CRAN Package Check Results for Package RxODE

Last updated on 2019-09-15 23:46:31 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.1-4 181.28 253.04 434.32 NOTE
r-devel-linux-x86_64-debian-gcc 0.9.1-4 233.30 172.01 405.31 NOTE
r-devel-linux-x86_64-fedora-clang 0.9.1-4 556.32 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9.1-4 673.00 NOTE
r-devel-windows-ix86+x86_64 0.9.1-4 478.00 606.00 1084.00 ERROR
r-patched-linux-x86_64 0.9.1-4 216.62 219.08 435.70 NOTE
r-patched-solaris-x86 0.9.1-4 627.40 WARN
r-release-linux-x86_64 0.9.1-4 221.04 218.58 439.62 NOTE
r-release-windows-ix86+x86_64 0.9.1-4 359.00 419.00 778.00 NOTE
r-release-osx-x86_64 0.9.1-4 WARN
r-oldrel-windows-ix86+x86_64 0.9.1-4 479.00 597.00 1076.00 NOTE
r-oldrel-osx-x86_64 0.9.1-4 WARN

Check Details

Version: 0.9.1-4
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-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.9.1-4
Check: installed package size
Result: NOTE
     installed size is 21.3Mb
     sub-directories of 1Mb or more:
     doc 1.3Mb
     libs 18.9Mb
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: 0.9.1-4
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: 0.9.1-4
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [114s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > Sys.setenv("R_TESTS" = "")
     > library(testthat)
     > library(RxODE)
     Rtools is not set up correctly!
    
     You need a working Rtools installation for RxODE to work.
     You can set up Rtools using the command 'rxWinSetup()'.
    
     > test_check("RxODE")
     [====|====|====|====|====|====|====|====|====|====
     [====|====|====|====|====|====|====|====|====|====-- 1. Error: (unknown) (@test-steady-state.R#1) -------------------------------
     object 'package' not found
     1: rxPermissive({
     ms <- c("liblsoda", "lsoda", "dop853")
     if (grepl("SunOS", Sys.info()["sysname"]))
     ms <- "lsoda"
     for (m in ms) {
     et <- eventTable() %>% add.dosing(dose = 3, nbr.doses = 6, dosing.interval = 8) %>%
     add.sampling(seq(0, 48, length.out = 200))
     ode.1c <- RxODE({
     V <- 20
     Cl <- 1
     fc <- 1
     C2 = center/V
     d/dt(center) ~ -Cl * C2
     f(center) = fc
     })
     ode.1cR <- RxODE({
     V <- 20
     Cl <- 1
     C2 = center/V
     fc = 1
     d/dt(center) ~ -Cl * C2
     rate(center) = rateIn
     f(center) = fc
     })
     ode.1cD <- RxODE({
     V <- 20
     Cl <- 1
     C2 = center/V
     fc = 1
     d/dt(center) ~ -Cl * C2
     dur(center) = durIn
     f(center) = fc
     })
     d <- 3
     et2 <- eventTable() %>% add.dosing(dose = d, nbr.doses = 2, dosing.interval = 8) %>%
     add.sampling(seq(0, 48, length.out = 200))
     x2 <- solve(ode.1c, et2, method = m)
     c0 <- setNames(d/rxInits(ode.1c)["V"], NULL)
     ke <- with(as.list(rxInits(ode.1c)), {
     Cl/V
     })
     context(sprintf("Steady state IV Bolus (%s)", m))
     test_that("Non steady state dose makes sense", {
     expect_equal(x2$C2[1], c0)
     })
     tol <- 0.001
     for (ii in seq(2, 24, by = 2)) {
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii) %>% et(amt = d, time = ii) %>%
     et(seq(0, 48, length.out = 200))
     x2 <- solve(ode.1c, et3, method = m)
     test_that(paste("Steady State dose makes sense for ii=", ii), {
     expect_equal(x2$C2[1], c0/(1 - exp(-ke * ii)), tolerance = tol)
     })
     }
     context(sprintf("Steady state Infusions (%s)", m))
     for (dur in c(0.5, 1)) {
     for (ii in seq(2, 24, by = 2)) {
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = d/dur) %>% et(time = ii,
     amt = d, ii = ii, addl = floor(24/ii), rate = d/dur) %>% et(c(dur,
     seq(0, 24, length.out = 200)))
     x2 <- solve(ode.1c, et3, method = m, maxsteps = 10000)
     infMax <- with(as.list(rxInit(ode.1c)), d/(Cl * dur) * (1 - exp(-ke *
     dur))/(1 - exp(-ke * ii)))
     inf0 <- with(as.list(rxInit(ode.1c)), infMax * exp(-ke * (ii - dur)))
     test_that(paste("Infusion Steady State dose makes sense for ii=",
     ii, " dur=", dur, "(rate)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, dur = dur) %>% et(c(dur,
     seq(0, 24, length.out = 19)))
     x2 <- solve(ode.1c, et3, method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for ii=",
     ii, " dur=", dur, "(dur)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = -1) %>% et(c(dur,
     seq(0, 24, length.out = 19)))
     x2 <- rxSolve(ode.1cR, et3, c(rateIn = d/dur), method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for ii=",
     ii, " dur=", dur, "(rate modeled)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = -2) %>% et(c(dur,
     seq(0, 24, length.out = 19)))
     x2 <- rxSolve(ode.1cD, et3, c(durIn = dur), method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for ii=",
     ii, " dur=", dur, "(dur modeled)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     for (f in c(0.5, 1)) {
     if (dur * f < ii) {
     infMax <- with(as.list(rxInit(ode.1c)), f * d/(Cl * dur * f) *
     (1 - exp(-ke * dur * f))/(1 - exp(-ke * ii)))
     inf0 <- with(as.list(rxInit(ode.1c)), infMax * exp(-ke * (ii -
     dur * f)))
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = d/dur) %>%
     et(time = ii, amt = d, ii = ii, addl = floor(24/ii), rate = d/dur) %>%
     et(c(dur * f, seq(0, 24, length.out = 200)))
     x2 <- solve(ode.1c, et3, c(fc = f), method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for f= ",
     f, "ii=", ii, " dur=", dur, "(rate)"), {
     expect_equal(x2$C2[x2 == dur * f], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = -1) %>% et(c(dur *
     f, seq(0, 24, length.out = 19)))
     x2 <- rxSolve(ode.1cR, et3, c(fc = f, rateIn = d/dur), method = m,
     maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for f= ",
     f, " ii=", ii, " dur=", dur, "(rate modeled)"), {
     expect_equal(x2$C2[x2 == dur * f], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     }
     infMax <- with(as.list(rxInit(ode.1c)), f * d/(Cl * dur) * (1 -
     exp(-ke * dur))/(1 - exp(-ke * ii)))
     inf0 <- with(as.list(rxInit(ode.1c)), infMax * exp(-ke * (ii -
     dur)))
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, dur = dur) %>% et(time = ii,
     amt = d, ii = ii, addl = floor(24/ii), dur = dur) %>% et(unique(c(dur,
     seq(0, 24, length.out = 200))))
     x2 <- solve(ode.1c, et3, c(fc = f), method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for f= ",
     f, "ii=", ii, " dur=", dur, "(dur)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = -2) %>% et(c(dur,
     seq(0, 24, length.out = 19)))
     x2 <- rxSolve(ode.1cD, et3, c(fc = f, durIn = dur), method = m,
     maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for f=",
     f, "ii=", ii, " dur=", dur, "(dur modeled)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     }
     }
     }
     context(sprintf("Bolus SS=2 (%s)", m))
     test_that("bolus SS=2", {
     e2 <- et(amt = 20, ii = 24, ss = 2, time = 12) %>% et(seq(0, 24, length.out = 100))
     s2 <- rxSolve(ode.1c, e2)
     e3 <- et(amt = 20, ii = 24, ss = 1, time = 12) %>% et(seq(0, 24, length.out = 100))
     s3 <- rxSolve(ode.1c, e3)
     expect_equal(as.data.frame(s2), as.data.frame(s3))
     e1 <- et(amt = 10, ii = 24, ss = 1, time = 0) %>% et(seq(0, 24, length.out = 100))
     s1 <- rxSolve(ode.1c, e1)
     e2 <- et(amt = 20, ii = 24, ss = 2, time = 12) %>% et(seq(0, 24, length.out = 100))
     s2 <- rxSolve(ode.1c, e2)
     e3 <- c(e1, e2, ii = 0) %>% et(seq(0, 24, length.out = 100))
     s3 <- rxSolve(ode.1c, e3)
     expect_equal(s1$C2 + s2$C2, s3$C2)
     for (f in c(0.5, 2)) {
     s1 <- rxSolve(ode.1c, e1, c(fc = f))
     s2 <- rxSolve(ode.1c, e2, c(fc = f))
     s3 <- rxSolve(ode.1c, e3, c(fc = f))
     expect_equal(s1$C2 + s2$C2, s3$C2)
     }
     })
     context(sprintf("IV Infusion SS=2 (%s)", m))
     d <- 10
     for (f in c(0.5, 1, 2)) {
     for (dur in c(1, 2)) {
     e1 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(seq(0,
     24, length.out = 200))
     s1 <- solve(ode.1c, e1, c(fc = f), method = m, maxsteps = 1e+06)
     e2 <- et() %>% et(time = 12, amt = 2 * d, ss = 2, ii = 24, rate = d *
     2/dur) %>% et(seq(0, 24, length.out = 200))
     if (f == 1) {
     s2 <- solve(ode.1c, e2, c(fc = f), method = m, maxsteps = 1e+06)
     e3 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(time = 12,
     amt = 2 * d, ss = 2, ii = 24, rate = d * 2/dur) %>% et(seq(0,
     24, length.out = 200))
     s3 <- solve(ode.1c, e3, c(fc = f), method = m, maxsteps = 1e+06)
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(rate)"), {
     expect_equal(s1$C2 + s2$C2, s3$C2, tolerance = 1e-04)
     })
     }
     else {
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(dur)"), {
     expect_error(solve(ode.1c, e2, c(fc = f), method = m, maxsteps = 1e+06))
     })
     }
     e1 <- et() %>% et(amt = d, ss = 1, ii = 24, dur = dur) %>% et(seq(0,
     24, length.out = 200))
     s1 <- solve(ode.1c, e1, c(fc = f), method = m, maxsteps = 1e+06)
     e2 <- et() %>% et(time = 12, amt = 2 * d, ss = 2, ii = 24, dur = dur) %>%
     et(seq(0, 24, length.out = 200))
     if (f == 1) {
     s2 <- solve(ode.1c, e2, c(fc = f), method = m, maxsteps = 1e+06)
     e3 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(time = 12,
     amt = 2 * d, ss = 2, ii = 24, rate = d * 2/dur) %>% et(seq(0,
     24, length.out = 200))
     s3 <- solve(ode.1c, e3, c(fc = f), method = m, maxsteps = 1e+06)
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(dur)"), {
     expect_equal(s1$C2 + s2$C2, s3$C2, tolerance = 1e-04)
     })
     }
     else {
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(dur)"), {
     expect_error(solve(ode.1c, e2, c(fc = f), method = m, maxsteps = 1e+06))
     })
     }
     e1 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(seq(0,
     24, length.out = 200))
     s1 <- solve(ode.1cR, e1, c(fc = f, rateIn = 2 * d/dur), method = m,
     maxsteps = 1e+06)
     e2 <- et() %>% et(time = 12, amt = 2 * d, ss = 2, ii = 24, rate = -1) %>%
     et(seq(0, 24, length.out = 200))
     if (f == 1) {
     s2 <- solve(ode.1cR, e2, c(fc = f, rateIn = 2 * d/dur), method = m,
     maxsteps = 1e+06)
     e3 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(time = 12,
     amt = 2 * d, ss = 2, ii = 24, rate = -1) %>% et(seq(0, 24, length.out = 200))
     s3 <- solve(ode.1cR, e3, c(fc = f, rateIn = 2 * d/dur), method = m,
     maxsteps = 1e+06)
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(modeled rate)"), {
     expect_equal(s1$C2 + s2$C2, s3$C2, tolerance = 1e-04)
     })
     }
     else {
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(modeled rate)"), {
     expect_error(solve(ode.1cR, e2, c(fc = f, rateIn = 2 * d/dur),
     method = m, maxsteps = 1e+06))
     })
     }
     e1 <- et() %>% et(amt = d, ss = 1, ii = 24, dur = dur) %>% et(seq(0,
     24, length.out = 200))
     s1 <- solve(ode.1cD, e1, c(fc = f, durIn = dur), method = m, maxsteps = 1e+06)
     e2 <- et() %>% et(time = 12, amt = 2 * d, ss = 2, ii = 24, rate = -2) %>%
     et(seq(0, 24, length.out = 200))
     if (f == 1) {
     s2 <- solve(ode.1cD, e2, c(fc = f, durIn = dur), method = m, maxsteps = 1e+06)
     e3 <- et() %>% et(amt = d, ss = 1, ii = 24, dur = dur) %>% et(time = 12,
     amt = 2 * d, ss = 2, ii = 24, rate = -2) %>% et(seq(0, 24, length.out = 200))
     s3 <- solve(ode.1cD, e3, c(fc = f, durIn = dur), method = m, maxsteps = 1e+06)
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(modeled duration)"), {
     expect_equal(s1$C2 + s2$C2, s3$C2, tolerance = 1e-04)
     })
     }
     else {
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(modeled duration)"), {
     expect_error(solve(ode.1cD, e2, c(fc = f, durIn = dur), method = m,
     maxsteps = 1e+06))
     })
     }
     }
     }
     }
     }, cran = TRUE, silent = TRUE) at testthat/test-steady-state.R:1
     2: do.call(getFromNamespace("rxOptions", "RxODE"), args, envir = parent.frame(1))
     3: (function (expr, op.rx = NULL, silent = .isTestthat(), respect = FALSE, rxclean = .isTestthat(),
     cran = FALSE, on.validate = FALSE)
     {
     rxSetSilentErr(1L)
     on.exit(rxSetSilentErr(0L))
     do.it <- TRUE
     if (!identical(Sys.getenv("NOT_CRAN"), "true") && !cran) {
     do.it <- FALSE
     }
     if (is(on.validate, "character")) {
     val.txt <- on.validate
     on.validate <- TRUE
     }
     else {
     val.txt <- "RxODE_VALIDATION_FULL"
     }
     if (on.validate && !identical(Sys.getenv(val.txt), "true")) {
     do.it <- FALSE
     }
     if (!on.validate && identical(Sys.getenv(val.txt), "true")) {
     do.it <- FALSE
     }
     if (do.it) {
     if (missing(expr) && is.null(op.rx)) {
     op <- options()
     op <- op[regexpr(rex::rex("RxODE."), names(op)) != -1]
     op <- op[order(names(op))]
     sapply(names(op), function(n) {
     rxCat(sprintf("%s: %s\n", n, op[[n]]))
     })
     return(invisible(op))
     }
     else {
     if (is(op.rx, "character")) {
     if (op.rx == "strict") {
     op.rx <- 1
     }
     else {
     op.rx <- 2
     }
     }
     if (is(op.rx, "numeric")) {
     if (op.rx <= 2) {
     x <- op.rx
     op.rx <- list()
     for (v in names(rxOpt)) {
     op.rx[[v]] <- rxOpt[[v]][x]
     }
     }
     }
     if (!missing(silent)) {
     op.rx$RxODE.verbose = !silent
     op.rx$RxODE.suppress.syntax.info = silent
     }
     if (!missing(expr)) {
     if (rxclean) {
     rxClean()
     }
     opOld <- options()
     .oldProg <- getProgSupported()
     if (silent) {
     setProgSupported(-1)
     }
     on.exit({
     options(opOld)
     setProgSupported(.oldProg)
     rxSyncOptions()
     if (rxclean) {
     rxClean()
     }
     })
     }
     if (respect) {
     op <- options()
     w <- !(names(op.rx) %in% names(op))
     if (any(w))
     options(op.rx[w])
     rxSyncOptions()
     }
     else if (length(op.rx) > 0) {
     options(op.rx)
     rxSyncOptions()
     }
     if (is(substitute(expr), "{")) {
     if (silent) {
     return(suppressMessages(eval(substitute(expr), envir = parent.frame(1))))
     }
     else {
     return(eval(substitute(expr), envir = parent.frame(1)))
     }
     }
     }
     }
     })(expr = {
     ms <- c("liblsoda", "lsoda", "dop853")
     if (grepl("SunOS", Sys.info()["sysname"]))
     ms <- "lsoda"
     for (m in ms) {
     et <- eventTable() %>% add.dosing(dose = 3, nbr.doses = 6, dosing.interval = 8) %>%
     add.sampling(seq(0, 48, length.out = 200))
     ode.1c <- RxODE({
     V <- 20
     Cl <- 1
     fc <- 1
     C2 = center/V
     d/dt(center) ~ -Cl * C2
     f(center) = fc
     })
     ode.1cR <- RxODE({
     V <- 20
     Cl <- 1
     C2 = center/V
     fc = 1
     d/dt(center) ~ -Cl * C2
     rate(center) = rateIn
     f(center) = fc
     })
     ode.1cD <- RxODE({
     V <- 20
     Cl <- 1
     C2 = center/V
     fc = 1
     d/dt(center) ~ -Cl * C2
     dur(center) = durIn
     f(center) = fc
     })
     d <- 3
     et2 <- eventTable() %>% add.dosing(dose = d, nbr.doses = 2, dosing.interval = 8) %>%
     add.sampling(seq(0, 48, length.out = 200))
     x2 <- solve(ode.1c, et2, method = m)
     c0 <- setNames(d/rxInits(ode.1c)["V"], NULL)
     ke <- with(as.list(rxInits(ode.1c)), {
     Cl/V
     })
     context(sprintf("Steady state IV Bolus (%s)", m))
     test_that("Non steady state dose makes sense", {
     expect_equal(x2$C2[1], c0)
     })
     tol <- 0.001
     for (ii in seq(2, 24, by = 2)) {
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii) %>% et(amt = d, time = ii) %>%
     et(seq(0, 48, length.out = 200))
     x2 <- solve(ode.1c, et3, method = m)
     test_that(paste("Steady State dose makes sense for ii=", ii), {
     expect_equal(x2$C2[1], c0/(1 - exp(-ke * ii)), tolerance = tol)
     })
     }
     context(sprintf("Steady state Infusions (%s)", m))
     for (dur in c(0.5, 1)) {
     for (ii in seq(2, 24, by = 2)) {
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = d/dur) %>% et(time = ii,
     amt = d, ii = ii, addl = floor(24/ii), rate = d/dur) %>% et(c(dur,
     seq(0, 24, length.out = 200)))
     x2 <- solve(ode.1c, et3, method = m, maxsteps = 10000)
     infMax <- with(as.list(rxInit(ode.1c)), d/(Cl * dur) * (1 - exp(-ke *
     dur))/(1 - exp(-ke * ii)))
     inf0 <- with(as.list(rxInit(ode.1c)), infMax * exp(-ke * (ii - dur)))
     test_that(paste("Infusion Steady State dose makes sense for ii=",
     ii, " dur=", dur, "(rate)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, dur = dur) %>% et(c(dur,
     seq(0, 24, length.out = 19)))
     x2 <- solve(ode.1c, et3, method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for ii=",
     ii, " dur=", dur, "(dur)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = -1) %>% et(c(dur,
     seq(0, 24, length.out = 19)))
     x2 <- rxSolve(ode.1cR, et3, c(rateIn = d/dur), method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for ii=",
     ii, " dur=", dur, "(rate modeled)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = -2) %>% et(c(dur,
     seq(0, 24, length.out = 19)))
     x2 <- rxSolve(ode.1cD, et3, c(durIn = dur), method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for ii=",
     ii, " dur=", dur, "(dur modeled)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     for (f in c(0.5, 1)) {
     if (dur * f < ii) {
     infMax <- with(as.list(rxInit(ode.1c)), f * d/(Cl * dur * f) *
     (1 - exp(-ke * dur * f))/(1 - exp(-ke * ii)))
     inf0 <- with(as.list(rxInit(ode.1c)), infMax * exp(-ke * (ii -
     dur * f)))
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = d/dur) %>%
     et(time = ii, amt = d, ii = ii, addl = floor(24/ii), rate = d/dur) %>%
     et(c(dur * f, seq(0, 24, length.out = 200)))
     x2 <- solve(ode.1c, et3, c(fc = f), method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for f= ",
     f, "ii=", ii, " dur=", dur, "(rate)"), {
     expect_equal(x2$C2[x2 == dur * f], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = -1) %>% et(c(dur *
     f, seq(0, 24, length.out = 19)))
     x2 <- rxSolve(ode.1cR, et3, c(fc = f, rateIn = d/dur), method = m,
     maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for f= ",
     f, " ii=", ii, " dur=", dur, "(rate modeled)"), {
