CRAN Package Check Results for Package RxODE

Last updated on 2019-07-22 06:47:48 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.1-0 170.97 236.22 407.19 NOTE
r-devel-linux-x86_64-debian-gcc 0.9.1-0 216.89 169.52 386.41 NOTE
r-devel-linux-x86_64-fedora-clang 0.9.1-0 506.98 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9.1-0 645.00 NOTE
r-devel-windows-ix86+x86_64 0.9.1-0 330.00 436.00 766.00 NOTE
r-patched-linux-x86_64 0.9.1-0 220.96 187.44 408.40 ERROR
r-patched-solaris-x86 0.9.1-0 668.80 ERROR
r-release-linux-x86_64 0.9.1-0 222.06 215.74 437.80 NOTE
r-release-windows-ix86+x86_64 0.9.1-0 288.00 429.00 717.00 NOTE
r-release-osx-x86_64 0.9.1-0 WARN
r-oldrel-windows-ix86+x86_64 0.9.1-0 473.00 652.00 1125.00 NOTE
r-oldrel-osx-x86_64 0.9.1-0 WARN

Additional issues

ATLAS OpenBLAS valgrind

Check Details

Version: 0.9.1-0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'installr'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.9.1-0
Check: installed package size
Result: NOTE
     installed size is 16.9Mb
     sub-directories of 1Mb or more:
     doc 1.3Mb
     libs 14.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9.1-0
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘n1qn1’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.9.1-0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'SnakeCharmR'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9.1-0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [119s/138s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > Sys.setenv("R_TESTS" = "")
     > library(testthat)
     > library(RxODE)
     > test_check("RxODE")
     ── 1. Error: Issue #56 (@test-issue-56.R#9) ───────────────────────────────────
     Error building model
     1: RxODE(model = ode, modName = "m1", wd = "/tmp") at testthat/test-issue-56.R:9
     2: .env$compile()
     3: with(<environment>, {
     .lwd <- getwd()
     if (!file.exists(wd))
     dir.create(wd, recursive = TRUE)
     if (file.exists(wd))
     setwd(wd)
     on.exit(setwd(.lwd))
     if (missing.modName) {
     .rxDll <- RxODE::rxCompile(.mv, extraC = extraC, debug = debug, package = NULL)
     }
     else {
     .rxDll <- RxODE::rxCompile(.mv, dir = mdir, extraC = extraC, debug = debug,
     modName = modName, package = NULL)
     }
     assign("rxDll", .rxDll, envir = <environment>)
     assign(".mv", .rxDll$modVars, envir = <environment>)
     })
     4: with.default(<environment>, {
     .lwd <- getwd()
     if (!file.exists(wd))
     dir.create(wd, recursive = TRUE)
     if (file.exists(wd))
     setwd(wd)
     on.exit(setwd(.lwd))
     if (missing.modName) {
     .rxDll <- RxODE::rxCompile(.mv, extraC = extraC, debug = debug, package = NULL)
     }
     else {
     .rxDll <- RxODE::rxCompile(.mv, dir = mdir, extraC = extraC, debug = debug,
     modName = modName, package = NULL)
     }
     assign("rxDll", .rxDll, envir = <environment>)
     assign(".mv", .rxDll$modVars, envir = <environment>)
     })
     5: eval(substitute(expr), data, enclos = parent.frame())
     6: eval(substitute(expr), data, enclos = parent.frame())
     7: RxODE::rxCompile(.mv, dir = mdir, extraC = extraC, debug = debug, modName = modName,
     package = NULL)
     8: rxCompile.rxModelVars(.mv, dir = mdir, extraC = extraC, debug = debug, modName = modName,
     package = NULL)
     9: .badBuild("Error building model")
     10: stop(msg, call. = FALSE)
    
