• 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 ‘ctsemOMX/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ctsemOMX’ version ‘1.0.7’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] 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 ‘ctsemOMX’ can be installed ... OK See the install log 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 ... [6s/8s] OK
• checking whether the package can be loaded with stated dependencies ... [7s/8s] OK
• checking whether the package can be unloaded cleanly ... [5s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/7s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
• checking loading without being on the library search path ... [9s/10s] 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 ... [29s/36s] OK
• checking Rd files ... [0s/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 ... [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 ... [14s/17s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10s/13s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [9s/12s] 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
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs