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

Tue Apr 5 19:09:50 CEST 2011

Le 05/04/11 18:58, Jay Emerson a écrit :
> 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

This is it I guess. IIRC R is only currently supported for versions 
greater than leopard (10.5).

(adding simon to the cc, he probably knows better than my vague memory)

> 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
>>
>
>
>

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