* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/LSJM.Rcheck’
* using R Under development (unstable) (2026-08-22 r90441)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
    GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-22 21:13:22 UTC
* checking for file ‘LSJM/DESCRIPTION’ ... OK
* this is package ‘LSJM’ version ‘0.1.0’
* 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 ‘LSJM’ can be installed ... [688s/386s] OK
* used C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
* checking package 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 ... [160s/191s] 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [13s/32s] OK
* checking examples with --run-donttest ... [112s/131s] ERROR
Running examples in ‘LSJM-Ex.R’ failed
The error most likely occurred in:

> ### Name: dynpred
> ### Title: dynpred: compute the dynamic predictions of an event.
> ### Aliases: dynpred dynpred.lsjm_classicCR dynpred.lsjm_classicIDM
> ###   dynpred.lsjm_classicSingle dynpred.lsjm_covDepCR
> ###   dynpred.lsjm_covDepIDM dynpred.lsjm_covDepSingle
> ###   dynpred.lsjm_interintraCR dynpred.lsjm_interintraIDM
> ###   dynpred.lsjm_interintraSingle
> 
> ### ** Examples
> 
> 
> set.seed(123)
> data <- data.frame(
+          ID = rep(1:100, each = 3),
+          time = rep(1:3, 100),
+          y = rnorm(300),
+          event = rep(rbinom(100,1,0.5), each = 3),
+          time_event = rep(runif(100), each = 3)
+          )
> 
> 
> m0 <- lsmm(
+    formFixed = y ~ time,
+    formRandom = ~ time,
+    formGroup = ~ ID,
+    formVar = "standard",
+    timeVar = "time",
+    data.long = data,
+    S1 = 5,
+    S2 = 5,
+    nproc = 1
+    )
> 
>  fit <- lsjm(
+       Objectlsmm = m0,
+       survival_type = "Single",
+       formSurv_01 = ~ 1,
+       sharedtype_01 = "value",
+       hazardBase_01 = "Weibull",
+       delta1 = ~ event,
+       Time_T = ~ time_event,
+       S1 = 10,
+       S2 = 10,
+       nproc = 1
+       )
> 
>  ind1 <- data[which(data$ID == 1),]
>  dynpEvent <- dynpred(fit, ind1,  s = 2, horizon = seq(2.1,3,0.1),
+                   event = 1, nb.draws = 100)
> 
> 
> ## No test: 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> 
> # Begin by running the examples from the lsjm function (see ?lsjm).
> data(threeC)
> threeC$age.visit65 <- (threeC$age.visit-65)/10
> threeC$SBP <- threeC$SBP/10
> 
> 
> # Example: prediction of the risk to be diagnosed with dementia
> # (dynpDementia) and to die (dynpDeath) between 85 and 95 years old
> # given the blood pressure measurements before 85 years old for
> # individual "10003", with a competing risk model
> threeC_ex2 <- threeC[,c("ID", "SBP", "age.visit65", "age0_65",
+                         "age.final65", "age.last65", "age.first65",
+                         "dem", "death", "sex","num.visit")]
> 
> threeC_ex2$age65_CR <- NA
> threeC_ex2$age65_CR[which(threeC_ex2$dem == 1)] <-
+   (threeC_ex2$age.last65[which(threeC_ex2$dem == 1)] +
+      threeC_ex2$age.first65[which(threeC_ex2$dem == 1)])/2
> threeC_ex2$age65_CR[which(threeC_ex2$dem == 0)] <-
+   threeC_ex2$age.final65[which(threeC_ex2$dem == 0)]
> 
> threeC_ex2$demCR <- threeC_ex2$dem
> threeC_ex2$deathCR <- NA
> threeC_ex2$deathCR[which(threeC_ex2$dem == 1)] <- 0
> threeC_ex2$deathCR[which(threeC_ex2$dem == 0)] <-
+   threeC_ex2$death[which(threeC_ex2$dem == 0)]
> 
> threeC_ex2 <- threeC_ex2 %>% group_by(ID) %>% dplyr::filter(age.visit65 <= age65_CR)
> 
> threeC_ex2 <- threeC_ex2[,c("ID","SBP","age.visit65","num.visit","age0_65",
+                             "demCR","deathCR","age65_CR","sex")]
> 
> ind2 <- threeC_ex2[which(threeC_ex2$ID == 3),]
> 
> m2 <- lsmm(formFixed = SBP ~ age.visit65,
+                formRandom = ~ age.visit65,
+                formGroup = ~ ID,
+                timeVar = 'age.visit65',
+                data.long = threeC_ex2,
+                formVar = "inter-intra",
+                random_inter = TRUE,
+                random_intra = TRUE,
+                formGroupVisit = ~num.visit,
+                correlated_re = FALSE,
+                S1 = 500,
+                S2 = 1000,
+                nproc = 1)
> 
> 
> l2 <- lsjm(Objectlsmm = m2,
+            survival_type = 'CR',
+            formSurv_01 = ~ sex,
+            formSurv_02 = ~ sex,
+            sharedtype_01 = c("value", "variability inter"),
+            sharedtype_02 = c("value", "variability inter",
+                              "variability intra"),
+            hazardBase_01 = "Weibull",
+            hazardBase_02 = "Weibull",
+            delta1 = ~ demCR,
+            delta2 = ~ deathCR,
+            Time_T0 = ~ age0_65,
+            Time_T = ~ age65_CR,
+            nproc = 5,
+            S1 = 1000,
+            S2 = 2000)
Error in .check_ncores(length(names)) : 5 simultaneous processes spawned
Calls: lsjm ... marqLevAlg -> <Anonymous> -> makePSOCKcluster -> .check_ncores
Execution halted
* checking PDF version of manual ... 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
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-donttest/LSJM.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 14:05.71, 1008.14 + 47.90