Merge pull request #795 from nlmixr2/795-cran-issue

CRAN issues
nlmixr2 · Sep 26, 2024 · b1fd587 · b1fd587
2 parents 096e100 + ad80998
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: rxode2
-Version: 3.0.0
+Version: 3.0.1
 Title: Facilities for Simulating from ODE-Based Models
 Authors@R: c(
    person("Matthew L.","Fidler", role = c("aut", "cre"), email = "matthew.fidler@gmail.com", comment=c(ORCID="0000-0001-8538-6691")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# rxode2 3.0.1
+
+- explicitly initialize the order vector to stop valgrind warning (requested from CRAN)
+
 # rxode2 3.0.0
 
 ## Breaking Changes

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,3 @@
-- This works with the new dparser, PreciseSums and lotri to reduce abi linkages
-- This rxode2 combines the rxode2parse rxode2random and rxode2et (as
-  requested by CRAN)
+- explicitly initialized C integer vector `ordS` in rxode2 code to
+  avoid valgrind warning (as requested by CRAN).
+- all other warnings come from the `units` package
diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/man/rmdhunks/rxode2-create-models.Rmd b/man/rmdhunks/rxode2-create-models.Rmd
@@ -1,8 +1,8 @@
-The ODE-based model specification may be coded inside four places: 
+The ODE-based model specification may be coded inside four places:
 
 - Inside a `rxode2({})` block statements:
 
-```{r modBracket}
+``` r
 library(rxode2)
 mod <- rxode2({
   # simple assignment
@@ -15,7 +15,7 @@ mod <- rxode2({
 
 - Inside a `rxode2("")` string statement:
 
-```{r modString}
+``` r
 mod <- rxode2("
   # simple assignment
   C2 <- centr/V2
@@ -27,7 +27,7 @@ mod <- rxode2("
 
 - In a file name to be loaded by rxode2:
 
-```{r modFile} 
+``` r
 writeLines("
   # simple assignment
   C2 <- centr/V2
@@ -38,10 +38,10 @@ writeLines("
 mod <- rxode2(filename='modelFile.rxode2')
 unlink("modelFile.rxode2")
 ```
-  
+
 - In a model function which can be parsed by `rxode2`:
 
-```{r modFun}
+``` r
 mod <- function() {
   model({
     # simple assignment
@@ -94,10 +94,10 @@ For the last type of model (a model function), a call to `rxode2`
 creates a parsed `rxode2` ui that can be translated to the `rxode2`
 compilation model.
 
-```{r}
+``` r
 mod$simulationModel
 
-# or 
+# or
 mod$simulationIniModel
 ```
 

diff --git a/src/genModelVars.h b/src/genModelVars.h
@@ -227,6 +227,9 @@ static inline int sortStateVectorsErrHandle(int prop, int pass, int i) {
 
 static inline SEXP sortStateVectors(SEXP ordS) {
   int *ord = INTEGER(ordS);
+  for (int i = 0; i < Rf_length(ordS); i++) {
+    ord[i] = 0; // explicitly initialize to avoid valgrind warning
+  }
   sbt.o = 0; // we can use sbt.o since all the code has already been output
   sbt.s[0] = 0;
   for (int i = 0; i < tb.de.n; i++) {

diff --git a/tests/testthat/test-000-modelVars.R b/tests/testthat/test-000-modelVars.R
@@ -20,6 +20,7 @@ d/dt(y3) = a3*y1*y2
     et <- eventTable()
     et$add.sampling(seq(0, 20, by = 0.01))
 
+
     out <- solve(rigid, et)
 
     expect_equal(rxModelVars(rigid), rxModelVars(rigid$cmpMgr$rxDll()))

