* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/metaforest.Rcheck’ * using R Under development (unstable) (2023-03-24 r84037) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2) GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2) * running under: Fedora 34 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘metaforest/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metaforest’ version ‘0.1.3’ * 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 ‘metaforest’ can be installed ... 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 R 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 ... [13s/13s] 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 ... ERROR Running examples in ‘metaforest-Ex.R’ failed The error most likely occurred in: > ### Name: ClusterMF-deprecated > ### Title: Clustered MetaForest analysis for dependent data. > ### Aliases: ClusterMF-deprecated > ### Keywords: internal > > ### ** Examples > > #Load and clean data from metafor > data <- get(data(dat.bourassa1996)) > data <- escalc(measure = "OR", ai = lh.le, bi = lh.re, ci = rh.le, di= rh.re, + data = data, add = 1/2, to = "all") > data$mage[is.na(data$mage)] <- median(data$mage, na.rm = TRUE) > data[c(5:8)] <- lapply(data[c(5:8)], factor) > data$yi <- as.numeric(data$yi) > mf.cluster.b1996 <- MetaForest(formula = yi~ selection + investigator + + hand_assess + eye_assess + mage +sex, + data, study = "sample", + whichweights = "unif", num.trees = 300) > #Print MetaForest object > mf.cluster.b1996 Call: MetaForest(formula = yi ~ selection + investigator + hand_assess + eye_assess + mage + sex, data = data, study = "sample", whichweights = "unif", num.trees = 300) R squared (OOB): 0.0223 Residual heterogeneity (tau2): 0.3100 > #Check convergence plot > plot(mf.cluster.b1996) > #Check summary > summary(mf.cluster.b1996, digits = 4) MetaForest results Type of analysis: Clustered MetaForest Number of studies: Forest 1: 47, Forest 2: 49 Number of moderators: 6 Number of trees in forest: Two forests of length 150 Candidate variables per split: 2 Minimum terminal node size: 5 OOB prediction error (MSE): 0.8357 R squared (OOB): 0.0223 Tests for Heterogeneity: tau2 tau2_SE I^2 H^2 Q-test df Q_p Raw effect sizes: 0.4096 0.0894 86.5418 7.4304 561.0564 95 0.0000 Residuals (after MetaForest): 0.3100 0.0725 82.9545 5.8666 346.0612 95 0.0000 Random intercept meta-analyses: Intercept se ci.lb ci.ub p Raw effect sizes: 1.3075 0.0825 1.1457 1.4693 0.0000 Residuals (after MetaForest): -0.0691 0.0750 -0.2161 0.0778 0.3564 > #Check variable importance plot > VarImpPlot(mf.cluster.b1996) > #Univariate partial dependence plot > PartialDependence(mf.cluster.b1996, vars = "eye_assess") > #Interpolated partial dependence plot for a bivariate interaction > ## No test: > PartialDependence(mf.cluster.b1996, vars = c("mage", "eye_assess"), interaction = TRUE) Error in PartialDependence.MetaForest(mf.cluster.b1996, vars = c("mage", : The argument 'interaction' has been deprecated, and is replaced by the argument 'moderator'. See ?PartialDependence for help on how to use the 'moderator' argument. Calls: PartialDependence -> PartialDependence.MetaForest Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [23s/22s] [23s/22s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * checking PDF 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/blackswan/ripley/R/packages/tests-devel/metaforest.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:49.07, 98.72 + 13.57