* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/nlpsem.Rcheck’
* using R Under development (unstable) (2025-11-17 r89032)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘nlpsem/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nlpsem’ version ‘0.3’
* package encoding: UTF-8
* 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 ‘nlpsem’ can be installed ... [84s/86s] OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [171s/174s] OK
* checking Rd files ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [30m/30m] ERROR
Running examples in ‘nlpsem-Ex.R’ failed
The error most likely occurred in:

> ### Name: getEstimateStats
> ### Title: Calculate p-Values and Confidence Intervals of Parameters for a
> ###   Fitted Model
> ### Aliases: getEstimateStats
> 
> ### ** Examples
> 
> mxOption(model = NULL, key = "Default optimizer", "CSOLNP", reset = FALSE)
> # Load ECLS-K (2011) data
> data("RMS_dat")
> RMS_dat0 <- RMS_dat
> # Re-baseline the data so that the estimated initial status is for the starting point of the study
> baseT <- RMS_dat0$T1
> RMS_dat0$T1 <- RMS_dat0$T1 - baseT
> RMS_dat0$T2 <- RMS_dat0$T2 - baseT
> RMS_dat0$T3 <- RMS_dat0$T3 - baseT
> RMS_dat0$T4 <- RMS_dat0$T4 - baseT
> RMS_dat0$T5 <- RMS_dat0$T5 - baseT
> RMS_dat0$T6 <- RMS_dat0$T6 - baseT
> RMS_dat0$T7 <- RMS_dat0$T7 - baseT
> RMS_dat0$T8 <- RMS_dat0$T8 - baseT
> RMS_dat0$T9 <- RMS_dat0$T9 - baseT
> # Standardized time-invariant covariates
> RMS_dat0$ex1 <- scale(RMS_dat0$Approach_to_Learning)
> RMS_dat0$ex2 <- scale(RMS_dat0$Attention_focus)
> ## No test: 
> # Fit bilinear spline latent growth curve model (fixed knots)
> paraBLS_LGCM.r <- c(
+   "mueta0", "mueta1", "mueta2", "knot",
+   paste0("psi", c("00", "01", "02", "11", "12", "22")),
+   "residuals"
+   )
> BLS_LGCM_r <- getLGCM(
+   dat = RMS_dat0, t_var = "T", y_var = "M", curveFun = "BLS", intrinsic = FALSE,
+   records = 1:9, res_scale = 0.1, paramOut = TRUE, names = paraBLS_LGCM.r)
Running LGCM, Bilinear Spline Functional Form, Fixed knot with 11 parameters
Treating first argument as an expression
Treating first argument as an expression
Treating first argument as an expression
Treating first argument as an expression
> ## Generate P value and Wald confidence intervals
> getEstimateStats(
+   est_in = BLS_LGCM_r@Estimates, CI_type = "Wald"
+   )
An object of class "StatsOutput"
Slot "wald":
          Estimate     SE p.value wald_lbound wald_ubound
mueta0     39.4122 0.5314 <0.0001     38.3707     40.4537
mueta1      1.7669 0.0164 <0.0001      1.7348      1.7990
mueta2      0.6906 0.0172 <0.0001      0.6569      0.7243
knot       34.7703 0.3626 <0.0001     34.0596     35.4810
psi00     123.7682 8.8735 <0.0001    106.3765    141.1599
psi01       0.6017 0.1853  0.0012      0.2385      0.9649
psi02      -1.2618 0.1634 <0.0001     -1.5821     -0.9415
psi11       0.0813 0.0078 <0.0001      0.0660      0.0966
psi12      -0.0094 0.0050  0.0601     -0.0192      0.0004
psi22       0.0311 0.0058 <0.0001      0.0197      0.0425
residuals  34.0030 0.8793 <0.0001     32.2796     35.7264

Slot "likelihood":
data frame with 0 columns and 0 rows

Slot "bootstrap":
data frame with 0 columns and 0 rows

> # Fit bilinear spline latent growth curve model (random knots) with time-invariant covariates for
> # mathematics development
> ## Define parameter names
> paraBLS.TIC_LGCM.f <- c(
+   "alpha0", "alpha1", "alpha2", "alphag",
+   paste0("psi", c("00", "01", "02", "0g", "11", "12", "1g", "22", "2g", "gg")), "residuals",
+   paste0("beta1", c(0:2, "g")), paste0("beta2", c(0:2, "g")), paste0("mux", 1:2),
+   paste0("phi", c("11", "12", "22")), "mueta0", "mueta1", "mueta2", "mu_knot"
+   )
> ## Fit the model
> BLS_LGCM.TIC_f <- getLGCM(
+   dat = RMS_dat0, t_var = "T", y_var = "M", curveFun = "BLS", intrinsic = TRUE, records = 1:9,
+   growth_TIC = c("ex1", "ex2"), res_scale = 0.1, paramOut = TRUE, names = paraBLS.TIC_LGCM.f
+   )
Running LGCM_TICs, Bilinear Spline Functional Form, Random knot with 28 parameters
Treating first argument as an expression
Treating first argument as an expression
Treating first argument as an expression
Treating first argument as an expression
Treating first argument as an expression
Treating first argument as an expression
> ## Change optimizer to "SLSQP" for getting likelihood-based confidence interval
> mxOption(model = NULL, key = "Default optimizer", "SLSQP", reset = FALSE)
> ## Generate P value and all three types of confidence intervals
> getEstimateStats(
+   model = BLS_LGCM.TIC_f@mxOutput, est_in = BLS_LGCM.TIC_f@Estimates, CI_type = "all", rep = 1000
+   )
Running LGCM_TICs, Bilinear Spline Functional Form, Random knot with 28 parameters

Beginning initial fit attempt
Running LGCM_TICs, Bilinear Spline Functional Form, Random knot with 28 parameters

 Lowest minimum so far:  33537.4152746348

Solution found

Final run, for Hessian and/or standard errors and/or confidence intervals

Running LGCM_TICs, Bilinear Spline Functional Form, Random knot with 28 parameters
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [141s/145s] OK
* checking PDF version of manual ... [11s/11s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/nlpsem.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 39:34.50, 2286.38 + 43.22