[Rcpp-devel] Unable to install RcppArmadillo from CRAN or from SVN archive on Ubuntu 10.10

Douglas Bates bates at stat.wisc.edu
Thu Apr 28 22:14:36 CEST 2011


By way of a postscript, "R CMD check Rcpp" still fails for me on a
segmentation fault in the unit test called test.sugar.asvector on this
setup (Ubuntu 10.10, g++ 4.4.5 and R-2.13.0 installed from the CRAN
repository for Ubuntu packages).


Executing test function test.sugar.asvector  ...
 *** caught segfault ***
address 0x3, cause 'memory not mapped'

Traceback:
 1: .Primitive(".Call")(<pointer: 0x7fdd3f2ae4c7>, x, y, z)
 2: fx(1:4, 1:5, diag(1:5))
 3: func()
...

I'm thinking of becoming a theoretician.  The worst that can happen by
way of hardware/software problems is your pencil point breaking.

On Thu, Apr 28, 2011 at 2:53 PM, Douglas Bates <bates at stat.wisc.edu> wrote:
> I have been facing this problem for months now and I still don't know
> why other users of Ubuntu 10.10 using
>
> $ g++ --version
> g++ (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
> Copyright (C) 2010 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.
>
> can install RcppArmadillo and I can't.  Most recently I tried to
> install the source package from CRAN and got the same error as I have
> been getting for months.
>
>
>> install.packages("RcppArmadillo", repos="http://cran.fhcrc.org")
> Installing package(s) into ‘/home/bates/R/x86_64-unknown-linux-gnu-library/2.13’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.2.19.tar.gz'
> Content type 'application/x-gzip' length 259638 bytes (253 Kb)
> opened URL
> ==================================================
> downloaded 253 Kb
>
> * installing *source* package ‘RcppArmadillo’ ...
> ** libs
> ccache g++ -I/usr/share/R/include
> -I"/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/include"
> -I../inst/include -fpic  -g -Wall -pipe -pedantic -c RcppArmadillo.cpp
> -o RcppArmadillo.o
> ccache g++ -I/usr/share/R/include
> -I"/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/include"
> -I../inst/include -fpic  -g -Wall -pipe -pedantic -c fastLm.cpp -o
> fastLm.o
> g++ -shared -o RcppArmadillo.so RcppArmadillo.o fastLm.o
> -L/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/lib -lRcpp
> -Wl,-rpath,/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/lib
> -llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR
> installing to /home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object
> '/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo/libs/RcppArmadillo.so':
>  /home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo/libs/RcppArmadillo.so:
> undefined symbol: _ZN4arma12arma_version5majorE
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ‘/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo’
> * restoring previous
> ‘/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo’
>
> The downloaded packages are in
>        ‘/tmp/RtmpoJ3I0u/downloaded_packages’
> Warning message:
> In install.packages("RcppArmadillo", repos = "http://cran.fhcrc.org") :
>  installation of package 'RcppArmadillo' had non-zero exit status
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.13.0
>
>
> The version of the source file RcppArmadillo/src/RcppArmadillo.cpp
> that I have (SVN version 3012 for the file - the source code package
> is at SVN version 3023) does indeed use arma::version::major,
> arma::version:minor and arma::version::patch but they aren't defined
> any place that I can see.
>
> What am I missing here?
>


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