CRAN Package Check Results for Package jomo

Last updated on 2020-01-20 01:50:24 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.6-10 108.70 207.45 316.15 WARN
r-devel-linux-x86_64-debian-gcc 2.6-10 106.50 150.23 256.73 OK
r-devel-linux-x86_64-fedora-clang 2.6-10 391.68 WARN
r-devel-linux-x86_64-fedora-gcc 2.6-10 406.48 OK
r-devel-windows-ix86+x86_64 2.6-10 261.00 262.00 523.00 OK
r-devel-windows-ix86+x86_64-gcc8 2.6-10 224.00 342.00 566.00 OK
r-patched-linux-x86_64 2.6-10 116.78 179.80 296.58 OK
r-patched-solaris-x86 2.6-10 642.60 ERROR
r-release-linux-x86_64 2.6-10 117.02 178.67 295.69 OK
r-release-windows-ix86+x86_64 2.6-10 261.00 257.00 518.00 OK
r-release-osx-x86_64 2.6-10 WARN
r-oldrel-windows-ix86+x86_64 2.6-10 180.00 240.00 420.00 OK
r-oldrel-osx-x86_64 2.6-10 WARN

Check Details

Version: 2.6-10
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
     jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
     jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
     jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
     jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 2.6-10
Check: examples
Result: ERROR
    Running examples in ‘jomo-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: jomo.clmm
    > ### Title: Joint Modelling Imputation Compatible with Cumulative Link Mixed
    > ### Model
    > ### Aliases: jomo.clmm
    >
    > ### ** Examples
    >
    >
    >
    > # make sure social is a factor:
    >
    > cldata<-within(cldata, social<-factor(social))
    >
    > # we define the data frame with all the variables
    >
    > data<-cldata[,c("measure","age", "social", "city")]
    >
    > # And the formula of the substantive lm model
    > # social as an outcome only because it is the only ordinal variable in the dataset...
    >
    > formula<-as.formula(social~age+measure+(1|city))
    >
    > #And finally we run the imputation function:
    >
    > imp<-jomo.clmm(formula,data, nburn=2, nbetween=2, nimp=2)
    This function is beta software. Please use carefully and report any bug to the package mantainer
    
     *** caught segfault ***
    address 3ff00008, cause 'memory not mapped'
    
    Traceback:
     1: drop(B1 %*% par[1:(nalpha + nbeta)])
     2: eval(substitute(expr), data, enclos = parent.frame())
     3: eval(substitute(expr), data, enclos = parent.frame())
     4: with.default(rho, { tau <- exp(par[nalpha + nbeta + 1:ntau]) eta1Fix <- drop(B1 %*% par[1:(nalpha + nbeta)]) eta2Fix <- drop(B2 %*% par[1:(nalpha + nbeta)])})
     5: with(rho, { tau <- exp(par[nalpha + nbeta + 1:ntau]) eta1Fix <- drop(B1 %*% par[1:(nalpha + nbeta)]) eta2Fix <- drop(B2 %*% par[1:(nalpha + nbeta)])})
     6: nllBase.uC(rho)
     7: update.uC(rho)
     8: obj.fun(rho, par)
     9: objective(.par, ...)
    10: nlminb(rho$par, function(par) obj.fun(rho, par), control = control)
    11: doTryCatch(return(expr), name, parentenv, handler)
    12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    13: tryCatchList(expr, classes, parentenv, handlers)
    14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
    15: try(nlminb(rho$par, function(par) obj.fun(rho, par), control = control), silent = TRUE)
    16: clmm.fit.ssr(rho, control = control$optCtrl, method = control$method, Hess)
    17: ordinal::clmm(formula, data = data, na.action = na.omit, Hess = T, link = "probit")
    18: jomo.clmm(formula, data, nburn = 2, nbetween = 2, nimp = 2)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86