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

Last updated on 2025-12-28 09:51:03 CET.

Package	ERROR	NOTE	OK
ctsem	1	2	8
ctsemOMX	4		9

Package ctsem

Current CRAN status: ERROR: 1, NOTE: 2, OK: 8

Additional issues

donttest M1mac

Version: 3.10.4
Flags: --no-vignettes
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 Flavor: r-devel-windows-x86_64

Version: 3.10.4
Flags: --no-vignettes
Check: tests
Result: ERROR Running 'testthat.R' [91s] 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=23108 on localhost:32309 at 01:15:19.839 starting worker pid=42640 on localhost:32309 at 01:15:20.112 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=52704 on localhost:33785 at 01:15:39.515 starting worker pid=65808 on localhost:33785 at 01:15:39.879 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% starting worker pid=16308 on localhost:11418 at 01:15:43.560 starting worker pid=33432 on localhost:11418 at 01:15:43.802 SAMPLING FOR MODEL 'ctsm' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.005846 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 58.46 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 0.0076 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 76 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: 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 2: Iteration: 120 / 300 [ 40%] (Warmup) Chain 1: Iteration: 120 / 300 [ 40%] (Warmup) Chain 1: Iteration: 140 / 300 [ 46%] (Warmup) Chain 2: Iteration: 140 / 300 [ 46%] (Warmup) Chain 1: Iteration: 151 / 300 [ 50%] (Sampling) Chain 2: Iteration: 151 / 300 [ 50%] (Sampling) Chain 1: Iteration: 170 / 300 [ 56%] (Sampling) Chain 2: Iteration: 170 / 300 [ 56%] (Sampling) Chain 1: Iteration: 190 / 300 [ 63%] (Sampling) Chain 2: 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 2: Iteration: 300 / 300 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 19.139 seconds (Warm-up) Chain 2: 10.512 seconds (Sampling) Chain 2: 29.651 seconds (Total) Chain 2: Chain 1: Iteration: 300 / 300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 19.344 seconds (Warm-up) Chain 1: 10.955 seconds (Sampling) Chain 1: 30.299 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-windows-x86_64

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: 4, OK: 9

Version: 1.0.7
Flags: --no-vignettes
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-windows-x86_64

Version: 1.0.7
Flags: --no-vignettes
Check: tests
Result: ERROR Running 'testthat.R' [14s] 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-windows-x86_64

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