• using R Under development (unstable) (2025-12-19 r89206)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘ctsem/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ctsem’ version ‘3.10.4’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• 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 ‘ctsem’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’
• checking C++ specification ... OK
• 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 ... [5s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/7s] OK
• checking whether the package can be unloaded cleanly ... [5s/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
• checking loading without being on the library search path ... [8s/9s] OK
• checking whether startup messages can be suppressed ... [5s/6s] 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 ... [46s/55s] OK
• checking Rd files ... [1s/1s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [7s/8s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [8s/9s] ERROR Running examples in ‘ctsem-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ctACF > ### Title: Continuous Time Autocorrelation Function (ctACF) > ### Aliases: ctACF > > ### ** Examples > > data.table::setDTthreads(1) #ignore this line > # Example usage: > head(ctstantestdat)   id time Y1 Y2 TD1 TI1 TI2 TI3 4 1 0.000000 8.628419 13.55213 0 -0.05380504 -1.366299 -0.2074973 5 1 0.123705 NA 11.34075 NA -0.05380504 -1.366299 -0.2074973 6 1 0.594186 7.500058 12.33738 0 -0.05380504 -1.366299 -0.2074973 7 1 0.888842 6.834832 12.63265 1 -0.05380504 -1.366299 -0.2074973 8 1 1.186905 7.010044 11.90834 0 -0.05380504 -1.366299 -0.2074973 9 1 1.624510 6.791367 10.21116 0 -0.05380504 -1.366299 -0.2074973 > ctACF(ctstantestdat,varnames=c('Y1'),idcol='id',timecol='time',nboot=5) Loading required namespace: collapse Error in `[.data.table`(dat, , `:=`(.timediff, c(NA, diff(get(timecol)))), :   attempt access index 8/8 in VECTOR_ELT Calls: ctACF -> quantile -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [74s/101s] ERROR   Running ‘testthat.R’ [74s/100s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(ctsem)   Loading required package: Rcpp   ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions   > pdf(NULL)   > test_check("ctsem")   Saving _problems/test-intervalise-12.R   Saving _problems/test-reshaping-30.R        [,1] [,2]   [1,] "0" "0"   [2,] "0" "diff"        [,1]   [1,] "0"          [,1]   [1,] "0"   [2,] "cint"   ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions   starting worker pid=899587 on localhost:28290 at 15:36:47.735   ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions   starting worker pid=899582 on localhost:28290 at 15:36:49.505   Loading required package: data.table   Loading required package: data.table      Attaching package: ‘data.table’      The following object is masked from ‘package:base’:          %notin%         Attaching package: ‘data.table’      The following object is masked from ‘package:base’:          %notin%      ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions   starting worker pid=1010750 on localhost:24314 at 15:37:20.798   ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX'), and for discussion https://github.com/cdriveraus/ctsem/discussions   starting worker pid=1010748 on localhost:24314 at 15:37:22.613   Loading required package: data.table   Loading required package: data.table      Attaching package: ‘data.table’      The following object is masked from ‘package:base’:          %notin%         Attaching package: ‘data.table’      The following object is masked from ‘package:base’:          %notin%         SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 1).      SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 2).   Chain 1:   Chain 1: Gradient evaluation took 0.010442 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 104.42 seconds.   Chain 1: Adjust your expectations accordingly!   Chain 1:   Chain 1:   Chain 2:   Chain 2: Gradient evaluation took 0.014697 seconds   Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 146.97 seconds.   Chain 2: Adjust your expectations accordingly!   Chain 2:   Chain 2:   Chain 1: Iteration: 1 / 300 [ 0%] (Warmup)   Chain 2: Iteration: 1 / 300 [ 0%] (Warmup)   Chain 1: Iteration: 20 / 300 [ 6%] (Warmup)   Chain 2: Iteration: 20 / 300 [ 6%] (Warmup)   Chain 1: Iteration: 40 / 300 [ 13%] (Warmup)   Chain 2: Iteration: 40 / 300 [ 13%] (Warmup)   Chain 1: Iteration: 60 / 300 [ 20%] (Warmup)   Chain 2: Iteration: 60 / 300 [ 20%] (Warmup)   Chain 1: Iteration: 80 / 300 [ 26%] (Warmup)   Chain 1: Iteration: 100 / 300 [ 33%] (Warmup)   Chain 2: Iteration: 80 / 300 [ 26%] (Warmup)   Chain 1: Iteration: 120 / 300 [ 40%] (Warmup)   Chain 2: Iteration: 100 / 300 [ 33%] (Warmup)   Chain 1: Iteration: 140 / 300 [ 46%] (Warmup)   Chain 1: Iteration: 151 / 300 [ 50%] (Sampling)   Chain 1: Iteration: 170 / 300 [ 56%] (Sampling)   Chain 2: Iteration: 120 / 300 [ 40%] (Warmup)   Chain 1: Iteration: 190 / 300 [ 63%] (Sampling)   Chain 1: Iteration: 210 / 300 [ 70%] (Sampling)   Chain 2: Iteration: 140 / 300 [ 46%] (Warmup)   Chain 1: Iteration: 230 / 300 [ 76%] (Sampling)   Chain 2: Iteration: 151 / 300 [ 50%] (Sampling)   Chain 1: Iteration: 250 / 300 [ 83%] (Sampling)   Chain 2: Iteration: 170 / 300 [ 56%] (Sampling)   Chain 1: Iteration: 270 / 300 [ 90%] (Sampling)   Chain 1: Iteration: 290 / 300 [ 96%] (Sampling)   Chain 1: Iteration: 300 / 300 [100%] (Sampling)   Chain 1:   Chain 1: Elapsed Time: 16.433 seconds (Warm-up)   Chain 1: 7.603 seconds (Sampling)   Chain 1: 24.036 seconds (Total)   Chain 1:   Chain 2: Iteration: 190 / 300 [ 63%] (Sampling)   Chain 2: Iteration: 210 / 300 [ 70%] (Sampling)   Chain 2: Iteration: 230 / 300 [ 76%] (Sampling)   Chain 2: Iteration: 250 / 300 [ 83%] (Sampling)   Chain 2: Iteration: 270 / 300 [ 90%] (Sampling)   Chain 2: Iteration: 290 / 300 [ 96%] (Sampling)   Chain 2: Iteration: 300 / 300 [100%] (Sampling)   Chain 2:   Chain 2: Elapsed Time: 20.905 seconds (Warm-up)   Chain 2: 11.367 seconds (Sampling)   Chain 2: 32.272 seconds (Total)   Chain 2:   [ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]      ══ Skipped tests (16) ══════════════════════════════════════════════════════════   • empty test (16): , , , , , , , , , , , , , , ,      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-intervalise.R:10:3'): intervals ────────────────────────────────   Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT   Backtrace:       ▆    1. └─ctsem::ctLongToWide(...) at test-intervalise.R:10:3    2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]    3. └─data.table:::`[.data.table`(...)   ── Error ('test-reshaping.R:29:3'): reshaping1 ─────────────────────────────────   Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 8/8 in VECTOR_ELT   Backtrace:       ▆    1. └─ctsem::ctLongToWide(...) at test-reshaping.R:29:3    2. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id]    3. └─data.table:::`[.data.table`(...)      [ FAIL 2 | WARN 0 | SKIP 16 | PASS 6 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [13s/18s] OK
• checking PDF version of manual ... [6s/9s] OK
• checking HTML version of manual ... [4s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs