* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/semPLS.Rcheck’ * using R Under development (unstable) (2022-04-03 r82074) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘semPLS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘semPLS’ version ‘1.0-10’ * 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 ‘semPLS’ can be installed ... [7s/25s] OK * 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 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 use of S3 registration ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘XML’ ‘boot’ ‘sem’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported objects imported by ':::' calls: ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’ ‘resempls’ ‘residuals.sempls’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [18s/41s] NOTE AIC.sempls : aic: no visible global function definition for ‘logLik’ BIC.sempls : bic: no visible global function definition for ‘logLik’ bootsempls: no visible global function definition for ‘runif’ centroid: no visible global function definition for ‘cor’ densityplot.bootsempls: no visible global function definition for ‘var’ densityplot.sempls: no visible global function definition for ‘predict’ densityplot.sempls: no visible global function definition for ‘residuals’ extractAIC.semplslv: no visible global function definition for ‘deviance’ factorial: no visible global function definition for ‘cor’ ic.sempls: no visible global function definition for ‘deviance’ mvpairs.plsm: no visible global function definition for ‘par’ mvplot.plsm: no visible global function definition for ‘reshape’ mvplot.plsm: no visible global function definition for ‘par’ mvplot.plsm: no visible global function definition for ‘xtabs’ outerApprx: no visible global function definition for ‘cor’ outerApprx2: no visible global function definition for ‘cor’ pairs: no visible binding for global variable ‘points’ pairs : textPanel: no visible global function definition for ‘text’ pairs : localAxis: no visible global function definition for ‘Axis’ pairs: no visible global function definition for ‘par’ pairs: no visible global function definition for ‘box’ pairs: no visible global function definition for ‘strwidth’ pairs: no visible global function definition for ‘mtext’ panel.bars: no visible global function definition for ‘par’ panel.bars: no visible global function definition for ‘barplot’ panel.bars: no visible global function definition for ‘rect’ panel.cor: no visible global function definition for ‘par’ panel.cor: no visible global function definition for ‘cor’ panel.cor: no visible global function definition for ‘complete.cases’ panel.cor: no visible global function definition for ‘strwidth’ panel.cor: no visible global function definition for ‘text’ panel.jitter: no visible global function definition for ‘par’ panel.jitter: no visible global function definition for ‘points’ panel.jitter: no visible global function definition for ‘lines’ panel.jitter: no visible global function definition for ‘abline’ pathCoeff.default: no visible global function definition for ‘cor’ pathWeighting: no visible global function definition for ‘cor’ plot.sempls: no visible global function definition for ‘trellis.par.get’ plot.sempls: no visible global function definition for ‘trellis.par.set’ plot.sempls: no visible global function definition for ‘xyplot’ plsm: no visible global function definition for ‘edit’ plsm: no visible global function definition for ‘read.csv’ plsm2sem.plsm: no visible global function definition for ‘packageVersion’ plsm2sem.plsm: no visible global function definition for ‘specifyModel’ plsm2sem.plsm: no visible global function definition for ‘specify.model’ plsmEdit.plsm: no visible global function definition for ‘edit’ predict.sempls: no visible global function definition for ‘complete.cases’ print.bootsempls: no visible binding for global variable ‘sd’ qSquared.sempls : sse: no visible global function definition for ‘complete.cases’ rSquared.sempls: no visible global function definition for ‘predict’ rSquared.sempls: no visible binding for global variable ‘var’ rSquared2.sempls: no visible global function definition for ‘predict’ rSquared2.sempls: no visible binding for global variable ‘var’ read.splsm: no visible global function definition for ‘xmlInternalTreeParse’ read.splsm: no visible global function definition for ‘xpathApply’ read.splsm: no visible binding for global variable ‘xmlGetAttr’ resempls: no visible global function definition for ‘cor’ resempls: no visible global function definition for ‘coefficients’ residuals.sempls: no visible global function definition for ‘predict’ sempls.plsm: no visible global function definition for ‘complete.cases’ sempls.plsm: no visible global function definition for ‘na.omit’ sempls.plsm: no visible binding for global variable ‘sd’ sempls.plsm: no visible global function definition for ‘reshape’ sempls.plsm: no visible global function definition for ‘cor’ sempls.plsm: no visible global function definition for ‘coefficients’ summary.bootsempls: no visible binding for global variable ‘sd’ summary.bootsempls: no visible global function definition for ‘boot.ci’ Undefined global functions or variables: Axis abline barplot boot.ci box coefficients complete.cases cor deviance edit lines logLik mtext na.omit packageVersion par points predict read.csv rect reshape residuals runif sd specify.model specifyModel strwidth text trellis.par.get trellis.par.set var xmlGetAttr xmlInternalTreeParse xpathApply xtabs xyplot Consider adding importFrom("graphics", "Axis", "abline", "barplot", "box", "lines", "mtext", "par", "points", "rect", "strwidth", "text") importFrom("stats", "coefficients", "complete.cases", "cor", "deviance", "logLik", "na.omit", "predict", "reshape", "residuals", "runif", "sd", "var", "xtabs") importFrom("utils", "edit", "packageVersion", "read.csv") to your NAMESPACE file. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘semPLS-Ex.R’ failed The error most likely occurred in: > ### Name: hanafi2007 > ### Title: Hanafi (2007): Example Data > ### Aliases: hanafi2007 > > ### ** Examples > > ### get the Data from Hanafi's Example > data(hanafi2007) > hanafi2007 x11 x12 x13 x21 x22 x23 x31 x32 x33 x34 x35 1 165 -43 142 -79 -73 140 159 -111 -47 -91 100 2 -11 70 10 -23 -23 -106 -108 103 -63 -42 -37 3 -29 145 105 17 76 -71 28 -18 15 -91 47 4 94 -197 -53 -55 13 -20 12 139 170 254 41 5 -13 -57 16 -18 -190 -41 -109 -22 -51 -81 56 6 -50 54 -214 -60 -4 19 -94 23 -183 55 10 7 -219 73 -111 255 -70 24 10 -172 112 -49 92 8 -30 -76 -10 -96 158 202 135 -2 -39 64 59 9 -7 -69 43 -37 143 -8 -120 141 115 0 -183 10 103 101 70 97 -30 -139 86 -79 -27 -18 -188 > > ### 1st Example: the 11 MVs relate to formative 3 LVs > Ex1mfrom <- names(hanafi2007) > Ex1mto <- paste("z", c(rep(1:3, each=3), 3, 3), sep="") > Ex1mm <- cbind(source=Ex1mfrom, target=Ex1mto) > > Ex1sfrom <- paste("z", 1:2, sep="") > Ex1sto <- paste("z", 2:3, sep="") > Ex1sm <- cbind(source=Ex1sfrom, target=Ex1sto) > > library(semPLS) > EX1 <- plsm(data=hanafi2007, strucmod=Ex1sm, measuremod=Ex1mm) ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- semPLS --- call from context --- plsm(data = hanafi2007, strucmod = Ex1sm, measuremod = Ex1mm) --- call from argument --- ncol(strucmod) != 2 || mode(strucmod) != "character" || class(strucmod) != "matrix" --- R stacktrace --- where 1: plsm(data = hanafi2007, strucmod = Ex1sm, measuremod = Ex1mm) --- value of length: 2 type: logical --- [1] FALSE TRUE --- function from context --- function (data, strucmod, measuremod, order = c("generic", "alphabetical"), interactive = FALSE) { if (class(data) != "data.frame") stop("The argument 'data' must be of class 'data.frame'.") if (interactive & missing(strucmod)) { cat("Edit the structural model!