install.html' for details. * checking package directory ... OK * checking for future file timestamps ... 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 ... [3s/4s] OK * checking whether the package can be loaded with stated dependencies ... [3s/5s] OK * checking whether the package can be unloaded cleanly ... [3s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK * checking whether the namespace can be unloaded cleanly ... [3s/4s] OK * checking loading without being on the library search path ... [3s/3s] 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 ... [17s/22s] OK * checking Rd files ... [0s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: coef.wqs.Rd: glm2 estimate.wqs.Rd: glm2 Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. 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 ... [0s/0s] 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 ... [5s/6s] ERROR Running examples in ‘miWQS-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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 ... [4s/5s] OK Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [3s/4s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [5s/7s] OK * checking PDF version of manual ... [4s/5s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR, 1 NOTE