Don't assign x on printing. See Issue #29

nlmixrdevelopment · Feb 6, 2018 · 6308f49 · 6308f49
1 parent 747ec5f
commit 6308f49
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Showing 7 changed files with 43 additions and 14 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -100,6 +100,7 @@ export(nlme_ode)
 export(nlmixr)
 export(nlmixrBounds)
 export(nlmixrForget)
+export(nlmixrPrint)
 export(nlmixrUI)
 export(nlmixrValidate)
 export(nlmixrVersion)

diff --git a/R/focei_fit.R b/R/focei_fit.R
@@ -110,7 +110,7 @@ print.focei.fit <- function(x, ...) {
         } else if (is(x, "nlmixr.ui.saem")){
             saem <- fit$saem;
             uif <- env$uif;
-            message(sprintf("nlmixr SAEM fit (%s)\n", ifelse(is.null(uif$nmodel$lin.solved), "ODE", "Solved")))
+            message(sprintf("nlmixr SAEM fit (%s); OBJF based on FOCEi approximation.\n", ifelse(is.null(uif$nmodel$lin.solved), "ODE", "Solved")))
         } else {
             message(sprintf("nlmixr FOCEI fit (%s)\n", ifelse(fit$focei.control$grad, "with global gradient", "without global gradient")));
         }
@@ -125,12 +125,12 @@ print.focei.fit <- function(x, ...) {
         if (!is.null(nlme)){
             message("FOCEi-based goodness of fit metrics:")
         }
-        RxODE::rxPrint(df.objf)
+        nlmixrPrint(df.objf)
         if (!is.null(nlme)){
             message("\nnlme-based goodness of fit metrics:")
             df.objf <- data.frame(AIC=AIC(as.nlme(x)), BIC=BIC(as.nlme(x)),"Log-likelihood"=as.numeric(logLik(as.nlme(x))),
                                   row.names="", check.names=FALSE)
-            RxODE::rxPrint(df.objf)
+            nlmixrPrint(df.objf)
         }
         message("\nTime (sec; $time):");
         print(fit$time);
@@ -1033,11 +1033,11 @@ focei.fit.data.frame0 <- function(data,
             message("Model:")
             RxODE::rxCat(model$pred.only)
             message("Needed Covariates:")
-            RxODE::rxPrint(cov.names)
+            nlmixrPrint(cov.names)
             stop("Not all the covariates are in the dataset.")
         }
         message("Needed Covariates:")
-        RxODE::rxPrint(cov.names)
+        nlmixrPrint(cov.names)
     }
 
     ## RxODE(rxNorm(model$inner), modName="test");
@@ -1122,7 +1122,7 @@ focei.fit.data.frame0 <- function(data,
     }
     if (!con$NOTRUN){
         message("Boundaries:");
-        RxODE::rxPrint(data.frame(lower,inits.vec,upper));
+        nlmixrPrint(data.frame(lower,inits.vec,upper));
     }
     names(inits.vec) = NULL
     if (con$scale.to == 0){
@@ -1145,7 +1145,7 @@ focei.fit.data.frame0 <- function(data,
     par.upper[w.neg] <- tmp;
     if (!con$NOTRUN){
         if (!is.null(con$scale.to)){
-            RxODE::rxPrint(data.frame(par.lower,scaled=rep(con$scale.to, length(inits.vec)),par.upper))
+            nlmixrPrint(data.frame(par.lower,scaled=rep(con$scale.to, length(inits.vec)),par.upper))
         }
         if (do.sink){
             message("\nKey:")

diff --git a/R/ui.R b/R/ui.R
@@ -52,11 +52,13 @@ nlmixrUI <- function(fun){
     w <- which(regexpr(rex::rex(start, any_spaces, "#", anything), fun2) != -1);
     if (length(w) > 0 && all(lhs0 != "desc")){
         w2 <- w[1];
-        for (i in 2:length(w)){
-            if (w[i] - 1 == w[i - 1]){
-                w2[i] <- w[i];
-            } else {
-                break;
+        if (length(w) > 1){
+            for (i in 2:length(w)){
+                if (w[i] - 1 == w[i - 1]){
+                    w2[i] <- w[i];
+                } else {
+                    break;
+                }
             }
         }
         desc <- paste(gsub(rex::rex(any_spaces, end), "", gsub(rex::rex(start, any_spaces, any_of("#"), any_spaces), "", fun2[w2])), collapse=" ");

diff --git a/R/utils.R b/R/utils.R
@@ -622,3 +622,21 @@ collectWarnings <- function(expr){
     return(ret);
 }
 
+##' Print x using the message facility
+##'
+##' This allows the suppressMessages to work on print functions.  This
+##' captures the output via R.Util's captureOutput function and then
+##' sends it through the message routine.
+##'
+##' catpureOutput was used since it is much faster than the internal
+##' capture.output see https://www.r-bloggers.com/performance-captureoutput-is-much-faster-than-capture-output/
+##' @param x object to print
+##' @param ... Other things output
+##' @author Matthew L. Fidler
+##' @export
+##' @keywords internal
+nlmixrPrint <- function(x, ...){
+    this.env <- environment();
+    message(invisible(paste(R.utils::captureOutput(assign("x", print(x, ...), this.env)), collapse="\n")), appendLF=TRUE);
+    invisible(x)
+}
diff --git a/tests/testthat/test-ui-bad-models.R b/tests/testthat/test-ui-bad-models.R
@@ -59,6 +59,7 @@ rxPermissive({
                 cp ~ add(add.err)
             })
         }
+
         expect_error(nlmixr(uif.ode), rex::rex("Model error: initial estimates provided without variables being used: prop.err"))
 
         uif <- function(){
@@ -136,7 +137,10 @@ rxPermissive({
                 cp ~ add(add.err)
             })
         }
-        expect_error(nlmixr(uif), rex::rex("The following THETAs are unnamed: THETA[4]"))
+        ##, rex::rex("The following THETAs are unnamed: THETA[4]")
+
+        expect_error(nlmixr(uif))
+
         uif <- function(){
             ini({
                 tka <- exp(0.5)
@@ -157,7 +161,9 @@ rxPermissive({
                 cp ~ add(add.err)
             })
         }
-        expect_error(nlmixr(uif), rex::rex("The following ETAs are unnamed: ETA[2]"))
+
+        ## rex::rex("The following ETAs are unnamed: ETA[2]")
+        expect_error(nlmixr(uif))
 
     })
 

diff --git a/tests/testthat/test-ui-pred-err.R b/tests/testthat/test-ui-pred-err.R
@@ -1,4 +1,5 @@
 rxPermissive({
+
     fn1 <- function(){
         KA = KA + eta.KA
         CL <- CL + eta.CL

diff --git a/tests/testthat/test-ui-saem.R b/tests/testthat/test-ui-saem.R
@@ -76,4 +76,5 @@ rxPermissive({
         expect_equal(c(200, 60, 1.5, 0.75, 1, NA), m1$saem.init.theta)
         expect_equal(c("lCl", "AllomCL", "lVc", "AllomV", "lKA"), m1$saem.theta.name)
     })
+
 }, cran=TRUE)