use tryCatch with error = print around code that throws exceptions

this enables us to set the knitr error=FALSE chunk option to not allow articles with errors to render

Author: jjallaire

_posts/2013-01-13-intro-to-exceptions.md

@@ -22,7 +22,6 @@ by a block of <code>try</code> and <code>catch</code>.
 A simple example will help.
 
 
-
 {% highlight cpp %}
 #include <Rcpp.h>
 
@@ -44,11 +43,11 @@ double takeLog(double val) {
 }
 {% endhighlight %}
 
-
 We can look at this example with a valid, and an invalid argument:
 
 {% highlight r %}
-  takeLog(exp(1))   # works
+# works
+takeLog(exp(1))
 {% endhighlight %}
 
 
@@ -60,16 +59,17 @@ We can look at this example with a valid, and an invalid argument:
 
 
 {% highlight r %}
-  takeLog(-1.0)     # throws exception
+# throws exception
+tryCatch(takeLog(-1.0),
+         error = print)
 {% endhighlight %}
 
 
 
 <pre class="output">
-Error: Inadmissible value
+&lt;std::range_error: Inadmissible value&gt;
 </pre>
 
-
 As we can see, execptions works as expected. By throwing an
 exception derived from the standard exception call, we arrive in
 the case first <code>catch</code> branch where the exception text
@@ -96,11 +96,11 @@ double takeLog2(double val) {
 }
 {% endhighlight %}
 
-
 Again, we can look at this example with a valid, and an invalid argument:
 
 {% highlight r %}
-  takeLog2(exp(1))   # works
+# works
+takeLog2(exp(1))
 {% endhighlight %}
 
 
@@ -112,16 +112,17 @@ Again, we can look at this example with a valid, and an invalid argument:
 
 
 {% highlight r %}
-  takeLog2(-1.0)     # throws exception
+# throws exception
+tryCatch(takeLog2(-1.0),    
+         error = print)
 {% endhighlight %}
 
 
 
 <pre class="output">
-Error: Inadmissible value
+&lt;std::range_error: Inadmissible value&gt;
 </pre>
 
-
 This shows that due to the automatic addition of the needed
 infrastructure, exception handling can add a useful mechanism to
 signal error conditions back to R.
@@ -142,9 +143,9 @@ double takeLog3(double val) {
 }
 {% endhighlight %}
 
-
 {% highlight r %}
-  takeLog3(exp(1))   # works
+# works
+takeLog3(exp(1))
 {% endhighlight %}
 
 
@@ -156,12 +157,13 @@ double takeLog3(double val) {
 
 
 {% highlight r %}
-  takeLog3(-1.0)     # throws exception
+# throws exception
+tryCatch(takeLog3(-1.0), 
+         error = print)
 {% endhighlight %}
 
 
 
 <pre class="output">
-Error: Inadmissible value
+&lt;Rcpp::exception: Inadmissible value&gt;
 </pre>
-

_posts/2013-04-08-rcpp-wrap-and-recurse.md

@@ -64,7 +64,6 @@ List do_stuff( List x_ ) {
 }
 {% endhighlight %}
 
-
 A quick test:
 
 
@@ -86,7 +85,6 @@ print(tmp)
 [[2]]
 [1]  2  4  6  8 10
 </pre>
-
 
 Some notes on the above:
 
@@ -108,7 +106,7 @@ We also check that we fail gracefully when we encounter a non-accepted `SEXP`:
 
 {% highlight r %}
 tryCatch(do_stuff(list(new.env())),
-         error = function(e) print(e))
+         error = print)
 {% endhighlight %}
 
 
@@ -157,7 +155,6 @@ List recurse(List x_) {
 }
 {% endhighlight %}
 
-
 A test case:
 
 
@@ -191,7 +188,6 @@ $z$zy
 [1] 40
 </pre>
 
-
 Note that all we had to do was add a `VECSXP` case in our `switch` statement.
 If we see a list, we call the same `recurse` function on that list, and then
 re-assign the result of that recursive call. Neat!

_posts/2014-03-20-dynamic-dispatch-for-sparse-matrices.md

@@ -54,7 +54,6 @@ arma::mat matmult_cpp(SEXP Xr, const arma::mat Y) {
 }
 {% endhighlight %}
 
-
 **Set up test cases:**
 
 {% highlight r %}
@@ -82,20 +81,19 @@ X_ind <- as(sample(1:d, n, rep=TRUE), "indMatrix")
 Y <- matrix(1:(d*p), d, p)
 {% endhighlight %}
 
-
 **Check exception handling:**
 
 {% highlight r %}
-matmult_cpp(as(X_ind, "ngTMatrix"), Y)
+tryCatch(matmult_cpp(as(X_ind, "ngTMatrix"), Y),
+         error = print)
 {% endhighlight %}
 
 
 
 <pre class="output">
-Error: unknown class of Xr
+&lt;Rcpp::exception: unknown class of Xr&gt;
 </pre>
 
-
 **Dense times dense:**
 
 {% highlight r %}
@@ -150,11 +148,10 @@ benchmark(X_sp%*%Y,
 
 <pre class="output">
                   test replications elapsed relative
-2 matmult_cpp(X_sp, Y)          100   0.009    1.000
-1           X_sp %*% Y          100   0.025    2.778
+2 matmult_cpp(X_sp, Y)          100   0.006    1.000
+1           X_sp %*% Y          100   0.013    2.167
 </pre>
 
-
 **`indMatrix` times dense:**
 
 {% highlight r %}
@@ -179,10 +176,9 @@ benchmark(X_ind%*%Y,
 
 <pre class="output">
                    test replications elapsed relative
-2 matmult_cpp(X_ind, Y)          100   0.013    1.000
-1           X_ind %*% Y          100   0.025    1.923
+2 matmult_cpp(X_ind, Y)          100   0.008      1.0
+1           X_ind %*% Y          100   0.012      1.5
 </pre>
-
 
 Based on [this](http://stackoverflow.com/a/22531129/295025) Q&A on StackOverflow,
 thanks again to Kevin Ushey for his helpful comment.

src/2013-01-13-intro-to-exceptions.cpp

@@ -46,8 +46,12 @@ double takeLog(double val) {
  */
 
 /*** R
-  takeLog(exp(1))   # works
-  takeLog(-1.0)     # throws exception
+# works
+takeLog(exp(1))
+  
+# throws exception
+tryCatch(takeLog(-1.0),
+         error = print)
 */
 
 /**
@@ -81,8 +85,12 @@ double takeLog2(double val) {
  */
 
 /*** R
-  takeLog2(exp(1))   # works
-  takeLog2(-1.0)     # throws exception
+# works
+takeLog2(exp(1))
+  
+# throws exception
+tryCatch(takeLog2(-1.0),    
+         error = print)
 */
 
 /**
@@ -106,6 +114,11 @@ double takeLog3(double val) {
 }
 
 /*** R
-  takeLog3(exp(1))   # works
-  takeLog3(-1.0)     # throws exception
+# works
+takeLog3(exp(1))
+
+# throws exception
+tryCatch(takeLog3(-1.0), 
+         error = print)
 */
+

src/2013-04-08-rcpp-wrap-and-recurse.Rmd

@@ -91,7 +91,7 @@ We also check that we fail gracefully when we encounter a non-accepted `SEXP`:
 
 ```{r tidy=FALSE}
 tryCatch(do_stuff(list(new.env())),
-         error = function(e) print(e))
+         error = print)
 ```
 
 However, this only operates on top-level objects within the list. What if your

src/2014-03-20-dynamic-dispatch-for-sparse-matrices.Rmd

@@ -68,7 +68,8 @@ Y <- matrix(1:(d*p), d, p)
 
 **Check exception handling:**
 ```{r}
-matmult_cpp(as(X_ind, "ngTMatrix"), Y)
+tryCatch(matmult_cpp(as(X_ind, "ngTMatrix"), Y),
+         error = print)
 ```
 
 **Dense times dense:**