* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/semEff.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* 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
* 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 ‘semEff’ can be installed ... [26s/30s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/semEff-00install.html' for details.
* checking installed package size ... 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 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/34s] 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 ... [35s/52s] 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 ... [52s/67s] OK
* checking PDF version of manual ... [9s/11s] 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