CRAN Package Check Results for Maintainer ‘Charles Driver <charles.driver2 at uzh.ch>’

Last updated on 2025-12-21 17:51:04 CET.

Package ERROR NOTE OK
ctsem 4 2 5
ctsemOMX 6 7

Package ctsem

Current CRAN status: ERROR: 4, NOTE: 2, OK: 5

Version: 3.10.4
Check: examples
Result: 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 Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 3.10.4
Check: tests
Result: ERROR Running ‘testthat.R’ [102s/125s] 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 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=444135 on localhost:30668 at 23:40:58.510 starting worker pid=444134 on localhost:30668 at 23:40:59.456 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 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=452726 on localhost:30212 at 23:41:28.696 starting worker pid=452727 on localhost:30212 at 23:41:29.649 Loading required package: data.table Loading required package: data.table Attaching package: ‘data.table’ Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% The following object is masked from ‘package:base’: %notin% SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.01074 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 107.4 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.017811 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 178.11 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 2: Iteration: 20 / 300 [ 6%] (Warmup) Chain 1: Iteration: 20 / 300 [ 6%] (Warmup) Chain 2: Iteration: 40 / 300 [ 13%] (Warmup) Chain 1: Iteration: 40 / 300 [ 13%] (Warmup) Chain 2: Iteration: 60 / 300 [ 20%] (Warmup) Chain 1: Iteration: 60 / 300 [ 20%] (Warmup) Chain 2: Iteration: 80 / 300 [ 26%] (Warmup) Chain 1: Iteration: 80 / 300 [ 26%] (Warmup) Chain 2: Iteration: 100 / 300 [ 33%] (Warmup) Chain 1: Iteration: 100 / 300 [ 33%] (Warmup) Chain 1: Iteration: 120 / 300 [ 40%] (Warmup) Chain 2: Iteration: 120 / 300 [ 40%] (Warmup) Chain 1: Iteration: 140 / 300 [ 46%] (Warmup) Chain 2: Iteration: 140 / 300 [ 46%] (Warmup) Chain 2: Iteration: 151 / 300 [ 50%] (Sampling) Chain 1: Iteration: 151 / 300 [ 50%] (Sampling) Chain 2: Iteration: 170 / 300 [ 56%] (Sampling) Chain 1: Iteration: 170 / 300 [ 56%] (Sampling) Chain 2: Iteration: 190 / 300 [ 63%] (Sampling) Chain 1: Iteration: 190 / 300 [ 63%] (Sampling) Chain 1: Iteration: 210 / 300 [ 70%] (Sampling) Chain 2: Iteration: 210 / 300 [ 70%] (Sampling) Chain 2: Iteration: 230 / 300 [ 76%] (Sampling) Chain 1: Iteration: 230 / 300 [ 76%] (Sampling) Chain 2: Iteration: 250 / 300 [ 83%] (Sampling) Chain 1: Iteration: 250 / 300 [ 83%] (Sampling) Chain 2: Iteration: 270 / 300 [ 90%] (Sampling) Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) Chain 2: Iteration: 290 / 300 [ 96%] (Sampling) Chain 1: Iteration: 290 / 300 [ 96%] (Sampling) Chain 1: Iteration: 300 / 300 [100%] (Sampling) Chain 2: Iteration: 300 / 300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 26.635 seconds (Warm-up) Chain 1: 13.441 seconds (Sampling) Chain 1: 40.076 seconds (Total) Chain 1: Chain 2: Chain 2: Elapsed Time: 26.34 seconds (Warm-up) Chain 2: 13.743 seconds (Sampling) Chain 2: 40.083 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 Flavor: r-devel-linux-x86_64-debian-clang