     expect_equal(x2$C2[x2 == dur * f], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     }
     infMax <- with(as.list(rxInit(ode.1c)), f * d/(Cl * dur) * (1 -
     exp(-ke * dur))/(1 - exp(-ke * ii)))
     inf0 <- with(as.list(rxInit(ode.1c)), infMax * exp(-ke * (ii -
     dur)))
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, dur = dur) %>% et(time = ii,
     amt = d, ii = ii, addl = floor(24/ii), dur = dur) %>% et(unique(c(dur,
     seq(0, 24, length.out = 200))))
     x2 <- solve(ode.1c, et3, c(fc = f), method = m, maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for f= ",
     f, "ii=", ii, " dur=", dur, "(dur)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     et3 <- et() %>% et(amt = d, ss = 1, ii = ii, rate = -2) %>% et(c(dur,
     seq(0, 24, length.out = 19)))
     x2 <- rxSolve(ode.1cD, et3, c(fc = f, durIn = dur), method = m,
     maxsteps = 10000)
     test_that(paste("Infusion Steady State dose makes sense for f=",
     f, "ii=", ii, " dur=", dur, "(dur modeled)"), {
     expect_equal(x2$C2[x2 == dur], infMax, tolerance = tol)
     expect_equal(x2$C2[1], inf0, tolerance = tol)
     })
     }
     }
     }
     context(sprintf("Bolus SS=2 (%s)", m))
     test_that("bolus SS=2", {
     e2 <- et(amt = 20, ii = 24, ss = 2, time = 12) %>% et(seq(0, 24, length.out = 100))
     s2 <- rxSolve(ode.1c, e2)
     e3 <- et(amt = 20, ii = 24, ss = 1, time = 12) %>% et(seq(0, 24, length.out = 100))
     s3 <- rxSolve(ode.1c, e3)
     expect_equal(as.data.frame(s2), as.data.frame(s3))
     e1 <- et(amt = 10, ii = 24, ss = 1, time = 0) %>% et(seq(0, 24, length.out = 100))
     s1 <- rxSolve(ode.1c, e1)
     e2 <- et(amt = 20, ii = 24, ss = 2, time = 12) %>% et(seq(0, 24, length.out = 100))
     s2 <- rxSolve(ode.1c, e2)
     e3 <- c(e1, e2, ii = 0) %>% et(seq(0, 24, length.out = 100))
     s3 <- rxSolve(ode.1c, e3)
     expect_equal(s1$C2 + s2$C2, s3$C2)
     for (f in c(0.5, 2)) {
     s1 <- rxSolve(ode.1c, e1, c(fc = f))
     s2 <- rxSolve(ode.1c, e2, c(fc = f))
     s3 <- rxSolve(ode.1c, e3, c(fc = f))
     expect_equal(s1$C2 + s2$C2, s3$C2)
     }
     })
     context(sprintf("IV Infusion SS=2 (%s)", m))
     d <- 10
     for (f in c(0.5, 1, 2)) {
     for (dur in c(1, 2)) {
     e1 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(seq(0,
     24, length.out = 200))
     s1 <- solve(ode.1c, e1, c(fc = f), method = m, maxsteps = 1e+06)
     e2 <- et() %>% et(time = 12, amt = 2 * d, ss = 2, ii = 24, rate = d *
     2/dur) %>% et(seq(0, 24, length.out = 200))
     if (f == 1) {
     s2 <- solve(ode.1c, e2, c(fc = f), method = m, maxsteps = 1e+06)
     e3 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(time = 12,
     amt = 2 * d, ss = 2, ii = 24, rate = d * 2/dur) %>% et(seq(0,
     24, length.out = 200))
     s3 <- solve(ode.1c, e3, c(fc = f), method = m, maxsteps = 1e+06)
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(rate)"), {
     expect_equal(s1$C2 + s2$C2, s3$C2, tolerance = 1e-04)
     })
     }
     else {
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(dur)"), {
     expect_error(solve(ode.1c, e2, c(fc = f), method = m, maxsteps = 1e+06))
     })
     }
     e1 <- et() %>% et(amt = d, ss = 1, ii = 24, dur = dur) %>% et(seq(0,
     24, length.out = 200))
     s1 <- solve(ode.1c, e1, c(fc = f), method = m, maxsteps = 1e+06)
     e2 <- et() %>% et(time = 12, amt = 2 * d, ss = 2, ii = 24, dur = dur) %>%
     et(seq(0, 24, length.out = 200))
     if (f == 1) {
     s2 <- solve(ode.1c, e2, c(fc = f), method = m, maxsteps = 1e+06)
     e3 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(time = 12,
     amt = 2 * d, ss = 2, ii = 24, rate = d * 2/dur) %>% et(seq(0,
