Merge pull request #213 from metrumresearchgroup/dev

Release 0.8.6
metrumresearchgroup · Mar 16, 2017 · 261e00a · 261e00a
2 parents ec76cb1 + e199adc
commit 261e00a
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,4 @@
+mrgsolve/
 cran-comments.md
 Rchecks
 .github

diff --git a/.github/.gitkeep b/.github/.gitkeep
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mrgsolve
 Type: Package
-Version: 0.8.3.9000
+Version: 0.8.6
 Title: Simulate from ODE-Based Population PK/PD and Systems Pharmacology
     Models
 Authors@R: c(

diff --git a/Makefile b/Makefile
@@ -10,9 +10,18 @@ CHKDIR=Rchecks
 ## Set libPaths:
 ##export R_LIBS=${LIBDIR}
 
+gut_check:
+	Rscript "inst/maintenance/gut_check.R"
+
 pkgdown:
 	Rscript -e 'library(pkgdown)' -e 'build_home()' -e 'build_reference(examples=FALSE)' -e 'build_news()'
 
+test-all:
+	Rscript -e 'library(testthat)' -e 'test_dir("tests/testthat")' -e 'test_dir("inst/maintenance/unit")'
+
+unit:
+	Rscript -e 'library(testthat)' -e 'test_dir("inst/maintenance/unit")'
+
 cran:
 	make doc
 	make build
@@ -53,7 +62,7 @@ check:
 	make doc
 	make build
 	R CMD check ${TARBALL} -o ${CHKDIR}
-
+	make unit
 qcheck: 
 	make doc
 	make build 
@@ -67,11 +76,8 @@ check-cran:
 
 test:
 	R CMD INSTALL ${PKGDIR}
-	Rscript -e 'library(testthat)' -e 'test_dir("tests/testthat")'
+	make test-all
 
-.PHONY: tests
-tests:
-	Rscript inst/maintenance/tests.R
 
 clean:
 	if test -d ${CHKDIR}/mrgsolve.Rcheck; then rm -rf ${CHKDIR}/mrgsolve.Rcheck;fi
@@ -82,3 +88,4 @@ datasets:
 travis:
 	make build
 	R CMD check --as-cran ${TARBALL} -o ${CHKDIR}
+	make test
diff --git a/R/library.R b/R/library.R
@@ -88,14 +88,14 @@ pred_KA = KA*exp(ETA(5));
 ##'
 ##' @examples
 ##'
+##' \dontrun{
 ##' mod <- pkmodel(1)
 ##'
 ##' mod %>% ev(amt=1000, ii=24, addl=3) %>% mrgsim(end=120)
-##'
-##' \dontrun{
 ##' mod <- pkmodel(1,TRUE)
 ##' mod <- pkmodel(2)
 ##' mod <- pkmodel(2,TRUE)
+##' 
 ##' }
 ##'
 ##'

diff --git a/R/mread.R b/R/mread.R
@@ -32,6 +32,7 @@ NULL
 ##'
 ##' @examples
 ##'
+##' \dontrun{ 
 ##' code <- '
 ##' $CMT DEPOT CENT
 ##' $PKMODEL ncmt=1, depot=TRUE
@@ -42,7 +43,7 @@ NULL
 ##' '
 ##'
 ##' mod <- mcode("example",code)
-##'
+##' }
 ##' @export
 mcode <- function(model,code, project=tempdir(),...) {
   mread(model=model,project=project,code=code,...)
@@ -94,7 +95,7 @@ mcode <- function(model,code, project=tempdir(),...) {
 ##' 
 ##' @examples
 ##'
-##'
+##' \dontrun{
 ##' code <- '
 ##' $PARAM CL = 1, VC = 5
 ##' $CMT CENT
@@ -111,7 +112,7 @@ mcode <- function(model,code, project=tempdir(),...) {
 ##' mod <- mread("irm3", modlib())
 ##' 
 ##' mod
-##'
+##' }
 mread <- function(model=character(0),project=getwd(),code=NULL,udll=TRUE,
                   ignore.stdout=TRUE,
                   raw=FALSE,compile=TRUE,audit=TRUE,

diff --git a/R/package.R b/R/package.R
@@ -139,13 +139,13 @@
 ##'
 ##'
 ##' # Internal model library
-##' 
+##' \dontrun{
 ##' mod <- mread("irm1", modlib())
 ##' 
 ##' mod
 ##' 
 ##' mod %>% ev(amt=300, ii=12, addl=3) %>% mrgsim
-##' 
+##' }
 ##'
 NULL
 

diff --git a/R/simtime.R b/R/simtime.R
@@ -41,13 +41,14 @@
 ##' day1 <- c(peak,sparse)
 ##'
 ##' design <- c(day1, day1+72, day1+240)
-##'
+##' 
+##' \dontrun{
 ##' mod <- mrgsolve:::house()
 ##'
 ##' out <- mod %>% ev(amt=1000, ii=24, addl=10) %>% mrgsim(tgrid=design)
 ##'
 ##' plot(out,CP~., type='b')
-##'
+##' }
 tgrid <-  function(start=0,end=24,delta=1,add=numeric(0),.offset=0, .scale=1,...) {
     new("tgrid", start=start, end=end, delta=delta, add=add, offset=.offset, scale=.scale)
 }

