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

[Dirk Eddelbuettel]

Dan,

[ Impossible Subject:, there is no Rcpp 0.11.1 amywhere yet. ]

On 12 February 2014 at 17:19, Dan Tenenbaum wrote:
| 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:
| 
| lm.br
| RSofia 

They all passed when I did my checks -- Ubuntu 13.10, g++-4.8.  I do not
claim to have the resources to test all package against all compilers.

If you want to retest all CRAN package, I'll happily walk you through my
scripts. Preferably off-list.

| 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:

I was under the impression that you knew you needed to _recompile_. 

| > 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, 

Yes, we knew. That is from the release announcement dated Feb 3 where I say

   [...]  This does however mean that your current packages using Rcpp will
   break, so you need rebuild all packages using Rcpp this one time.  [...]

| and either patched to deal with the compiler/constructor issue, or perhaps
| that issue can be addressed in Rcpp itself. 

Kevin has taken care of the mzR / constructor issue.  May I once again
suggest that you take advantage of the fact he works in your building /
institution and try to sort this out locally?

Thanks so much.

Dirk

| 
| Thanks,
| Dan
| 
| > sessionInfo()
| R version 3.0.2 Patched (2013-12-18 r64488)
| Platform: x86_64-apple-darwin10.8.0 (64-bit)
| 
| locale:
| [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    
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-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com