[Rcpp-devel] Mac problem (possibly not Rcpp's fault)

Jay Emerson jayemerson at gmail.com
Tue Apr 5 18:58:01 CEST 2011


I'm making a guess that the R-Forge setup is having the same problems
as we are, though -- more than just RcppModels show that same bus
error.  Executive summary: I now have a local success, with his
information given below, as well as information on one of the
failures; it does indeed appear to be a compiler version issue, as
Romain suspected.  I'll badger the students again to make sure they
are up to date.

Thanks!

The success setup:

R version 2.12.2 (2011-02-25)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

$ g++ --version
i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5664)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ uname -a
Darwin Taylors-MacBook-Pro.local 10.6.0 Darwin Kernel Version 10.6.0:
Wed Nov 10 18:13:17 PST 2010; root:xnu-1504.9.26~3/RELEASE_I386 i386

-------------------------------------
My other student (who couldn't succeed) has an older version it
appears.  She seems to think she installed the newest version of
everything, up apparently not.

dhcp128036180037:R-2.12.2 Grace$ g++ --version
i686-apple-darwin9-g++-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5493)
Copyright (C) 2005 Free Software Foundation, Inc.

dhcp128036180037:Week10 Grace$ uname -a
Darwin dhcp128036046230.central.yale.edu 9.8.0 Darwin Kernel Version
9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386
i386



On Tue, Apr 5, 2011 at 12:14 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
>
> Hi Jay,
>
> Thanks for posting here!
>
> On 5 April 2011 at 11:59, Jay Emerson wrote:
> | I've Rcpp-ified the new package bcp (Bayesian change point analysis)
> | and it seems to work on Linux and Windows.  We're having some Mac
> | problems (and I don't have a Mac).  I have one current and one past
> | student, both getting similar problems in different ways.  For one,
> | she started with (I think) Rcpp installing properly, but the RESULT 1
> | bus error when trying to build bcp.  I recommended she rebuild R from
> | scratch using updated everyting; after doing so, she got a similar bus
> | error RESULT 2, this time in the process of trying to install Rcpp.
> | The other student has the same bus error.
> |
> | I've exhausted my guesses and recommendations.  I note the same bus
> | error appears in some RcppModel logs, at
> |
> | https://r-forge.r-project.org/R/?group_id=155&log=build_mac&pkg=RcppModels&flavor=patched
> |
> | ?? Any advice ??
>
> Hm, it so happens that Romain committed something today (r2950) which seems
> to be around the same or similar spot -- I have not been hit by anything like
> it.  OS X uses g++ 4.2.1 which is starting to pose challenges as we are being
> pushed at the same time to use g++ 4.5 and even 4.6 (now in Debian unstable
> and already used by Kurt on CRAN tests).
>
> We sort-of have 0.9.3 pre-releases; we are being hang-up by a modules issue
> right now we are debugging. Rcpp 0.9.3 may help you -- can you and your
> students try the version from my site at
>
>   http://dirk.eddelbuettel.com/code/rcpp/Rcpp_0.9.3.tar.gz
>
> I just put a new tarball there that corresponds to r2956 which is very
> current.  Passes R CMD check here... but it not 'officially released' so it
> bites your cat and sets your car on fire none of that is our business :)
>
> Romain may have more pertinent help for the OS X issues.
>
> Dirk
>
> | Jay
> |
> |
> | RESULT 1:
> | xiao-yangs-macbook:Week10 Grace$ R CMD INSTALL bcp
> | * installing to library '/Library/Frameworks/R.framework/Resources/library'
> | * installing *source* package 'bcp' ...
> | ** libs
> | make: *** No rule to make target `Cbcp.o', needed by `bcp.so'.  Stop.
> | *** arch - i386
> | g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
> | -I/Library/Frameworks/R.framework/Resources/include/i386
> | -I/usr/local/include
> | -I"/Library/Frameworks/R.framework/Resources/library/Rcpp/include"
> | -fPIC  -g -O2 -c Cbcp.cpp -o Cbcp.o
> | /Library/Frameworks/R.framework/Resources/library/Rcpp/include/Rcpp/internal/export.h:
> | In function 'void Rcpp::internal::export_range__dispatch(SEXPREC*,
> | InputIterator, Rcpp::traits::r_type_primitive_tag)':
> | /Library/Frameworks/R.framework/Resources/library/Rcpp/include/Rcpp/internal/export.h:56:
> | internal compiler error: Bus error
> |
> | Please submit a full bug report,
> | with preprocessed source if appropriate.
> | See <URL:http://developer.apple.com/bugreporter> for instructions.
> | make: *** [Cbcp.o] Error 1
> | ERROR: compilation failed for package 'bcp'
> | * removing '/Library/Frameworks/R.framework/Resources/library/bcp'
> |
> |
> | RESULT 2:
> | I downloaded Xcode 3.1.3 from the web and restarted the computer and
> | compiled R again. But Rcpp still cannot be installed; the error
> | message is the same:
> |
> | > install.packages("Rcpp")
> | --- Please select a CRAN mirror for use in this session ---
> | Loading Tcl/Tk interface ... done
> | trying URL 'http://cran.stat.ucla.edu/src/contrib/Rcpp_0.9.2.tar.gz'
> | Content type 'application/x-tar' length 1921635 bytes (1.8 Mb)
> |
> | opened URL
> | ==================================================
> | downloaded 1.8 Mb
> |
> | * installing *source* package 'Rcpp' ...
> | ** libs
> | g++ -I/Users/Grace/Study/Statistics/2011Spring/STAT662/Week10/R-2.12.2/include
> | -I../inst/include/ -I/usr/local/include    -fPIC  -g -O2 -c Date.cpp
> | -o Date.o
> | ../inst/include/Rcpp/internal/export.h: In function 'void
> | Rcpp::internal::export_range__dispatch(SEXPREC*, InputIterator,
> | Rcpp::traits::r_type_primitive_tag)':
> | ../inst/include/Rcpp/internal/export.h:56: internal compiler error: Bus error
> | Please submit a full bug report,
> | with preprocessed source if appropriate.
> | See <URL:http://developer.apple.com/bugreporter> for instructions.
> | make: *** [Date.o] Error 1
> | ERROR: compilation failed for package 'Rcpp'
> | * removing '/Users/Grace/Study/Statistics/2011Spring/STAT662/Week10/R-2.12.2/library/Rcpp'
> |
> | The downloaded packages are in
> |        '/private/var/folders/rB/rByzYYffEzadShxSslfirU+++TI/-Tmp-/RtmpNVHfDM/downloaded_packages'
> |
> | Updating HTML index of packages in '.Library'
> | Warning message:
> | In install.packages("Rcpp") :
> |  installation of package 'Rcpp' had non-zero exit status
> |
> |
> |
> |
> | --
> | John W. Emerson (Jay)
> | Associate Professor of Statistics
> | Department of Statistics
> | Yale University
> | http://www.stat.yale.edu/~jay
> | _______________________________________________
> | 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
>



-- 
John W. Emerson (Jay)
Associate Professor of Statistics
Department of Statistics
Yale University
http://www.stat.yale.edu/~jay


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