    
     *** caught segfault ***
     address 84ace14, cause 'memory not mapped'
    
     Traceback:
     1: remove(list = setdiff(allObjects, direct), envir = allTable)
     2: .resetInheritedMethods(fenv, mtable)
     3: .updateMethodsInTable(getGeneric(g), where, attach)
     4: .updateMethodsInTable(fdef, where, attach)
     5: methods::cacheMetaData(ns, TRUE, ns)
     6: loadNamespace(name)
     7: getNamespace(ns)
     8: asNamespace(ns)
     9: getExportedValue(pkg, name)
     10: Matrix::.bdiag
     11: (function (mat, diag.xform = c("sqrt", "log", "identity")) { diag.xform <- match.arg(diag.xform) mat2 <- mat mat2 <- rxInv(mat2) mat2 <- try({ chol(mat2) }) if (inherits(mat2, "try-error")) { stop("Initial Omega matrix inverse is non-positive definite.") } mat3 = mat2 if (diag.xform == "sqrt") { diag(mat3) <- sqrt(diag(mat3)) } else if (diag.xform == "log") { diag(mat3) <- log(diag(mat3)) } w <- which(as.vector(lower.tri(mat3, TRUE)) * 1 == 1) elts <- as.vector(mat3)[w] ini <- as.vector(mat3)[as.vector(upper.tri(mat3, TRUE))] th.unscaled <- c() for (i in seq_along(elts)) { if (elts[i] != 0) { th.unscaled[length(th.unscaled) + 1] <- elts[i] } } mat1 <- (mat != 0) * 1 if (length(mat1) == 1) { mat1 <- matrix(mat1, 1) } dmat <- dim(mat1)[1] - 1 block <- list() last <- 1 if (dmat != 0) { for (i in 1:dmat) { if (all(mat1[rxBlockZeros(mat1, i)] == 0)) { s <- seq(last, i) cur <- matrix(as.double(mat[s, s]), length(s)) last <- i + 1 block[[length(block) + 1]] <- cur } } } if (length(block) != 0) { s <- seq(last, dmat + 1) cur <- matrix(as.double(mat[s, s]), length(s)) block[[length(block) + 1]] <- cur } if (length(block) == 0) { if (diag.xform == "sqrt" && dim(mat1)[1] <= .Call(`_rxCholInv`, 0L, NULL, NULL)) { fmat <- mat1 num <- as.vector(mat1[upper.tri(mat1, TRUE)]) i <- 0 num <- sapply(num, function(x) { if (x == 1) { i <<- i + 1 return(i) } else { return(0) } }) fmat[upper.tri(fmat, TRUE)] <- num - 1 fmat[lower.tri(fmat)] <- t(fmat)[lower.tri(fmat)] d <- dim(fmat)[1] fmat <- paste0("t", fmat) fmat[fmat == "t-1"] <- "0" fmat <- matrix(fmat, d) if (diag.xform == "sqrt") { diag(fmat) <- sprintf("%s^2", diag(fmat)) } else if (diag.xform == "log") { diag(fmat) <- sprintf("exp(%s)", diag(fmat)) } else { diag(fmat) <- sprintf("(%s)", diag(fmat)) } w <- which(fmat[upper.tri(fmat, TRUE)] != "0") if (length(w) == 0) { stop("zero matrix.") } fn <- eval(bquote(function(theta, tn) { if (is.null(tn)) { .ret <- matrix(rep(TRUE, .(d * d)), nrow = .(d)) .ret[lower.tri(.ret)] <- FALSE return(.ret[lower.tri(.ret, TRUE)]) } else if (is.na(tn)) { new.theta <- rep(0, .((d + 1) * d/2)) new.theta[.(w)] <- theta return(.Call(`_rxCholInv`, .(as.integer(d)), as.double(new.theta), NA_integer_)) } if (tn == -2L) { return(.(length(w))) } new.theta <- rep(0, .((d + 1) * d/2)) new.theta[.(w)] <- theta return(.Call(`_rxCholInv`, .(as.integer(d)), as.double(new.theta), as.integer(tn))) })) ret <- list(fmat = fmat, fn = fn, ini = ini, cache = TRUE) class(ret) <- "rxSymInvChol" return(ret) } else { ret <- rxSymInvC2(mat1 = mat1, diag.xform = diag.xform) th <- th.unscaled ret <- list(fmat = ret[[2]], ini = ini, fn = rxSymInvCreate2C(ret[[1]])) class(ret) <- "rxSymInvChol" return(ret) } } else { mat <- Matrix::.bdiag(block) matI <- lapply(block, rxSymInvCreateC_, diag.xform = diag.xform) ini <- unlist(lapply(matI, function(x) { x$ini })) ntheta <- sum(sapply(matI, function(x) { return(x$fn(NULL, -2L)) })) i <- 1 theta.part <- lapply(matI, function(x) { len <- x$fn(NULL, -2L) ret <- as.integer(seq(i, by = 1, length = len)) i <<- max(ret) + 1 return(ret) }) fn <- eval(bquote(function(theta, tn) { force(matI) theta.part <- .