Version: 3.10.4
Check: tests
Result: 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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 3.10.4
Check: examples
Result: ERROR Running examples in ‘ctsem-Ex.R’ failed The error most likely occurred in: > ### 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 3.10.4
Check: tests
Result: ERROR Running ‘testthat.R’ [181s/327s] 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=1558680 on localhost:28220 at 17:45:03.882 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=1558681 on localhost:28220 at 17:45:07.151 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 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=1564202 on localhost:38575 at 17:46:17.958 starting worker pid=1564201 on localhost:38575 at 17:46:18.762 Loading required package: data.table Loading required package: data.table Attaching package: ‘data.table’ Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% The following object is masked from ‘package:base’: %notin% SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.039327 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 393.27 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.061976 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 619.76 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 300 [ 0%] (Warmup) Chain 1: Iteration: 1 / 300 [ 0%] (Warmup) Chain 2: Iteration: 20 / 300 [ 6%] (Warmup) Chain 1: Iteration: 20 / 300 [ 6%] (Warmup) Chain 2: Iteration: 40 / 300 [ 13%] (Warmup) Chain 1: Iteration: 40 / 300 [ 13%] (Warmup) Chain 2: Iteration: 60 / 300 [ 20%] (Warmup) Chain 2: Iteration: 80 / 300 [ 26%] (Warmup) Chain 1: Iteration: 60 / 300 [ 20%] (Warmup) Chain 2: Iteration: 100 / 300 [ 33%] (Warmup) Chain 1: Iteration: 80 / 300 [ 26%] (Warmup) Chain 1: Iteration: 100 / 300 [ 33%] (Warmup) Chain 2: Iteration: 120 / 300 [ 40%] (Warmup) Chain 1: Iteration: 120 / 300 [ 40%] (Warmup) Chain 2: Iteration: 140 / 300 [ 46%] (Warmup) Chain 1: Iteration: 140 / 300 [ 46%] (Warmup) Chain 2: Iteration: 151 / 300 [ 50%] (Sampling) Chain 1: Iteration: 151 / 300 [ 50%] (Sampling) Chain 2: Iteration: 170 / 300 [ 56%] (Sampling) Chain 1: Iteration: 170 / 300 [ 56%] (Sampling) Chain 2: Iteration: 190 / 300 [ 63%] (Sampling) Chain 1: Iteration: 190 / 300 [ 63%] (Sampling) Chain 2: Iteration: 210 / 300 [ 70%] (Sampling) Chain 1: Iteration: 210 / 300 [ 70%] (Sampling) Chain 2: Iteration: 230 / 300 [ 76%] (Sampling) Chain 1: Iteration: 230 / 300 [ 76%] (Sampling) Chain 2: Iteration: 250 / 300 [ 83%] (Sampling) Chain 1: Iteration: 250 / 300 [ 83%] (Sampling) Chain 2: Iteration: 270 / 300 [ 90%] (Sampling) Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) Chain 2: Iteration: 290 / 300 [ 96%] (Sampling) Chain 1: Iteration: 290 / 300 [ 96%] (Sampling) Chain 2: Iteration: 300 / 300 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 84.339 seconds (Warm-up) Chain 2: 36.809 seconds (Sampling) Chain 2: 121.148 seconds (Total) Chain 2: Chain 1: Iteration: 300 / 300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 85.138 seconds (Warm-up) Chain 1: 38.077 seconds (Sampling) Chain 1: 123.215 seconds (Total) Chain 1: [ 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 Flavor: r-devel-linux-x86_64-fedora-clang

Version: 3.10.4
Check: tests
Result: ERROR Running ‘testthat.R’ [141s/220s] 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 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=345245 on localhost:22525 at 13:04:44.900 starting worker pid=345246 on localhost:22525 at 13:04:45.328 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=346892 on localhost:20870 at 13:05:23.625 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=346891 on localhost:20870 at 13:05:39.566 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). Chain 1: Chain 1: Gradient evaluation took 0.013328 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 133.28 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 300 [ 0%] (Warmup) SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.047282 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 472.82 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 300 [ 0%] (Warmup) Chain 1: Iteration: 20 / 300 [ 6%] (Warmup) Chain 2: Iteration: 20 / 300 [ 6%] (Warmup) Chain 2: Iteration: 40 / 300 [ 13%] (Warmup) Chain 1: Iteration: 40 / 300 [ 13%] (Warmup) Chain 2: Iteration: 60 / 300 [ 20%] (Warmup) Chain 1: Iteration: 60 / 300 [ 20%] (Warmup) Chain 2: Iteration: 80 / 300 [ 26%] (Warmup) Chain 2: Iteration: 100 / 300 [ 33%] (Warmup) Chain 1: Iteration: 80 / 300 [ 26%] (Warmup) Chain 1: Iteration: 100 / 300 [ 33%] (Warmup) Chain 2: Iteration: 120 / 300 [ 40%] (Warmup) Chain 1: Iteration: 120 / 300 [ 40%] (Warmup) Chain 2: Iteration: 140 / 300 [ 46%] (Warmup) Chain 2: Iteration: 151 / 300 [ 50%] (Sampling) Chain 1: Iteration: 140 / 300 [ 46%] (Warmup) Chain 1: Iteration: 151 / 300 [ 50%] (Sampling) Chain 2: Iteration: 170 / 300 [ 56%] (Sampling) Chain 1: Iteration: 170 / 300 [ 56%] (Sampling) Chain 2: Iteration: 190 / 300 [ 63%] (Sampling) Chain 1: Iteration: 190 / 300 [ 63%] (Sampling) Chain 1: Iteration: 210 / 300 [ 70%] (Sampling) Chain 2: Iteration: 210 / 300 [ 70%] (Sampling) Chain 1: Iteration: 230 / 300 [ 76%] (Sampling) Chain 2: Iteration: 230 / 300 [ 76%] (Sampling) Chain 1: Iteration: 250 / 300 [ 83%] (Sampling) Chain 2: Iteration: 250 / 300 [ 83%] (Sampling) Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) Chain 2: 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: 49.497 seconds (Warm-up) Chain 1: 18.163 seconds (Sampling) Chain 1: 67.66 seconds (Total) Chain 1: Chain 2: Iteration: 290 / 300 [ 96%] (Sampling) Chain 2: Iteration: 300 / 300 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 46.718 seconds (Warm-up) Chain 2: 23.734 seconds (Sampling) Chain 2: 70.452 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 Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 3.10.4
Check: installed package size
Result: NOTE installed size is 201.7Mb sub-directories of 1Mb or more: R 2.0Mb data 1.7Mb libs 196.6Mb Flavor: r-oldrel-macos-arm64

Version: 3.10.4
Check: for GNU extensions in Makefiles
Result: NOTE GNU make is a SystemRequirements. Flavor: r-oldrel-macos-arm64

Version: 3.10.4
Flags: --no-vignettes
Check: installed package size
Result: NOTE installed size is 11.6Mb sub-directories of 1Mb or more: R 1.2Mb data 1.7Mb libs 7.3Mb Flavor: r-oldrel-windows-x86_64

Package ctsemOMX

Current CRAN status: ERROR: 6, OK: 7

Version: 1.0.7
Check: examples
Result: ERROR Running examples in ‘ctsemOMX-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ctGenerateFromFit > ### Title: Generates data according to the model estimated in a ctsemFit > ### object. > ### Aliases: ctGenerateFromFit > > ### ** Examples > > > data(AnomAuth) > AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2), + Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2)) Type "omx" is still supported but requires ctsemOMX package installation. "ct" or "dt" are recommended types. CINT specified via single value -- filling 2 * 1 matrix: [,1] [1,] "0" [2,] "0" > AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel) wide format data detected Running ctsemCarefulFit with 14 parameters Running ctsem with 14 parameters Beginning initial fit attempt Running ctsem with 14 parameters Lowest minimum so far: 23415.9290488409 Solution found Solution found! Final fit=23415.929 (started at 85069.46) (1 attempt(s): 1 valid, 0 errors) > > dwide <- ctGenerateFromFit(AnomAuthfit,timestep=1,n.subjects=5,wide=TRUE) Error in `[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), : attempt access index 4/4 in VECTOR_ELT Calls: ctGenerateFromFit ... withCallingHandlers -> ctGenerate -> ctLongToWide -> [ -> [.data.table Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.7
Check: tests
Result: ERROR Running ‘testthat.R’ [14s/17s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ctsemOMX) Loading required package: 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 Loading required package: OpenMx Attaching package: 'ctsemOMX' The following objects are masked from 'package:ctsem': ctFit, ctIndplot > pdf(NULL) > test_check("ctsemOMX") Saving _problems/test-intervalise-12.R Saving _problems/test-kalmanVram-35.R Saving _problems/test-reshaping-30.R [ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • empty test (3): , , ══ 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-kalmanVram.R:35:1'): time calc ───────────────────────────────── Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─ctsemOMX::ctRefineTo(...) at test-kalmanVram.R:35:1 2. └─ctsemOMX::ctFit(datawide, m, nofit = TRUE, ...) 3. └─ctsem::ctLongToWide(...) 4. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id] 5. └─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 3 | WARN 0 | SKIP 3 | PASS 0 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.7
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘ctsemOMX.rnw’ using knitr Quitting from ctsemOMX.rnw:315-323 [longformatconversion] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 8/8 in VECTOR_ELT --- Backtrace: x 1. \-ctsem::ctLongToWide(...) 2. +-data_long[, `:=`(discrete.time.point = 1:.N), by = id] 3. \-data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'ctsemOMX.rnw' failed with diagnostics: attempt access index 8/8 in VECTOR_ELT --- failed re-building ‘ctsemOMX.rnw’ SUMMARY: processing the following file failed: ‘ctsemOMX.rnw’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.7
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/12s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ctsemOMX) Loading required package: 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 Loading required package: OpenMx Attaching package: 'ctsemOMX' The following objects are masked from 'package:ctsem': ctFit, ctIndplot > pdf(NULL) > test_check("ctsemOMX") Saving _problems/test-intervalise-12.R Saving _problems/test-kalmanVram-35.R Saving _problems/test-reshaping-30.R [ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • empty test (3): , , ══ 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-kalmanVram.R:35:1'): time calc ───────────────────────────────── Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─ctsemOMX::ctRefineTo(...) at test-kalmanVram.R:35:1 2. └─ctsemOMX::ctFit(datawide, m, nofit = TRUE, ...) 3. └─ctsem::ctLongToWide(...) 4. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id] 5. └─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 3 | WARN 0 | SKIP 3 | PASS 0 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.7
