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

Thu Feb 13 04:13:49 CET 2014

----- Original Message -----
> From: "Kevin Ushey" <kevinushey at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Dirk Eddelbuettel" <edd at debian.org>, "rcpp-devel" <rcpp-devel at lists.r-forge.r-project.org>
> Sent: Wednesday, February 12, 2014 6:53:01 PM
> Subject: Re: [Rcpp-devel] CRAN package does not build with Rcpp 0.11.1 and g++ 4.2.1
> 
> 
> Yes, the patch is trivial. Dan, we can try installing the latest
> version of Rcpp on GitHub on the BioC Mac build machine and confirm
> that these packages do build on Mac with llvm-g++4.2. 

OK, I will do that and get back to you.

> And I agree
> that either 1. CRAN needs to rebuild the binaries for packages
> linking to Rcpp, or 2. these package maintainers need to send a
> maintenance bump. Of course, they can do neither until we submit a
> fixed version of Rcpp to CRAN, because essentially the bug means,
> IIUC, that any package using Rcpp Modules cannot be built with
> llvm-g++4.2.
> 
> 
> My opinion is that we should submit a maintenance release after
> issues on everyone's favourite OS, Solaris, are confirmed to be
> worked out.

That's great. 

Thanks,
Dan

> 
> 
> Cheers,
> Kevin
> 
> 
> 
> On Wed, Feb 12, 2014 at 6:44 PM, Dan Tenenbaum < dtenenba at fhcrc.org >
> wrote:
> 
> 
> Hi Dirk,
> 
> Sorry for the typo in my subject.
> 
> Very briefly:
> 
> There are three CRAN packages (probably more) that can't be run from
> binaries and they can't be recompiled (with CRAN's default compiler
> for the platform).
> 
> Therefore anyone who wants to use these 3 packages on a Mac is SOL.
> They could compile them if they downloaded Xcode and clang. That's
> asking a lot more than we typically ask of CRAN users on a Mac. I'm
> talking about ordinary end users, not developers.
> 
> All three packages can be fixed with a patch like the one Kevin made
> for mzR. But that patch belongs in Rcpp. If the patch is not applied
> to Rcpp, it does no good to other packages which we still haven't
> discovered won't build with g++ 4.2.1.
> 
> If you knew that all packages with dependencies on Rcpp would need to
> be rebuilt, why did you not ask the maintainers of all these
> packages to bump their version numbers? That would solve the problem
> in many cases (or at least expose cases where there were g++ 4.2.1
> compilation problems). Instead CRAN is pushing out unusable binaries
> to the world. Seems to me it's a lot simpler to do the rebuilding
> once -- on CRAN -- than to ask Mac and Windows non-developer users
> to do it, over and over, using software not installed by default on
> those platforms. This means that all the automated building that
> CRAN does every day is for naught, as far as these
> packages/platforms are concerned.
> 
> I am trying to help, here. This is not about solving problems at
> Bioconductor--I'm trying to point out problems lurking on CRAN. It's
> wonderful that Kevin is in my building but that's not germane here.
> 
> I think the patch required for Rcpp is trivial--Kevin can correct me
> if I'm wrong.
> 
> Dan
> 
> 
> 
> 
> 
> 
> 
> ----- Original Message -----
> > 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
> > | _______________________________________________
> > | Rcpp-devel mailing list
> > | Rcpp-devel at lists.r-forge.r-project.org
> > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> > --
> > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
> > 
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