diff --git a/tests/testthat/test-phi.R b/tests/testthat/test-phi.R
@@ -1,106 +1,104 @@
 rxTest({
-  rxTest({
-    test_that("phi/pnorm/qnorm", {
-      expect_equal(phi(1:3), pnorm(1:3))
-      expect_equal(phi(as.double(1:3)), pnorm(as.double(1:3)))
-
-      o <- rxode2({
-        o <- phi(a)
-      })
-
-      expect_equal(
-        rxSolve(o, data.frame(a = 1:3), et(0))$o,
-        pnorm(as.double(1:3))
-      )
-
-      o <- rxode2({
-        o <- pnorm(a)
-      })
-
-      expect_equal(
-        rxSolve(o, data.frame(a = 1:3), et(0))$o,
-        pnorm(as.double(1:3))
-      )
-
-      o <- rxode2({
-        o <- pnorm(a, 0.5)
-      })
-
-      expect_equal(
-        rxSolve(o, data.frame(a = 1:3), et(0))$o,
-        pnorm(as.double(1:3), 0.5)
-      )
-
-      o <- rxode2({
-        o <- pnorm(a, 0.5, 2)
-      })
-
-      expect_equal(
-        rxSolve(o, data.frame(a = 1:3), et(0))$o,
-        pnorm(as.double(1:3), 0.5, 2)
-      )
-
-      suppressMessages(expect_error(rxode2({
-        o <- pnorm()
-      })))
-
-      suppressMessages(expect_error(rxode2({
-        o <- pnorm(a, b, c, d)
-      })))
-
-      o <- rxode2({
-        o <- qnorm(a)
-      })
-
-      expect_equal(
-        rxSolve(o, data.frame(a = 1:3), et(0))$o,
-        suppressWarnings(qnorm(as.double(1:3)))
-      )
-
-      o <- rxode2({
-        o <- qnorm(a, 0.5)
-      })
-
-      expect_equal(
-        rxSolve(o, data.frame(a = 1:3), et(0))$o,
-        suppressWarnings(qnorm(as.double(1:3), 0.5))
-      )
-
-      o <- rxode2({
-        o <- qnorm(a, 0.5, 2)
-      })
-
-      expect_equal(
-        rxSolve(o, data.frame(a = 1:3), et(0))$o,
-        suppressWarnings(qnorm(as.double(1:3), 0.5, 2))
-      )
-
-      suppressMessages(expect_error(rxode2({
-        o <- qnorm()
-      })))
-
-      suppressMessages(expect_error(rxode2({
-        o <- qnorm(a, b, c, d)
-      })))
-
-      m <- rxode2({
-        o <- pnorm(a)
-      })
-
-      skip_if_not_installed("units")
-      expect_error(rxS(m), NA)
-
-      m <- rxode2({
-        o <- pnorm(a, b)
-      })
-
-      expect_error(rxS(m), NA)
-
-      m <- rxode2({
-        o <- pnorm(a, b, c)
-      })
-
-      expect_error(rxS(m), NA)
+  test_that("phi/pnorm/qnorm", {
+    expect_equal(phi(1:3), pnorm(1:3))
+    expect_equal(phi(as.double(1:3)), pnorm(as.double(1:3)))
+
+    o <- rxode2({
+      o <- phi(a)
     })
+
+    expect_equal(
+      rxSolve(o, data.frame(a = 1:3), et(0))$o,
+      pnorm(as.double(1:3))
+    )
+
+    o <- rxode2({
+      o <- pnorm(a)
+    })
+
+    expect_equal(
+      rxSolve(o, data.frame(a = 1:3), et(0))$o,
+      pnorm(as.double(1:3))
+    )
+
+    o <- rxode2({
+      o <- pnorm(a, 0.5)
+    })
+
+    expect_equal(
+      rxSolve(o, data.frame(a = 1:3), et(0))$o,
+      pnorm(as.double(1:3), 0.5)
+    )
+
+    o <- rxode2({
+      o <- pnorm(a, 0.5, 2)
+    })
+
+    expect_equal(
+      rxSolve(o, data.frame(a = 1:3), et(0))$o,
+      pnorm(as.double(1:3), 0.5, 2)
+    )
+
+    suppressMessages(expect_error(rxode2({
+      o <- pnorm()
+    })))
+
+    suppressMessages(expect_error(rxode2({
+      o <- pnorm(a, b, c, d)
+    })))
+
+    o <- rxode2({
+      o <- qnorm(a)
+    })
+
+    expect_equal(
+      rxSolve(o, data.frame(a = 1:3), et(0))$o,
+      suppressWarnings(qnorm(as.double(1:3)))
+    )
+
+    o <- rxode2({
+      o <- qnorm(a, 0.5)
+    })
+
+    expect_equal(
+      rxSolve(o, data.frame(a = 1:3), et(0))$o,
+      suppressWarnings(qnorm(as.double(1:3), 0.5))
+    )
+
+    o <- rxode2({
+      o <- qnorm(a, 0.5, 2)
+    })
+
+    expect_equal(
+      rxSolve(o, data.frame(a = 1:3), et(0))$o,
+      suppressWarnings(qnorm(as.double(1:3), 0.5, 2))
+    )
+
+    suppressMessages(expect_error(rxode2({
+      o <- qnorm()
+    })))
+
+    suppressMessages(expect_error(rxode2({
+      o <- qnorm(a, b, c, d)
+    })))
+
+    m <- rxode2({
+      o <- pnorm(a)
+    })
+
+    skip_if_not_installed("units")
+    expect_error(rxS(m), NA)
+
+    m <- rxode2({
+      o <- pnorm(a, b)
+    })
+
+    expect_error(rxS(m), NA)
+
+    m <- rxode2({
+      o <- pnorm(a, b, c)
+    })
+
+    expect_error(rxS(m), NA)
   })
 })
diff --git a/vignettes/rxode2-syntax.Rmd b/vignettes/rxode2-syntax.Rmd
@@ -13,11 +13,12 @@ vignette: >
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>")
+library(rxode2)
 ```
 
 ## Introduction
 
-This briefly describes the syntax used to define models 
+This briefly describes the syntax used to define models
 that `rxode2` will translate into R-callable compiled code. It also
 describes the communication of variables between `R` and the
 `rxode2` modeling specification.
@@ -35,7 +36,7 @@ describes the communication of variables between `R` and the
 
 ## Bugs and/or deficiencies
 
-- The modulo operator `%%` is currently unsupported. 
+- The modulo operator `%%` is currently unsupported.
 
 ## Note
 
@@ -49,10 +50,10 @@ Below is a commented example to quickly show the capabilities of
 
 ## Example
 
-```{r}
+``` r
 f <- function() {
   ini({
-    
+
   })
   model({
     # An rxode2 model specification (this line is a comment).
@@ -86,18 +87,18 @@ via the `d/dt(identifier)` operator as part of the model specification,
 and which are model parameters via the `params=` argument in `rxode2`
 `solve()` method:
 
-```
+``` r
 m1 <- rxode2(model = ode, modName = "m1")
 
 # model parameters -- a named vector is required
-theta <- 
+theta <-
    c(KA=0.29, CL=18.6, V2=40.2, Q=10.5, V3=297, Kin=1, Kout=1, EC50=200)
 
 # state variables and their amounts at time 0 (the use of names is
 # encouraged, but not required)
 inits <- c(depot=0, centr=0, peri=0, eff=1)
 
-# qd1 is an eventTable specification with a set of dosing and sampling 
+# qd1 is an eventTable specification with a set of dosing and sampling
 # records (code not shown here)
 
 solve(theta, event = qd1, inits = inits)