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<e...@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@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
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
http://romain-francois.com
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