diff --git a/R/update.R b/R/update.R
@@ -42,9 +42,11 @@ sval <- unique(c("atol","rtol",
 ##' @name update
 ##' @aliases update,mrgmod-method
 ##' @examples
+##' \dontrun{
 ##'  mod <- mrgsolve:::house()
 ##'
 ##'  mod <- update(mod, end=120, delta=4, param=list(CL=19.1))
+##'  }
 setMethod("update", "mrgmod", function(object,..., merge=TRUE,open=FALSE,data=list()) {
 
     x <- object

diff --git a/inst/base/modelheader.h b/inst/base/modelheader.h
@@ -80,13 +80,13 @@ struct databox {
 // $MAIN, $ODE, and $TABLE get translated into these functions
 // We need ODEFUN___ and INITFUN___ and TABLECODE___ defined in the
 // .cpp.cpp model file
-#define __BEGIN_config__ extern "C" {void __CONFIGFUN___(MRGSOLVE_CONFIG_SIGNATURE) {
+#define __BEGIN_config__ extern "C" { void __CONFIGFUN___(MRGSOLVE_CONFIG_SIGNATURE) {
 #define __END_config__ __DONE__
-#define __BEGIN_ode__ extern "C" {void __ODEFUN___(MRGSOLVE_ODE_SIGNATURE) {
+#define __BEGIN_ode__ extern "C" { void __ODEFUN___(MRGSOLVE_ODE_SIGNATURE) {
 #define __END_ode__ __DONE__
-#define __BEGIN_main__ extern "C" {void __INITFUN___(MRGSOLVE_INIT_SIGNATURE) {
+#define __BEGIN_main__ extern "C" { void __INITFUN___(MRGSOLVE_INIT_SIGNATURE) {
 #define __END_main__ __DONE__
-#define __BEGIN_table__ extern "C" {void __TABLECODE___(MRGSOLVE_TABLE_SIGNATURE) {
+#define __BEGIN_table__ extern "C" { void __TABLECODE___(MRGSOLVE_TABLE_SIGNATURE) {
 #define __END_table__ __DONE__
 #define __DONE__ }}
 

diff --git a/inst/base/mrgsolv.h b/inst/base/mrgsolv.h
@@ -26,6 +26,7 @@
 #include <map>
 #include <string>
 
+
 //! vector of doubles
 typedef std::vector<double> dvec;
 
@@ -35,7 +36,7 @@ typedef std::vector<std::string > svec;
 //! vector of integers
 typedef std::vector<int> ivec;
 
-typedef void refun(void*);
+typedef void (*refun)(void*);
 
 /**
  * @brief Resim functor.
@@ -46,14 +47,14 @@ typedef void refun(void*);
  */
 struct resim {
   //! resim constructor
-  resim(refun* x, void* y) : fun(x), prob(y){}
+  resim(refun x, void* y) : fun(x), prob(y){}
   resim(){}
   void operator()() {
     return fun(prob);
   }
 
 protected:
-  refun* fun; ///< function to call to re-simulate
+  refun fun; ///< function to call to re-simulate
   void* prob; ///< object to pass to re-simulated function
 };
 

diff --git a/inst/include/datarecord.h b/inst/include/datarecord.h
@@ -136,9 +136,10 @@ bool CompByTimePosRec(const rec_ptr& a, const rec_ptr& b);
  */
 struct CompRec {
   inline bool operator()(const rec_ptr& a, const rec_ptr& b) {
-    if(a->time() == b->time())
-      return a->pos()  < b->pos();
-      return a->time() < b->time();
+    if(a->time() == b->time()) {
+      return a->pos() < b->pos();
+    }
+    return a->time() < b->time();
   }
 };
 

diff --git a/inst/include/modelheader.h b/inst/include/modelheader.h
@@ -80,13 +80,13 @@ struct databox {
 // $MAIN, $ODE, and $TABLE get translated into these functions
 // We need ODEFUN___ and INITFUN___ and TABLECODE___ defined in the
 // .cpp.cpp model file
-#define __BEGIN_config__ extern "C" {void __CONFIGFUN___(MRGSOLVE_CONFIG_SIGNATURE) {
+#define __BEGIN_config__ extern "C" { void __CONFIGFUN___(MRGSOLVE_CONFIG_SIGNATURE) {
 #define __END_config__ __DONE__
-#define __BEGIN_ode__ extern "C" {void __ODEFUN___(MRGSOLVE_ODE_SIGNATURE) {
+#define __BEGIN_ode__ extern "C" { void __ODEFUN___(MRGSOLVE_ODE_SIGNATURE) {
 #define __END_ode__ __DONE__
-#define __BEGIN_main__ extern "C" {void __INITFUN___(MRGSOLVE_INIT_SIGNATURE) {
+#define __BEGIN_main__ extern "C" { void __INITFUN___(MRGSOLVE_INIT_SIGNATURE) {
 #define __END_main__ __DONE__
-#define __BEGIN_table__ extern "C" {void __TABLECODE___(MRGSOLVE_TABLE_SIGNATURE) {
+#define __BEGIN_table__ extern "C" { void __TABLECODE___(MRGSOLVE_TABLE_SIGNATURE) {
 #define __END_table__ __DONE__
 #define __DONE__ }}
 

diff --git a/inst/include/mrgsolv.h b/inst/include/mrgsolv.h
@@ -26,6 +26,7 @@
 #include <map>
 #include <string>
 
