Improved way to have persistent DLLs for mkinmod

Depends on inline >= 0.16.2 (including the bug fixes from
eddelbuettel/inline#18), which provides 'moveDLL' to store the DLL for a
compiled function in a safe place in case the argument 'dll_dir' is
specified in the call to 'mkinmod'.

Huge thanks to Dirk @eddelbuettel for his review and support
for the work on the inline package.

7 files changed, 67 insertions, 51 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 0953d07e..f1e4f169 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,7 +17,7 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006,
   note that no warranty is implied for correctness of results or fitness for a
   particular purpose.
 Depends: R (>= 2.15.1), parallel
-Imports: stats, graphics, methods, deSolve, R6, inline (>= 0.3.17), numDeriv,
+Imports: stats, graphics, methods, deSolve, R6, inline (>= 0.3.16.2), numDeriv,
   lmtest, pkgbuild, nlme (>= 3.1-150.1), purrr, saemix (>= 3.1.9000)
 Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr,
   benchmarkme, tibble, stats4
diff --git a/R/mkinfit.R b/R/mkinfit.R
index e482285d..a6efc858 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -479,10 +479,6 @@ mkinfit <- function(mkinmod, observed,
       solution_type = "analytical"
     } else {
       if (!is.null(mkinmod$cf) & use_compiled[1] != FALSE) {
-        try_dynlib <- try(inline::getDynLib(mkinmod$cf)[["path"]])
-        if (inherits(try_dynlib, "try-error")) {
-          mkinmod$cf <- inline::readDynLib(mkinmod$cf_name, mkinmod$cf_dir)
-        }
         solution_type = "deSolve"
       } else {
         if (is.matrix(mkinmod$coefmat)) {
diff --git a/R/mkinmod.R b/R/mkinmod.R
index 434282fd..a7353e81 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -11,6 +11,7 @@
 #' of the system of differential equations is included in the resulting
 #' mkinmod object in some cases, speeding up the solution.
 #'
+#' If a C compiler is found by [pkgbuild::has_compiler()] and there
 #' is more than one observed variable in the specification, C code is generated
 #' for evaluating the differential equations, compiled using
 #' [inline::cfunction()] and added to the resulting mkinmod object.
@@ -34,15 +35,21 @@
 #'   formation fractions are always used (default).  If "min", a minimum use of
 #'   formation fractions is made, i.e. each pathway to a metabolite has its
 #'   own rate constant.
-#' @param name A name for the model. Should be a valid R object name.
 #' @param speclist The specification of the observed variables and their
 #'   submodel types and pathways can be given as a single list using this
 #'   argument. Default is NULL.
 #' @param quiet Should messages be suppressed?
 #' @param verbose If \code{TRUE}, passed to [inline::cfunction()] if
 #'   applicable to give detailed information about the C function being built.
-#' @param cf_dir Directory where CFunc objects should be saved. Specifying
-#'   'cf_dir' without specifying a 'name' for the object is an error.
+#' @param name A name for the model. Should be a valid R object name.
+#' @param dll_dir Directory where an DLL object, if generated internally by
+#'   [inline::cfunction()], should be saved.  The DLL will only be stored in a
+#'   permanent location for use in future sessions, if 'dll_dir' and 'name'
+#'   are specified.
+#' @param unload If a DLL from the target location in 'dll_dir' is already
+#'   loaded, should that be unloaded first?
+#' @param overwrite If a file exists at the target DLL location in 'dll_dir',
+#'   should this be overwritten?
 #' @importFrom methods signature
 #' @return A list of class \code{mkinmod} for use with [mkinfit()],
 #'   containing, among others,
@@ -95,12 +102,20 @@
 #' \dontrun{
 #'  fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
 #'
-#'  # Now supplying full names used for plotting, and write to user defined location
+#'  # Now supplying compound names used for plotting, and write to user defined location
+#'  # We need to choose a path outside the session tempdir because this gets removed
+#'  DLL_dir <- "~/.local/share/mkin"
+#'  if (!dir.exists(DLL_dir)) dir.create(DLL_dir)
 #'  SFO_SFO.2 <- mkinmod(
 #'    parent = mkinsub("SFO", "m1", full_name = "Test compound"),
 #'    m1 = mkinsub("SFO", full_name = "Metabolite M1"),
-#'    name = "SFOSFO", cf_dir = tempdir())
-#' fit_sfo_sfo <- mkinfit(SFO_SFO.2, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
+#'    name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE)
+#' # Now we can save the model and restore it in a new session
+#' saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds")
+#' # Terminate the R session here if you would like to check, and then do
+#' library(mkin)
+#' SFO_SFO.3 <- readRDS("~/SFO_SFO.rds")
+#' fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
 #'
 #' # Show details of creating the C function
 #' SFO_SFO <- mkinmod(
@@ -126,15 +141,17 @@
 #'
 #' @export mkinmod
 mkinmod <- function(..., use_of_ff = "max", name = NULL,
-  speclist = NULL, quiet = FALSE, verbose = FALSE, cf_dir = NULL)
+  speclist = NULL, quiet = FALSE, verbose = FALSE, dll_dir = NULL,
+  unload = FALSE, overwrite = FALSE)
 {
   if (is.null(speclist)) spec <- list(...)
   else spec <- speclist
   obs_vars <- names(spec)
 
-  if (!is.null(cf_dir)) {
-    if (!dir.exists(cf_dir)) stop(cf_dir, " does not exist")
-    if (is.null(name)) stop("You must give a name if you want to use 'cf_dir'")
+  save_msg <- "You need to specify both 'name' and 'dll_dir' to save a model DLL"
+  if (!is.null(dll_dir)) {
+    if (!dir.exists(dll_dir)) stop(dll_dir, " does not exist")
+    if (is.null(name)) stop(save_msg)
   }
 
   # Check if any of the names of the observed variables contains any other
@@ -310,7 +327,7 @@ mkinmod <- function(..., use_of_ff = "max", name = NULL,
     } #}}}
   } #}}}
 
-  model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff)
+  model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff, name = name)
 
   # Create coefficient matrix if possible #{{{
   if (mat) {
@@ -438,26 +455,19 @@ mkinmod <- function(..., use_of_ff = "max", name = NULL,
       "}\n\n")
 
     # Try to build a shared library
-    cf <- try(inline::cfunction(derivs_sig, derivs_code,
+    model$cf <- try(inline::cfunction(derivs_sig, derivs_code,
       otherdefs = initpar_code,
-      verbose = verbose,
+      verbose = verbose, name = "diffs",
       convention = ".C", language = "C"),
       silent = TRUE)
 
-    if (!inherits(cf, "try-error")) {
-      if (is.null(cf_dir)) {
-        model$cf <- cf
+    if (!inherits(model$cf, "try-error")) {
+      if (is.null(dll_dir)) {
         if (!quiet) message("Temporary DLL for differentials generated and loaded")
+        dll_info <- inline::getDynLib(model$cf)
       } else {
-        cf_file <- inline::writeDynLib(cf, name, cf_dir)
-        model$cf <- inline::readDynLib(name, cf_dir)
-        model$cf_name <- name
-        model$cf_dir <- cf_dir
-        fileDLL <- inline::getDynLib(model$cf)[["path"]]
-        if (!quiet) {
-          message("CFunc object written to ", cf_file)
-          message("DLL written to ", fileDLL)
-        }
+        dll_info <- inline::moveDLL(model$cf, name, dll_dir,
+          unload = unload, overwrite = overwrite, verbose = !quiet)
       }
     }
   }
diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index a294a114..277c3604 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -169,18 +169,13 @@ mkinpredict.mkinmod <- function(x,
 
   if (solution_type == "deSolve") {
     if (!is.null(x$cf) & use_compiled[1] != FALSE) {
-      DLL <- try(inline::getDynLib(x$cf))
-      if (inherits(DLL, "try-error")) {
-        x$cf <- inline::readDynLib(x$cf_name, x$cf_dir)
-      }
-      cf_env <- environment(x$cf)
 
       out <- deSolve::ode(
         y = odeini,
         times = outtimes,
-        func = cf_env$name,
+        func = "diffs",
         initfunc = "initpar",
-        dllname = cf_env$f,
+        dllname = inline::getDynLib(x$cf)[["name"]],
         parms = odeparms[x$parms], # Order matters when using compiled models
         method = method.ode,
         atol = atol,
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index f71ebfb3..77319aac 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -13,7 +13,9 @@ mkinmod(
   speclist = NULL,
   quiet = FALSE,
   verbose = FALSE,
-  cf_dir = NULL
+  dll_dir = NULL,
+  unload = FALSE,
+  overwrite = FALSE
 )
 