\n") strucmod <- matrix("Enter!", nrow = 1, ncol = 2, dimnames = list(NULL, c("source", "target"))) strucmod <- edit(strucmod, title = "Edit the structural model!") cat("Call for structural model:\n", paste("strucmod <- matrix(c(", paste(as.vector(t(strucmod)), collapse = ", "), "), ncol=2, byrow=TRUE, dimnames=list(NULL, c('source', 'target')))", sep = ""), "\n", sep = "") } if (interactive & missing(measuremod)) { cat("Edit the measurement model!\n") measuremod <- matrix("Enter!", nrow = 1, ncol = 2, dimnames = list(NULL, c("source", "target"))) measuremod <- edit(measuremod, title = "Edit the measurement model!") cat("Call for measurement model:\n", paste("measuremod <- matrix(c(", paste(as.vector(t(measuremod)), collapse = ", "), "), ncol=2, byrow=TRUE, dimnames=list(NULL, c('source', 'target')))", sep = ""), "\n", sep = "") } if (!is.matrix(strucmod)) { strucmod <- as.matrix(read.csv(strucmod)) } if (!is.matrix(measuremod)) { measuremod <- as.matrix(read.csv(measuremod)) } if (ncol(strucmod) != 2 || mode(strucmod) != "character" || class(strucmod) != "matrix") stop("The argument 'strucmod' must be a two column character matrix.") if (ncol(measuremod) != 2 || mode(measuremod) != "character" || class(measuremod) != "matrix") stop("The argument 'measuremod' must be a two column character matrix.") latent <- unique(as.vector(strucmod)) if (any(latent %in% colnames(data))) stop("The latent variables are not allowed to coincide with names of observed variables.") manifest <- sort(setdiff(as.vector(measuremod), latent)) if (!all(manifest %in% colnames(data))) stop("The manifest variables must be contained in the data.") order <- match.arg(order) D <- innerW(strucmod, latent) if (order == "generic") { tmp <- reorder(D) latent <- tmp$chain strucmod <- tmp$strucmod } if (order == "alphabetical") { latent <- sort(latent) } D <- D[latent, latent] blocks <- block(latent, manifest, measuremod) MVs <- NULL mm <- NULL for (i in names(blocks)) { MVs <- append(MVs, blocks[[i]]) if (attr(blocks[[i]], "mode") == "A") { mm <- rbind(mm, (cbind(i, blocks[[i]]))) } if (attr(blocks[[i]], "mode") == "B") { mm <- rbind(mm, (cbind(blocks[[i]], i))) } } dimnames(mm) <- dimnames(measuremod) measuremod <- mm result <- list() result$latent <- latent result$manifest <- MVs result$strucmod <- strucmod result$measuremod <- measuremod result$D <- D result$M <- initM1(model = result) result$blocks <- blocks result$order <- order class(result) <- "plsm" if (!connected(model = result)) stop("Structural model must be connected!") if (!acyclic(model = result)) stop("Structural model must be acyclic!") return(result) } --- function search by body --- Function plsm in namespace semPLS has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘regtest_ConstructLevelChanges.R’ Running ‘regtest_SmartPLS.R’ ERROR Running the tests in ‘tests/regtest_ConstructLevelChanges.R’ failed. Complete output: > ### Fixed Bug with version 1.0-3 (2011-10-06) > ### as reply to e-mail by Pratyush Nidhi Sharma (2011-10-05) > library("semPLS") Loading required package: lattice > > clcData <- read.table("./ConstructLevelChanges/clcData.csv", header=TRUE) > sm <- as.matrix(read.table("./ConstructLevelChanges/clcStruc.csv", header=TRUE)) > mm <- as.matrix(read.table("./ConstructLevelChanges/clcMeas.csv", header=TRUE)) > CLC <- plsm(data=clcData, strucmod=sm, measuremod=mm) ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- semPLS --- call from context --- plsm(data = clcData, strucmod = sm, measuremod = mm) --- call from argument --- ncol(strucmod) != 2 || mode(strucmod) != "character" || class(strucmod) != "matrix" --- R stacktrace --- where 1: plsm(data = clcData, strucmod = sm, measuremod = mm) --- value of length: 2 type: logical --- [1] FALSE TRUE --- function from context --- function (data, strucmod, measuremod, order = c("generic", "alphabetical"), interactive = FALSE) { if (class(data) != "data.frame") stop("The argument 'data' must be of class 'data.frame'.") if (interactive & missing(strucmod)) { cat("Edit the structural model!