     24, length.out = 200))
     s3 <- solve(ode.1c, e3, c(fc = f), method = m, maxsteps = 1e+06)
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(dur)"), {
     expect_equal(s1$C2 + s2$C2, s3$C2, tolerance = 1e-04)
     })
     }
     else {
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(dur)"), {
     expect_error(solve(ode.1c, e2, c(fc = f), method = m, maxsteps = 1e+06))
     })
     }
     e1 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(seq(0,
     24, length.out = 200))
     s1 <- solve(ode.1cR, e1, c(fc = f, rateIn = 2 * d/dur), method = m,
     maxsteps = 1e+06)
     e2 <- et() %>% et(time = 12, amt = 2 * d, ss = 2, ii = 24, rate = -1) %>%
     et(seq(0, 24, length.out = 200))
     if (f == 1) {
     s2 <- solve(ode.1cR, e2, c(fc = f, rateIn = 2 * d/dur), method = m,
     maxsteps = 1e+06)
     e3 <- et() %>% et(amt = d, ss = 1, ii = 24, rate = d/dur) %>% et(time = 12,
     amt = 2 * d, ss = 2, ii = 24, rate = -1) %>% et(seq(0, 24, length.out = 200))
     s3 <- solve(ode.1cR, e3, c(fc = f, rateIn = 2 * d/dur), method = m,
     maxsteps = 1e+06)
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(modeled rate)"), {
     expect_equal(s1$C2 + s2$C2, s3$C2, tolerance = 1e-04)
     })
     }
     else {
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(modeled rate)"), {
     expect_error(solve(ode.1cR, e2, c(fc = f, rateIn = 2 * d/dur),
     method = m, maxsteps = 1e+06))
     })
     }
     e1 <- et() %>% et(amt = d, ss = 1, ii = 24, dur = dur) %>% et(seq(0,
     24, length.out = 200))
     s1 <- solve(ode.1cD, e1, c(fc = f, durIn = dur), method = m, maxsteps = 1e+06)
     e2 <- et() %>% et(time = 12, amt = 2 * d, ss = 2, ii = 24, rate = -2) %>%
     et(seq(0, 24, length.out = 200))
     if (f == 1) {
     s2 <- solve(ode.1cD, e2, c(fc = f, durIn = dur), method = m, maxsteps = 1e+06)
     e3 <- et() %>% et(amt = d, ss = 1, ii = 24, dur = dur) %>% et(time = 12,
     amt = 2 * d, ss = 2, ii = 24, rate = -2) %>% et(seq(0, 24, length.out = 200))
     s3 <- solve(ode.1cD, e3, c(fc = f, durIn = dur), method = m, maxsteps = 1e+06)
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(modeled duration)"), {
     expect_equal(s1$C2 + s2$C2, s3$C2, tolerance = 1e-04)
     })
     }
     else {
     test_that(paste("Infusion SS=2 dose makes sense for f=", f, " dur=",
     dur, "(modeled duration)"), {
     expect_error(solve(ode.1cD, e2, c(fc = f, durIn = dur), method = m,
     maxsteps = 1e+06))
     })
     }
     }
     }
     }
     }, silent = TRUE, cran = TRUE, op.rx = 2)
     4: suppressMessages(eval(substitute(expr), envir = parent.frame(1)))
     5: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
     6: eval(substitute(expr), envir = parent.frame(1))
     7: eval(substitute(expr), envir = parent.frame(1))
     8: RxODE({
     V <- 20
     Cl <- 1
     fc <- 1
     C2 = center/V
     d/dt(center) ~ -Cl * C2
     f(center) = fc
     }) at testthat/test-steady-state.R:9
     9: RxODE::rxForget()
     10: memoise::is.memoised(getFromNamespace(fn, "RxODE"))
     11: getFromNamespace(fn, "RxODE")
     12: get(x, envir = ns, inherits = FALSE)
    
     == testthat results ===========================================================
     [ OK: 379 | SKIPPED: 13 | WARNINGS: 1 | FAILED: 1 ]
     1. Error: (unknown) (@test-steady-state.R#1)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.9.1-4
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
    --- 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’
    
    Segmentation Fault - core dumped
    --- 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.