(theta.part) if (is.null(tn)) { if (is.null(theta)) { return(unlist(lapply(theta.part, function(x) { .j <- .k <- 1 .ret <- logical(length(x)) for (.i in seq_along(x)) { if (.j == .k) { .ret[.i] <- TRUE .k <- .k + 1 .j <- 1 } else { .ret[.i] <- FALSE .j <- .j + 1 } } return(.ret) }))) } } else if (!is.na(tn)) { if (tn == -2L) { return(.(ntheta)) } } lst <- lapply(seq_along(theta.part), function(x) { mt <- matI[[x]] w <- theta.part[[x]] new.theta <- theta[w] ctn <- as.integer(tn) if (is.na(ctn)) { return(mt$fn(as.double(new.theta), ctn)) } else if (ctn == -1L || ctn == 0L) { return(mt$fn(as.double(new.theta), ctn)) } else { if (ctn > 0L) { if (ctn > max(w) | ctn < min(w)) { mat <- mt$fn(as.double(new.theta), 0L) d <- dim(mat)[1] return(matrix(rep(0, d * d), d)) } else { ctn <- as.integer(ctn - min(w) + 1) return(mt$fn(as.double(new.theta), ctn)) } } else { ctn <- as.integer(-ctn - 2) if (ctn > max(w) | ctn < min(w)) { vec <- mt$fn(as.double(new.theta), -3L) d <- length(vec) return(rep(0, d)) } else { ctn <- as.integer(-(ctn - min(w) + 1) - 2L) return(mt$fn(as.double(new.theta), ctn)) } } } }) if (is.na(tn)) { return(unlist(lst)) } else if (tn >= -1) { return(as.matrix(Matrix::.bdiag(lst))) } else { return(unlist(lst)) } })) ret <- list(fmat = mat, ini = ini, fn = fn) class(ret) <- "rxSymInvChol" return(ret) }})(mat = matrix(c(1, 0.9, 0, 0.9, 1, 0, 0, 0, 1), ncol = 3))
     12: do.call(rxSymInvCreateC_, args, envir = envir)
     13: rxSymInvCholCreate(matrix(c(1, 0.9, 0, 0.9, 1, 0, 0, 0, 1), ncol = 3))
     14: eval(code, test_env)
     15: eval(code, test_env)
     16: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     17: doTryCatch(return(expr), name, parentenv, handler)
     18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     20: doTryCatch(return(expr), name, parentenv, handler)
     21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     22: tryCatchList(expr, classes, parentenv, handlers)
     23: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     24: test_code(desc, code, env = parent.frame())
     25: test_that("diagonal indicator give correct values", { tmp <- rxSymInvCholCreate(matrix(c(1, 0.9, 0, 0.9, 1, 0, 0, 0, 1), ncol = 3)) expect_equal(tmp$theta.diag, c(TRUE, FALSE, TRUE, TRUE)) tmp <- rxSymInvCholCreate(matrix(c(1, 0.9, 0.9, 1), ncol = 2)) expect_equal(tmp$theta.diag, c(TRUE, FALSE, TRUE))})
     26: eval(code, test_env)
     27: eval(code, test_env)
     28: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     29: doTryCatch(return(expr), name, parentenv, handler)
     30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     31: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     32: doTryCatch(return(expr), name, parentenv, handler)
     33: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     34: tryCatchList(expr, classes, parentenv, handlers)
     35: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     36: test_code(NULL, exprs, env)
     37: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     38: force(code)
     39: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$end_context() reporter$end_file() })
     40: FUN(X[[i]], ...)
     41: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     42: force(code)
     43: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     45: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     46: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     47: test_check("RxODE")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 0.9.1-0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘RxODE-cmt.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-cmt.Rmd’
    