+
 //! vector of doubles
 typedef std::vector<double> dvec;
 
@@ -35,7 +36,7 @@ typedef std::vector<std::string > svec;
 //! vector of integers
 typedef std::vector<int> ivec;
 
-typedef void refun(void*);
+typedef void (*refun)(void*);
 
 /**
  * @brief Resim functor.
@@ -46,14 +47,14 @@ typedef void refun(void*);
  */
 struct resim {
   //! resim constructor
-  resim(refun* x, void* y) : fun(x), prob(y){}
+  resim(refun x, void* y) : fun(x), prob(y){}
   resim(){}
   void operator()() {
     return fun(prob);
   }
 
 protected:
-  refun* fun; ///< function to call to re-simulate
+  refun fun; ///< function to call to re-simulate
   void* prob; ///< object to pass to re-simulated function
 };
 

diff --git a/inst/include/odeproblem.h b/inst/include/odeproblem.h
@@ -62,16 +62,16 @@ typedef std::vector<rec_ptr> reclist;
 typedef std::vector<reclist> recstack;
 
 //! <code>$MAIN</code> function
-typedef void init_func(MRGSOLVE_INIT_SIGNATURE);
+typedef void (*init_func)(MRGSOLVE_INIT_SIGNATURE);
 
 //! <code>$TABLE</code> function
-typedef void table_func(MRGSOLVE_TABLE_SIGNATURE);
+typedef void (*table_func)(MRGSOLVE_TABLE_SIGNATURE);
 
 //! <code>$ODE</code> function
-typedef void deriv_func(MRGSOLVE_ODE_SIGNATURE);
+typedef void (*deriv_func)(MRGSOLVE_ODE_SIGNATURE);
 
 //! <code>$PREAMBLE</code> function
-typedef void config_func(MRGSOLVE_CONFIG_SIGNATURE);
+typedef void (*config_func)(MRGSOLVE_CONFIG_SIGNATURE);
 
 //! function to hand off to <code>DLSODA</code>
 typedef void main_deriv_func(int* neq, double* t,
@@ -201,6 +201,7 @@ class odeproblem : public odepack_dlsoda {
   void copy_parin(const Rcpp::List& parin);
   void copy_funs(const Rcpp::List& funs);
 
+
 protected:
 
   double* Param; ///< model parameters
@@ -212,10 +213,7 @@ class odeproblem : public odepack_dlsoda {
   dvec Init_dummy; ///< initial conditions for user input
   dvec F; ///< bioavability
   dvec Alag; ///< dosing lag time
-  deriv_func* Derivs; ///< <code>$ODE</code> function
-  init_func* Inits; ///< <code>$MAIN</code> function
-  table_func* Table; ///< <code>$TABLE</code> function
-  config_func* Config; ///< <code>$PREAMBLE</code> function
+
   std::vector<int> On; ///< compartment on/off indicator
   databox d; ///< various data passed to model functions
 
@@ -232,6 +230,12 @@ class odeproblem : public odepack_dlsoda {
   dvec pred; ///< brings clearances, volumes, and kas for advan 1/2/3/4 calculations
   dvec Capture; ///< captured data items
 
+  deriv_func Derivs; ///< <code>$ODE</code> function
+  init_func Inits; ///< <code>$MAIN</code> function
+  table_func Table; ///< <code>$TABLE</code> function
+  config_func Config; ///< <code>$PREAMBLE</code> function
+
+
 };
 
 

diff --git a/inst/maintenance/gut_check.R b/inst/maintenance/gut_check.R
@@ -0,0 +1,5 @@
+source(file.path("inst", "maintenance","maint.R"))
+pkg <- satellite_package(all_tests=TRUE)
+keepdir <- file.path("Rchecks", "gut_check")
+if(!dir.exists(keepdir)) dir.create(keepdir)
+devtools::check(basename(pkg),check_dir=keepdir)
diff --git a/inst/maintenance/maint.R b/inst/maintenance/maint.R
@@ -0,0 +1,20 @@
+
+
+satellite_package <- function(all_tests=FALSE,pkgname="mrgsolve") {
+
+  tmp <- tempdir()
+  chkdir <- file.path(tmp,paste0(pkgname,"_check"))
+  if(dir.exists(chkdir)) unlink(chkdir,recursive=TRUE)
+
+  foo <- devtools::build('.')
+  x <- utils::untar(foo,exdir=chkdir)
+
+  if(all_tests) {
+    xtests <- list.files(file.path("inst","maintenance", "unit"),
+                         full.names=TRUE)  
+    file.copy(xtests,
+              file.path(chkdir, pkgname, "tests", "testthat"),
+              overwrite=TRUE)
+  }
+  file.path(chkdir,pkgname)
+}