    
     *** caught segfault ***
    address 1bca6e8a, cause 'memory not mapped'
    
    Traceback:
     1: utf8::utf8_width(x, encode = FALSE, utf8 = TRUE)
     2: get_extent(x)
     3: get_max_extent(as.character(formatted))
     4: pillar::new_pillar_shaft_simple(out, align = "right", min_width = 8)
     5: pillar_shaft.units(X[[i]], ...)
     6: FUN(X[[i]], ...)
     7: lapply(.x, .f, ...)
     8: map(x[pillar_shown], pillar_shaft)
     9: colonnade_get_width(x, width, rowid_width)
    10: pillar::squeeze(x$mcf, width = width)
    11: format.trunc_mat(mat)
    12: format(mat)
    13: format.tbl(x, ..., n = n, width = width, n_extra = n_extra)
    14: format(x, ..., n = n, width = width, n_extra = n_extra)
    15: paste0(..., "\n")
    16: cat(paste0(..., "\n"), sep = "")
    17: cat_line(format(x, ..., n = n, width = width, n_extra = n_extra))
    18: print.tbl(dplyr::as.tbl(data.frame(x)))
    19: print(dplyr::as.tbl(data.frame(x)))
    20: print.rxEt(x)
    21: print(x)
    22: normal_print(x)
    23: knit_print.default(x, ...)
    24: knit_print(x, ...)
    25: withVisible(knit_print(x, ...))
    26: fun(x, options = options)
    27: value_fun(ev$value, ev$visible)
    28: withVisible(value_fun(ev$value, ev$visible))
    29: withCallingHandlers(withVisible(value_fun(ev$value, ev$visible)), warning = wHandler, error = eHandler, message = mHandler)
    30: handle(pv <- withCallingHandlers(withVisible(value_fun(ev$value, ev$visible)), warning = wHandler, error = eHandler, message = mHandler))
    31: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    32: evaluate::evaluate(...)
    33: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    34: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    35: block_exec(params)
    36: call_block(x)
    37: process_group.block(group)
    38: process_group(group)
    39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    40: process_file(text, output)
    41: knit(input, text = text, envir = envir, quiet = quiet)
    42: knit2html(..., force_v1 = TRUE)
    43: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    44: vweave(...)
    45: engine$weave(file, quiet = quiet, encoding = enc)
    46: doTryCatch(return(expr), name, parentenv, handler)
    47: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    48: tryCatchList(expr, classes, parentenv, handlers)
    49: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    50: tools:::.buildOneVignette("RxODE-events.Rmd", "/home/ripley/R/packages/tests32/RxODE.Rcheck/vign_test/RxODE", TRUE, FALSE, "RxODE-events", "UTF-8", "/tmp/RtmphaaOS4/file71654b8e39a0.rds")
    An irrecoverable exception occurred. R is aborting now ...
    --- re-building ‘RxODE-intro.Rmd’ using rmarkdown
    Warning in engine$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 files failed:
     ‘RxODE-events.Rmd’ ‘RxODE-model-types.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.9.1-4
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
    --- 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: 0.9.1-4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    udunits system database from /usr/local/share/udunits
    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.
    
    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