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

From: "Dirk Eddelbuettel" <edd at debian.org>
To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
Cc: "rcpp-devel" <rcpp-devel at lists.r-forge.r-project.org>
Sent: Wednesday, February 12, 2014 6:09:38 PM
Subject: Re: [Rcpp-devel] CRAN package does not build with Rcpp 0.11.1 and g++	4.2.1


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