    --- re-building ‘RxODE-covariates.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    udunits system database from /usr/local/share/udunits
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    --- finished re-building ‘RxODE-covariates.Rmd’
    
    --- re-building ‘RxODE-data-frame.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    udunits system database from /usr/local/share/udunits
    ___________________________________________________________________________
    ___________________________________________________________________________
    ___________________________________________________________________________
    
    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
    
    ___________________________________________________________________________
    ___________________________________________________________________________
    ___________________________________________________________________________
    ___________________________________________________________________________
    --- finished re-building ‘RxODE-data-frame.Rmd’
    
    --- re-building ‘RxODE-events.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-events.Rmd’
    
    --- re-building ‘RxODE-intro.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-intro.Rmd’
    
    --- re-building ‘RxODE-model-types.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 65-68 (RxODE-model-types.Rmd)
    Error: processing vignette 'RxODE-model-types.Rmd' failed with diagnostics:
    there is no package called 'webshot'
    --- failed re-building ‘RxODE-model-types.Rmd’
    
    --- re-building ‘RxODE-rxUse.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-rxUse.Rmd’
    
    --- re-building ‘RxODE-shiny.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-shiny.Rmd’
    
    --- re-building ‘RxODE-stiff.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-stiff.Rmd’
    
    --- re-building ‘RxODE-syntax.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-syntax.Rmd’
    
    --- re-building ‘RxODE-transit-compartments.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-transit-compartments.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘RxODE-model-types.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.9.1-0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘RxODE-cmt.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-cmt.Rmd’
    
    --- re-building ‘RxODE-covariates.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    udunits system database from /usr/local/share/udunits
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    --- finished re-building ‘RxODE-covariates.Rmd’
    
    --- re-building ‘RxODE-data-frame.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    udunits system database from /usr/local/share/udunits
    ___________________________________________________________________________
    ___________________________________________________________________________
    ___________________________________________________________________________
    
    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
    
    ___________________________________________________________________________
    ___________________________________________________________________________
    ___________________________________________________________________________
    ___________________________________________________________________________
    --- finished re-building ‘RxODE-data-frame.Rmd’
    
    --- re-building ‘RxODE-events.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-events.Rmd’
    
    --- re-building ‘RxODE-intro.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-intro.Rmd’
    
    --- re-building ‘RxODE-model-types.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 65-68 (RxODE-model-types.Rmd)
    Error: processing vignette 'RxODE-model-types.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘RxODE-model-types.Rmd’
    
    --- re-building ‘RxODE-rxUse.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-rxUse.Rmd’
    
    --- re-building ‘RxODE-shiny.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-shiny.Rmd’
    
    --- re-building ‘RxODE-stiff.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-stiff.Rmd’
    
    --- re-building ‘RxODE-syntax.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-syntax.Rmd’
    
    --- re-building ‘RxODE-transit-compartments.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    --- finished re-building ‘RxODE-transit-compartments.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘RxODE-model-types.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.9.1-0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
    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
    
    ________________________________________________________________________________
    ________________________________________________________________________________
    ________________________________________________________________________________
    ________________________________________________________________________________
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 65-68 (RxODE-model-types.Rmd)
    Error: processing vignette 'RxODE-model-types.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-oldrel-osx-x86_64