Last updated on 2026-07-11 05:52:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.2 | 16.28 | 143.76 | 160.04 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.7.2 | 12.37 | 104.20 | 116.57 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.7.2 | 29.00 | 308.13 | 337.13 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.7.2 | 26.00 | 281.39 | 307.39 | OK | |
| r-devel-windows-x86_64 | 0.7.2 | 19.00 | 146.00 | 165.00 | ERROR | |
| r-patched-linux-x86_64 | 0.7.2 | 16.99 | 139.09 | 156.08 | OK | |
| r-release-linux-x86_64 | 0.7.2 | 12.95 | 140.60 | 153.55 | OK | |
| r-release-macos-arm64 | 0.7.2 | 4.00 | 38.00 | 42.00 | OK | |
| r-release-macos-x86_64 | 0.7.2 | 12.00 | 157.00 | 169.00 | OK | |
| r-release-windows-x86_64 | 0.7.2 | 22.00 | 139.00 | 161.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.7.2 | OK | ||||
| r-oldrel-macos-x86_64 | 0.7.2 | 11.00 | 172.00 | 183.00 | OK | |
| r-oldrel-windows-x86_64 | 0.7.2 | 26.00 | 179.00 | 205.00 | ERROR |
Version: 0.7.2
Check: examples
Result: ERROR
Running examples in ‘semEff-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predEff
> ### Title: Predict Effects
> ### Aliases: predEff
>
> ### ** Examples
>
> # Predict effects (direct, total)
> m <- shipley.sem
> e <- shipley.sem.eff
> dir <- getDirEff(e)
> tot <- getTotEff(e)
> f.dir <- predEff(m, effects = dir, type = "response")
> f.tot <- predEff(m, effects = tot, type = "response")
> f.dir$Live[1:10]
1 2 3 4 5 6 7 8
0.9998907 0.9525798 0.9657500 0.9894445 0.9943723 0.9993621 0.9911463 0.9582557
9 10
0.9982749 0.9989735
> f.tot$Live[1:10]
1 2 3 4 5 6 7 8
0.9975858 0.5742006 0.5783691 0.7196629 0.9436709 0.9840953 0.8998478 0.5468860
9 10
0.9462890 0.9887104
>
> # Using new data for predictors
> d <- na.omit(shipley)
> xn <- c("lat", "DD", "Date", "Growth")
> seq100 <- function(x) seq(min(x), max(x), length = 100)
> nd <- data.frame(sapply(d[xn], seq100))
> f.dir <- predEff(m, nd, dir, type = "response")
> f.tot <- predEff(m, nd, tot, type = "response")
> f.dir$Live[1:10]
1 2 3 4 5 6 7 8
0.3000301 0.3279412 0.3571239 0.3874066 0.4185852 0.4504280 0.4826822 0.5150813
9 10
0.5473542 0.5792338
> f.tot$Live[1:10]
1 2 3 4 5 6 7
0.05467217 0.06338280 0.07337353 0.08479648 0.09781007 0.11257517 0.12924985
8 9 10
0.14798252 0.16890356 0.19211539
> # Add CIs
> # dir.b <- getDirEff(e, "boot")
> # tot.b <- getTotEff(e, "boot")
> # f.dir <- predEff(m, nd, dir, dir.b, type = "response")
> # f.tot <- predEff(m, nd, tot, tot.b, type = "response")
>
> # Predict an interactive effect (e.g. Live ~ Growth * DD)
> xn <- c("Growth", "DD")
> d[xn] <- scale(d[xn]) # scale predictors (improves fit)
> m <- lme4::glmer(Live ~ Growth * DD + (1 | site) + (1 | tree),
+ family = binomial, data = d)
Error: Downdated VtV is not positive definite
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
R2 5.863 0.32 8.512
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.7.2
Check: examples
Result: ERROR
Running examples in ‘semEff-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predEff
> ### Title: Predict Effects
> ### Aliases: predEff
>
> ### ** Examples
>
> # Predict effects (direct, total)
> m <- shipley.sem
> e <- shipley.sem.eff
> dir <- getDirEff(e)
> tot <- getTotEff(e)
> f.dir <- predEff(m, effects = dir, type = "response")
> f.tot <- predEff(m, effects = tot, type = "response")
> f.dir$Live[1:10]
1 2 3 4 5 6 7 8
0.9998907 0.9525798 0.9657500 0.9894445 0.9943723 0.9993621 0.9911463 0.9582557
9 10
0.9982749 0.9989735
> f.tot$Live[1:10]
1 2 3 4 5 6 7 8
0.9975858 0.5742006 0.5783691 0.7196629 0.9436709 0.9840953 0.8998478 0.5468860
9 10
0.9462890 0.9887104
>
> # Using new data for predictors
> d <- na.omit(shipley)
> xn <- c("lat", "DD", "Date", "Growth")
> seq100 <- function(x) seq(min(x), max(x), length = 100)
> nd <- data.frame(sapply(d[xn], seq100))
> f.dir <- predEff(m, nd, dir, type = "response")
> f.tot <- predEff(m, nd, tot, type = "response")
> f.dir$Live[1:10]
1 2 3 4 5 6 7 8
0.3000301 0.3279412 0.3571239 0.3874066 0.4185852 0.4504280 0.4826822 0.5150813
9 10
0.5473542 0.5792338
> f.tot$Live[1:10]
1 2 3 4 5 6 7
0.05467217 0.06338280 0.07337353 0.08479648 0.09781007 0.11257517 0.12924985
8 9 10
0.14798252 0.16890356 0.19211539
> # Add CIs
> # dir.b <- getDirEff(e, "boot")
> # tot.b <- getTotEff(e, "boot")
> # f.dir <- predEff(m, nd, dir, dir.b, type = "response")
> # f.tot <- predEff(m, nd, tot, tot.b, type = "response")
>
> # Predict an interactive effect (e.g. Live ~ Growth * DD)
> xn <- c("Growth", "DD")
> d[xn] <- scale(d[xn]) # scale predictors (improves fit)
> m <- lme4::glmer(Live ~ Growth * DD + (1 | site) + (1 | tree),
+ family = binomial, data = d)
> nd <- with(d, expand.grid(
+ Growth = seq100(Growth),
+ DD = mean(DD) + c(-sd(DD), sd(DD)) # two levels for DD
+ ))
> f <- predEff(m, nd, type = "response", interaction = "Growth:DD")
Warning: the ‘findbars’ function has moved to the reformulas package. Please update your imports, or ask an upstream package maintainer to do so.
This warning is displayed once per session.
Error: Downdated VtV is not positive definite
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.2
Check: examples
Result: ERROR
Running examples in 'semEff-Ex.R' failed
The error most likely occurred in:
> ### Name: bootEff
> ### Title: Bootstrap Effects
> ### Aliases: bootEff
>
> ### ** Examples
>
> # Bootstrap Shipley SEM (test – 1 rep)
> # (set 'site' as group for resampling – highest-level random effect)
> bootEff(shipley.sem, R = 1, ran.eff = "site", parallel = "no")
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64