Check: examples
Result: ERROR Running examples in ‘ctsemOMX-Ex.R’ failed The error most likely occurred in: > ### Name: ctGenerateFromFit > ### Title: Generates data according to the model estimated in a ctsemFit > ### object. > ### Aliases: ctGenerateFromFit > > ### ** Examples > > > data(AnomAuth) > AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2), + Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2)) Type "omx" is still supported but requires ctsemOMX package installation. "ct" or "dt" are recommended types. CINT specified via single value -- filling 2 * 1 matrix: [,1] [1,] "0" [2,] "0" > AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel) wide format data detected Running ctsemCarefulFit with 14 parameters Running ctsem with 14 parameters Beginning initial fit attempt Running ctsem with 14 parameters Lowest minimum so far: 23415.9290488409 Solution found Solution found! Final fit=23415.929 (started at 85069.46) (1 attempt(s): 1 valid, 0 errors) > > dwide <- ctGenerateFromFit(AnomAuthfit,timestep=1,n.subjects=5,wide=TRUE) Error in `[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), : attempt access index 4/4 in VECTOR_ELT Calls: ctGenerateFromFit ... withCallingHandlers -> ctGenerate -> ctLongToWide -> [ -> [.data.table Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.7
Check: tests
Result: ERROR Running ‘testthat.R’ [23s/63s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ctsemOMX) Loading required package: 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 Loading required package: OpenMx To take full advantage of multiple cores, use: mxOption(key='Number of Threads', value=parallel::detectCores()) #now Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx) Attaching package: 'ctsemOMX' The following objects are masked from 'package:ctsem': ctFit, ctIndplot > pdf(NULL) > test_check("ctsemOMX") Saving _problems/test-intervalise-12.R Saving _problems/test-kalmanVram-35.R Saving _problems/test-reshaping-30.R [ FAIL 3 | WARN 0 | SKIP 3 | PASS 0 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • empty test (3): , , ══ 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-kalmanVram.R:35:1'): time calc ───────────────────────────────── Error in ``[.data.table`(data_long, , `:=`(discrete.time.point = 1:.N), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─ctsemOMX::ctRefineTo(...) at test-kalmanVram.R:35:1 2. └─ctsemOMX::ctFit(datawide, m, nofit = TRUE, ...) 3. └─ctsem::ctLongToWide(...) 4. ├─data_long[, `:=`(discrete.time.point = 1:.N), by = id] 5. └─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 3 | WARN 0 | SKIP 3 | PASS 0 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.7
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘ctsemOMX.rnw’ using knitr Quitting from ctsemOMX.rnw:315-323 [longformatconversion] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 8/8 in VECTOR_ELT --- Backtrace: x 1. \-ctsem::ctLongToWide(...) 2. +-data_long[, `:=`(discrete.time.point = 1:.N), by = id] 3. \-data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'ctsemOMX.rnw' failed with diagnostics: attempt access index 8/8 in VECTOR_ELT --- failed re-building ‘ctsemOMX.rnw’ SUMMARY: processing the following file failed: ‘ctsemOMX.rnw’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.7
Check: package dependencies
Result: ERROR Package required but not available: ‘ctsem’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.0.7
Flags: --no-vignettes
Check: package dependencies
Result: ERROR Package required but not available: 'OpenMx' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. Flavor: r-oldrel-windows-x86_64