• using R Under development (unstable) (2025-02-15 r87723)
• 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
• using option ‘--no-stop-on-test-error’
• checking for file ‘semEff/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘semEff’ version ‘0.7.2’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
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• checking whether package ‘semEff’ can be installed ... [25s/32s] OK See the install log for details.
• 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 use of S3 registration ... OK
• checking dependencies in R code ... OK
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• checking R code for possible problems ... [26s/33s] OK
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• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
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• 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 ... [35s/46s] ERROR Running examples in ‘semEff-Ex.R’ failed The error most likely occurred in: > ### Name: stdEff > ### Title: Standardised Effects > ### Aliases: stdEff > > ### ** Examples > > library(lme4) Loading required package: Matrix Attaching package: ‘lme4’ The following object is masked from ‘package:semEff’:     getData > > # Standardised (direct) effects for SEM > m <- shipley.sem > stdEff(m) $DD (Intercept) lat -0.05600661 -0.68772025 $Date (Intercept) DD -0.01493651 -0.62813666 $Growth (Intercept) Date  -0.2917507 0.3824224 $Live (Intercept) Growth   0.3105220 0.3681961 > stdEff(m, cen.y = FALSE, std.y = FALSE) # x-only $DD (Intercept) lat  143.183138 -7.066909 $Date (Intercept) DD   126.79703 -5.11375 $Growth (Intercept) Date   48.955514 2.448161 $Live (Intercept) Growth    5.452982 2.226862 > stdEff(m, std.x = FALSE, std.y = FALSE) # centred only $DD (Intercept) lat  -0.5755154 -0.8354729 $Date (Intercept) DD  -0.1216002 -0.4976475 $Growth (Intercept) Date  -1.8677067 0.3007147 $Live (Intercept) Growth   1.8780467 0.3478536 > stdEff(m, cen.x = FALSE, cen.y = FALSE) # scaled only $DD (Intercept) lat  19.1373370 -0.6877202 $Date (Intercept) DD  24.3624481 -0.6281367 $Growth (Intercept) Date   1.6853620 0.3824224 $Live (Intercept) Growth  -2.0214940 0.3681961 > stdEff(m, unique.eff = FALSE) # include multicollinearity $DD (Intercept) lat -0.05600661 -0.68772025 $Date (Intercept) DD -0.01493651 -0.62813666 $Growth (Intercept) Date  -0.2917507 0.3824224 $Live (Intercept) Growth   0.3105220 0.3681961 > stdEff(m, R.squared = TRUE) # add R-squared $DD      (Intercept) lat (R.squared) (R.squared.adj)      -0.05600661 -0.68772025 0.70800826 0.70747906 (R.squared.pred)       0.68356361 $Date      (Intercept) DD (R.squared) (R.squared.adj)      -0.01493651 -0.62813666 0.98555565 0.98553510 (R.squared.pred)       0.98202414 $Growth      (Intercept) Date (R.squared) (R.squared.adj)       -0.2917507 0.3824224 0.7938367 0.7934879 (R.squared.pred)        0.7552854 $Live      (Intercept) Growth (R.squared) (R.squared.adj)        0.3105220 0.3681961 0.2668652 0.2655971 (R.squared.pred)               NA > stdEff(m, incl.raw = TRUE) # add unstandardised $DD       (Intercept) lat (raw)_(Intercept) (raw)_lat       -0.05600661 -0.68772025 196.65237838 -0.83547294 $Date       (Intercept) DD (raw)_(Intercept) (raw)_DD       -0.01493651 -0.62813666 198.33816379 -0.49764747 $Growth       (Intercept) Date (raw)_(Intercept) (raw)_Date        -0.2917507 0.3824224 10.7892162 0.3007147 $Live       (Intercept) Growth (raw)_(Intercept) (raw)_Growth         0.3105220 0.3681961 -12.2260588 0.3478536 > > # Demonstrate equality with effects from manually-standardised variables > # (gaussian models only) > m <- shipley.growth[[3]] > d <- data.frame(scale(na.omit(shipley))) > e1 <- stdEff(m, unique.eff = FALSE) > e2 <- coef(summary(update(m, data = d)))[, 1] Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :   convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera). Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :   Model failed to converge with max|grad| = 8.25548 (tol = 0.002, component 1) > stopifnot(all.equal(e1, e2)) Error: e1 and e2 are not equal:   Mean relative difference: 0.1456697 Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [63s/93s] OK
• checking PDF version of manual ... [9s/13s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR