----- Original Message ----- > From: "Kevin Ushey" <kevinus...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fhcrc.org> > Cc: "Dirk Eddelbuettel" <e...@debian.org>, "rcpp-devel" > <rcpp-devel@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 < dtene...@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" < e...@debian.org > > > To: "Dan Tenenbaum" < dtene...@fhcrc.org > > > Cc: "rcpp-devel" < rcpp-devel@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@lists.r-forge.r-project.org > > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > > -- > > Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com > > > _______________________________________________ > Rcpp-devel mailing list > Rcpp-devel@lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > _______________________________________________ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