\n") strucmod <- matrix("Enter!", nrow = 1, ncol = 2, dimnames = list(NULL, c("source", "target"))) strucmod <- edit(strucmod, title = "Edit the structural model!") cat("Call for structural model:\n", paste("strucmod <- matrix(c(", paste(as.vector(t(strucmod)), collapse = ", "), "), ncol=2, byrow=TRUE, dimnames=list(NULL, c('source', 'target')))", sep = ""), "\n", sep = "") } if (interactive & missing(measuremod)) { cat("Edit the measurement model!\n") measuremod <- matrix("Enter!", nrow = 1, ncol = 2, dimnames = list(NULL, c("source", "target"))) measuremod <- edit(measuremod, title = "Edit the measurement model!") cat("Call for measurement model:\n", paste("measuremod <- matrix(c(", paste(as.vector(t(measuremod)), collapse = ", "), "), ncol=2, byrow=TRUE, dimnames=list(NULL, c('source', 'target')))", sep = ""), "\n", sep = "") } if (!is.matrix(strucmod)) { strucmod <- as.matrix(read.csv(strucmod)) } if (!is.matrix(measuremod)) { measuremod <- as.matrix(read.csv(measuremod)) } if (ncol(strucmod) != 2 || mode(strucmod) != "character" || class(strucmod) != "matrix") stop("The argument 'strucmod' must be a two column character matrix.") if (ncol(measuremod) != 2 || mode(measuremod) != "character" || class(measuremod) != "matrix") stop("The argument 'measuremod' must be a two column character matrix.") latent <- unique(as.vector(strucmod)) if (any(latent %in% colnames(data))) stop("The latent variables are not allowed to coincide with names of observed variables.") manifest <- sort(setdiff(as.vector(measuremod), latent)) if (!all(manifest %in% colnames(data))) stop("The manifest variables must be contained in the data.") order <- match.arg(order) D <- innerW(strucmod, latent) if (order == "generic") { tmp <- reorder(D) latent <- tmp$chain strucmod <- tmp$strucmod } if (order == "alphabetical") { latent <- sort(latent) } D <- D[latent, latent] blocks <- block(latent, manifest, measuremod) MVs <- NULL mm <- NULL for (i in names(blocks)) { MVs <- append(MVs, blocks[[i]]) if (attr(blocks[[i]], "mode") == "A") { mm <- rbind(mm, (cbind(i, blocks[[i]]))) } if (attr(blocks[[i]], "mode") == "B") { mm <- rbind(mm, (cbind(blocks[[i]], i))) } } dimnames(mm) <- dimnames(measuremod) measuremod <- mm result <- list() result$latent <- latent result$manifest <- MVs result$strucmod <- strucmod result$measuremod <- measuremod result$D <- D result$M <- initM1(model = result) result$blocks <- blocks result$order <- order class(result) <- "plsm" if (!connected(model = result)) stop("Structural model must be connected!") if (!acyclic(model = result)) stop("Structural model must be acyclic!") return(result) } --- function search by body --- Function plsm in namespace semPLS has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘semPLS-intro.Rnw’ using Sweave Loading required package: lattice ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- semPLS --- call from context --- plsm(data = mobi, strucmod = ECSIsm, measuremod = ECSImm) --- call from argument --- ncol(strucmod) != 2 || mode(strucmod) != "character" || class(strucmod) != "matrix" --- R stacktrace --- where 1: plsm(data = mobi, strucmod = ECSIsm, measuremod = ECSImm) where 2: eval(expr, .GlobalEnv) where 3: eval(expr, .GlobalEnv) where 4: withVisible(eval(expr, .GlobalEnv)) where 5: doTryCatch(return(expr), name, parentenv, handler) where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 7: tryCatchList(expr, classes, parentenv, handlers) where 8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) }) where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE) where 10: evalFunc(ce, options) where 11: tryCatchList(expr, classes, parentenv, handlers) where 