[Rcpp-devel] CRAN package does not build with Rcpp 0.11.1 and g++ 4.2.1

Dan Tenenbaum dtenenba at fhcrc.org
Thu Feb 13 02:19:03 CET 2014


The CRAN package ConConPiWiFun does not compile under g++ 4.2.1 which is the default compiler on the CRAN build machine (see http://cran.us.r-project.org/web/checks/check_flavors.html, the row r-release-macosx-x86_64).

This has not been a problem so far because the package has not been rebuilt since November 5. But the next time the package is updated, it will fail to build on the CRAN mac build machine, unless the issue that causes the failure is addressed.

The error is:

/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:34: note:                 Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(const Rcpp::Reference_Impl<StoragePolicy>&) [with StoragePolicy = Rcpp::PreserveStorage]
make: *** [Modules.o] Error 1
ERROR: compilation failed for package ‘ConConPiWiFun’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ConConPiWiFun’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ConConPiWiFun’

This is the same error that has been discussed before on this list in the context of the Bioconductor package mzR. 

Apparently the problem is caused by the fact that g++ 4.2.1 does not create a default constructor; clang++ and newer versions of g++ can deal with this. 

This same problem occurs with other CRAN packages, among them:


I didn't test exhaustively; there could be more.

More concerning, installing the binary versions of these packages and then loading them causes errors that may be related to Rcpp:

> library(ConConPiWiFun)
Loading required package: Rcpp
Error in .doLoadActions(where, attach) : 
  error in load action .__A__.1 for package ConConPiWiFun: loadModule(module = "mod_cplfunction", what = TRUE, env = ns, : Unable to load module "mod_cplfunction": unimplemented type 'any' in 'eval'

Error: package or namespace load failed for ‘ConConPiWiFun’

> library(lm.br)
Loading required package: Rcpp

 *** caught segfault ***
address 0x1d00000031, cause 'memory not mapped'
Error in .doLoadActions(where, attach) : 
  error in load action .__A__.1 for package lm.br: loadModule(module = "Clmbr", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "Clmbr": 'getCharCE' must be called on a CHARSXP
Error: package or namespace load failed for ‘lm.br’

> library(RSofia)
Loading required package: Rcpp

 *** caught segfault ***
address 0x0, cause 'unknown'


This suggests that these packages need to be rebuilt against Rcpp 0.11.0, and either patched to deal with the compiler/constructor issue, or perhaps that issue can be addressed in Rcpp itself.


> sessionInfo()
R version 3.0.2 Patched (2013-12-18 r64488)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

More information about the Rcpp-devel mailing list