F. Privé F. Privé - 2 months ago 31
R Question

Can't use Rcpp engine in R Markdown

I tried to

Knit HTML
the following Rmd file:

---
title: "Untitled"
author: "Florian Privé"
date: "12 septembre 2016"
output: html_document
---

```{r fibCpp, engine='Rcpp'}
#include <Rcpp.h>

// [[Rcpp::export]]
int fibonacci(const int x) {
if (x == 0 || x == 1) return(x);
return (fibonacci(x - 1)) + fibonacci(x - 2);
}
```


I got the following error:

Building shared library for Rcpp code chunk...
Warning message:
l'exécution de la commande 'make -f "C:/PROGRA~1/R/R-33~1.1/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-33~1.1/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="sourceCpp_2.dll" WIN=64 TCLBIN=64 OBJECTS="file110c1d4643e9.o"' renvoie un statut 127


Quitting from lines 11-18 (test.Rmd)
Error in (function (file = "", code = NULL, env = globalenv(), embeddedR = TRUE, :
Error 1 occurred building shared library.
Calls: <Anonymous> ... block_exec -> in_dir -> engine -> do.call -> <Anonymous>
Exécution arrêtée


Am I doing something obviously wrong? Is it a problem related to Windows?

Environment Information from
sessionInfo()



R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] magrittr_1.5 rsconnect_0.4.3 htmltools_0.3.5 tools_3.3.1 yaml_2.1.13
[6] Rcpp_0.12.7 stringi_1.1.1 rmarkdown_1.0 stringr_1.1.0 digest_0.6.10
[11] evaluate_0.9


Rtools install check via
devtools::find_rtools()



[1] TRUE

Answer

Per the debug of Sys.getenv['PATH'] giving:

## PATH                  C:\Program
##                       Files\R\R-3.3.1\bin\x64;C:\ProgramData\Oracle\Java\javapath;C:\Program
##                       Files\NVIDIA GPU Computing
##                       Toolkit\CUDA\v7.5\bin;C:\Program
##                       Files\NVIDIA GPU Computing
##                       Toolkit\CUDA\v7.5\libnvvp;;C:\Program Files
##                       (x86)\Intel\iCLS Client\;C:\Program
##                       Files\Intel\iCLS
##                       Client\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program
##                       Files (x86)\Windows Live\Shared;C:\Program
##                       Files\Intel\Intel(R) Management Engine
##                       Components\DAL;C:\Program
##                       Files\Intel\Intel(R) Management Engine
##                       Components\IPT;C:\Program Files
##                       (x86)\Intel\Intel(R) Management Engine
##                       Components\DAL;C:\Program Files
##                       (x86)\Intel\Intel(R) Management Engine
##                       Components\IPT;C:\Program Files
##                       (x86)\Skype\Phone\;C:\Users\Florian\.dnx\bin;C:\Program
##                       Files\Microsoft DNX\Dnvm\;C:\Program Files
##                       (x86)\NVIDIA
##                       Corporation\PhysX\Common;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Users\Florian\Anaconda3;C:\Users\Florian\Anaconda3\Scripts;C:\Users\Florian\Anaconda3\Library\bin;C:\Program
##                       Files
##                       (x86)\Java\jre1.8.0_101\bin\client;C:\texlive\2015\bin\win32

I think you are falling victim to devtools::find_rtools() throwing a false positive on setup since if it is unable to find Rtools on the system path, it scans for Rtools within the registry and then sets an environment flag. The environment flag does not typically persist while running rmarkdown or during the package build stage.

E.g. If you close all open session R sessions, then open a new R session and only type Rcpp::evalCpp("2 + 2") you will likely trigger a compile error.

The fix for this is simple: Add the Rtools install location to the PATH system variable.

As of Rtools 3.4, the location that must be added to the PATH is:

c:\Rtools\bin;

To modify your PATH variable on windows see either: