Hopefully fix compiling on Solaris, verbose option

- Only declare the time variable in the C code when needed in the
  derivatives.
- Add the option to show verbose output of cfunction() when compiling
  the model to a shared library.

3 files changed, 39 insertions, 14 deletions

diff --git a/NEWS.md b/NEWS.md
index c9f7efe8..840aaade 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,7 +3,11 @@
 ## MINOR CHANGES
 
 - `vignettes/compiled_models.html`: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.
-- `GNUMakefile`,`vignettes/*`: Clean up vignette generation and include table of contents in HTML vignettes
+- `GNUMakefile`,`vignettes/*`: Clean up vignette generation and include table of contents in HTML vignettes.
+
+## BUG FIXES
+
+- `mkinmod.R()`: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the '-W-no-unused-variable' compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.
 
 # CHANGES in mkin VERSION 0.9-36
 
diff --git a/R/mkinmod.R b/R/mkinmod.R
index 72c4652a..27716899 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -16,7 +16,7 @@
 # You should have received a copy of the GNU General Public License along with

 # this program. If not, see <http://www.gnu.org/licenses/> }}}

 

-mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)

+mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)

 {

   if (is.null(speclist)) spec <- list(...)

   else spec <- speclist

@@ -273,11 +273,12 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
     model$coefmat <- m

   }#}}}

 

-  # Create a function compiled from C code if more than one observed {{{

+  # Try to create a function compiled from C code if more than one observed {{{

   # variable and gcc is available

   if (length(obs_vars) > 1) {

     if (Sys.which("gcc") != "") {

 

+      # Translate the R code for the derivatives to C code

       diffs.C <- paste(diffs, collapse = ";\n")

       diffs.C <- paste0(diffs.C, ";")

 

@@ -313,10 +314,18 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
         diffs.C <- gsub(pattern, replacement, diffs.C)

       }

 

-      if (!quiet) message("Compiling differential equation model from auto-generated C code...")

+      derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric",

+                              f = "numeric", rpar = "numeric", ipar = "integer")

+      

+      # Declare the time variable in the body of the function if it is used

+      derivs_code <- if (spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {

+        paste0("double time = *t;\n", diffs.C)

+      } else {

+        diffs.C

+      }

 

+      # Define the function initializing the parameters

       npar <- length(parms)

-

       initpar_code <- paste0(

         "static double parms [", npar, "];\n",

         paste0("#define ", parms, " parms[", 0:(npar - 1), "]\n", collapse = ""),

@@ -326,14 +335,17 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
         "    odeparms(&N, parms);\n",

         "}\n\n")

 

-      derivs_code <- paste0("double time = *t;\n", diffs.C)

-      derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric",

-                              f = "numeric", rpar = "numeric", ipar = "integer")

+      # Try to build a shared library

+      cf <- try(cfunction(list(func = derivs_sig), derivs_code,

+                          otherdefs = initpar_code,

+                          verbose = verbose,

+                          convention = ".C", language = "C"),

+                silent = TRUE)

 

-      model$cf <- cfunction(list(func = derivs_sig), derivs_code,

-                            otherdefs = initpar_code,

-                            cppargs = "-Wno-unused-variable",

-                            convention = ".C", language = "C")

+      if (!inherits(cf, "try-error")) {

+        if (!quiet) message("Successfully compiled differential equation model from auto-generated C code.")

+        model$cf <- cf

+      }

     }

   }

   # }}}

diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index f6a8fe5d..35372919 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -13,7 +13,7 @@
   in the FOCUS and NAFTA guidance documents are used.

 }

 \usage{

-mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)

+mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)

 }

 \arguments{

   \item{...}{

@@ -45,6 +45,10 @@ mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
   \item{quiet}{

     Should messages be suppressed?

   }

+  \item{verbose}{

+    If \code{TRUE}, passed to \code{\link{cfunction}} if applicable to give

+    detailed information about the C function being built.

+  }

 }

 \value{

   A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, containing 

@@ -80,7 +84,7 @@ mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
 # Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)

 SFO <- mkinmod(parent = list(type = "SFO"))

 

-# One parent compound, one metabolite, both single first order.

+# One parent compound, one metabolite, both single first order

 SFO_SFO <- mkinmod(

   parent = mkinsub("SFO", "m1"),

   m1 = mkinsub("SFO"))

@@ -90,6 +94,11 @@ SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1"),

   m1 = list(type = "SFO"))

 

+# Show details of creating the C function

+SFO_SFO <- mkinmod(

+  parent = mkinsub("SFO", "m1"),

+  m1 = mkinsub("SFO"), verbose = TRUE)

+

 # If we have several parallel metabolites 

 # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)

 m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),