 \method{print}{mkinmod}(x, ...)
@@ -53,8 +55,16 @@ argument. Default is NULL.}
 \item{verbose}{If \code{TRUE}, passed to \code{\link[inline:cfunction]{inline::cfunction()}} if
 applicable to give detailed information about the C function being built.}
 
-\item{cf_dir}{Directory where CFunc objects should be saved. Specifying
-'cf_dir' without specifying a 'name' for the object is an error.}
+\item{dll_dir}{Directory where an DLL object, if generated internally by
+\code{\link[inline:cfunction]{inline::cfunction()}}, should be saved.  The DLL will only be stored in a
+permanent location for use in future sessions, if 'dll_dir' and 'name'
+are specified.}
+
+\item{unload}{If a DLL from the target location in 'dll_dir' is already
+loaded, should that be unloaded first?}
+
+\item{overwrite}{If a file exists at the target DLL location in 'dll_dir',
+should this be overwritten?}
 
 \item{x}{An \code{\link{mkinmod}} object.}
 
@@ -120,6 +130,7 @@ For kinetic models with more than one observed variable, a symbolic solution
 of the system of differential equations is included in the resulting
 mkinmod object in some cases, speeding up the solution.
 
+If a C compiler is found by \code{\link[pkgbuild:has_compiler]{pkgbuild::has_compiler()}} and there
 is more than one observed variable in the specification, C code is generated
 for evaluating the differential equations, compiled using
 \code{\link[inline:cfunction]{inline::cfunction()}} and added to the resulting mkinmod object.
@@ -143,12 +154,16 @@ print(SFO_SFO)
 \dontrun{
  fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
 
- # Now supplying full names used for plotting, and write to user defined location
+ # Now supplying compound names used for plotting, and write to user defined location
  SFO_SFO.2 <- mkinmod(
    parent = mkinsub("SFO", "m1", full_name = "Test compound"),
    m1 = mkinsub("SFO", full_name = "Metabolite M1"),
-   name = "SFOSFO", cf_dir = tempdir())
-fit_sfo_sfo <- mkinfit(SFO_SFO.2, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
+   name = "SFO_SFO", dll_dir = "~/dll", unload = TRUE, overwrite = TRUE)
+# Now we can save the model and restore it in a new session
+saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds")
+# Terminate the R session here if you would like to check, and then do
+SFO_SFO.3 <- readRDS("~/SFO_SFO.rds")
+fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")
 
 # Show details of creating the C function
 SFO_SFO <- mkinmod(
diff --git a/test.log b/test.log
index 844c7542..67fd66c4 100644
--- a/test.log
+++ b/test.log
@@ -6,8 +6,8 @@ Testing mkin
 ✔ |   2       | Export dataset for reading into CAKE
 ✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ |   7       | Fitting the SFORB model [3.4 s]
-✔ |   5       | Analytical solutions for coupled models [3.1 s]
+✔ |   7       | Fitting the SFORB model [3.2 s]
+✔ |   5       | Analytical solutions for coupled models [2.9 s]
 ✔ |   5       | Calculation of Akaike weights
 ✔ |  10       | Confidence intervals and p-values [1.0 s]
 ✔ |  14       | Error model fitting [4.3 s]
@@ -33,15 +33,15 @@ Skip (test_plot.R:25:3): Plotting mkinfit and mmkin objects is reproducible
 Reason: getRversion() < "4.1.0"  is TRUE
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |   4       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
 ✔ |   4       | Summary [0.1 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s]
-✔ |   9       | Hypothesis tests [7.1 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.0 s]
+✔ |   9       | Hypothesis tests [6.4 s]
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 38.5 s
+Duration: 36.9 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 ● getRversion() < "4.1.0"  is TRUE (3)
diff --git a/vignettes/mkin.html b/vignettes/mkin.html
index 43481d8f..1f696c37 100644
--- a/vignettes/mkin.html
+++ b/vignettes/mkin.html
@@ -11,7 +11,7 @@
 
 <meta name="author" content="Johannes Ranke" />
 
-<meta name="date" content="2020-11-24" />
+<meta name="date" content="2020-11-27" />
 
 <title>Introduction to mkin</title>
 
@@ -1631,7 +1631,7 @@ div.tocify {
 
 <h1 class="title toc-ignore">Introduction to mkin</h1>
 <h4 class="author">Johannes Ranke</h4>
-<h4 class="date">2020-11-24</h4>
+<h4 class="date">2020-11-27</h4>
 
 </div>