12: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink() }) where 13: driver$runcode(drobj, chunk, chunkopts) where 14: utils::Sweave(...) where 15: engine$weave(file, quiet = quiet, encoding = enc) where 16: doTryCatch(return(expr), name, parentenv, handler) where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 18: tryCatchList(expr, classes, parentenv, handlers) where 19: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output) }, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) }) where 20: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/semPLS.Rcheck/vign_test/semPLS") --- value of length: 2 type: logical --- [1] FALSE TRUE --- function from context --- function (data, strucmod, measuremod, order = c("generic", "alphabetical"), interactive = FALSE) { if (class(data) != "data.frame") stop("The argument 'data' must be of class 'data.frame'.") if (interactive & missing(strucmod)) { cat("Edit the structural model!\n") strucmod <- matrix("Enter!", nrow = 1, ncol = 2, dimnames = list(NULL, c("source", "target"))) strucmod <- edit(strucmod, title = "Edit the structural model!") cat("Call for structural model:\n", paste("strucmod <- matrix(c(", paste(as.vector(t(strucmod)), collapse = ", "), "), ncol=2, byrow=TRUE, dimnames=list(NULL, c('source', 'target')))", sep = ""), "\n", sep = "") } if (interactive & missing(measuremod)) { cat("Edit the measurement model!\n") measuremod <- matrix("Enter!", nrow = 1, ncol = 2, dimnames = list(NULL, c("source", "target"))) measuremod <- edit(measuremod, title = "Edit the measurement model!") cat("Call for measurement model:\n", paste("measuremod <- matrix(c(", paste(as.vector(t(measuremod)), collapse = ", "), "), ncol=2, byrow=TRUE, dimnames=list(NULL, c('source', 'target')))", sep = ""), "\n", sep = "") } if (!is.matrix(strucmod)) { strucmod <- as.matrix(read.csv(strucmod)) } if (!is.matrix(measuremod)) { measuremod <- as.matrix(read.csv(measuremod)) } if (ncol(strucmod) != 2 || mode(strucmod) != "character" || class(strucmod) != "matrix") stop("The argument 'strucmod' must be a two column character matrix.") if (ncol(measuremod) != 2 || mode(measuremod) != "character" || class(measuremod) != "matrix") stop("The argument 'measuremod' must be a two column character matrix.") latent <- unique(as.vector(strucmod)) if (any(latent %in% colnames(data))) stop("The latent variables are not allowed to coincide with names of observed variables.") manifest <- sort(setdiff(as.vector(measuremod), latent)) if (!all(manifest %in% colnames(data))) stop("The manifest variables must be contained in the data.") order <- match.arg(order) D <- innerW(strucmod, latent) if (order == "generic") { tmp <- reorder(D) latent <- tmp$chain strucmod <- tmp$strucmod } if (order == "alphabetical") { latent <- sort(latent) } D <- D[latent, latent] blocks <- block(latent, manifest, measuremod) MVs <- NULL mm <- NULL for (i in names(blocks)) { MVs <- append(MVs, blocks[[i]]) if (attr(blocks[[i]], "mode") == "A") { mm <- rbind(mm, (cbind(i, blocks[[i]]))) } if (attr(blocks[[i]], "mode") == "B") { mm <- rbind(mm, (cbind(blocks[[i]], i))) } } dimnames(mm) <- dimnames(measuremod) measuremod <- mm result <- list() result$latent <- latent result$manifest <- MVs result$strucmod <- strucmod result$measuremod <- measuremod result$D <- D result$M <- initM1(model = result) result$blocks <- blocks result$order <- order class(result) <- "plsm" if (!connected(model = result)) stop("Structural model must be connected!") if (!acyclic(model = result)) stop("Structural model must be acyclic!") return(result) } --- function search by body --- Function plsm in namespace semPLS has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 ERRORs, 2 NOTEs See ‘/data/gannet/ripley/R/packages/tests-LENGTH1/semPLS.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:44.90, 59.24 + 7.72