[Rcpp-devel] Unable to install RcppArmadillo from CRAN or from SVN archive on Ubuntu 10.10
Sean Robert McGuffee
sean.mcguffee at gmail.com
Thu Apr 28 22:20:51 CEST 2011
I don't know if this is useful, but the results from a grep I did on a
different system suggest that include/armadillo_bits/arma_version.hpp might
be a file to look into:
grep -i arma * */* */*/* |grep -i ver
DESCRIPTION: Armadillo library (currently version 1.1.8). Thus users
do not
DESCRIPTION: Armadillo is licensed under the GNU LGPL version 3 or later,
while
NEWS: o Upgraded to Armadillo Version 1.1.8 "Kangaroo Steak"
NEWS: o Upgraded to Armadillo Version 1.1.6 ³Baby Carpet Shark²
NEWS: o Upgraded to Armadillo Version 1.1.4 ³Manta Lodge²
NEWS: o Upgraded to Armadillo Version 1.1.2 ³Flood Kayak²
NEWS: o Upgraded to Armadillo Version 1.1.0 ³Climate Vandal²
html/00Index.html:</div><h2>Documentation for package
‘RcppArmadillo’ version 0.2.16</h2>
include/armadillo: #include "armadillo_bits/arma_version.hpp"
unitTests/runTests.R: stop( "RcppArmadillo unit tests need at least the
version 0.3.5 of inline" )
include/armadillo_bits/arma_version.hpp:// This file is part of the
Armadillo C++ library.
include/armadillo_bits/arma_version.hpp://! \addtogroup arma_version
include/armadillo_bits/arma_version.hpp:#define ARMA_VERSION_MAJOR 1
include/armadillo_bits/arma_version.hpp:#define ARMA_VERSION_MINOR 1
include/armadillo_bits/arma_version.hpp:#define ARMA_VERSION_PATCH 8
include/armadillo_bits/arma_version.hpp:#define ARMA_VERSION_NAME "Kangaroo
Steak"
include/armadillo_bits/arma_version.hpp:struct arma_version
include/armadillo_bits/arma_version.hpp: static const unsigned int major =
ARMA_VERSION_MAJOR;
include/armadillo_bits/arma_version.hpp: static const unsigned int minor =
ARMA_VERSION_MINOR;
include/armadillo_bits/arma_version.hpp: static const unsigned int patch =
ARMA_VERSION_PATCH;
include/armadillo_bits/arma_version.hpp: const char* nickname =
ARMA_VERSION_NAME;
include/armadillo_bits/arma_version.hpp: ss << arma_version::major
include/armadillo_bits/arma_version.hpp: << arma_version::minor
include/armadillo_bits/arma_version.hpp: << arma_version::patch
include/armadillo_bits/arrayops_proto.hpp: convert_cx_scalar(out_eT& out,
const in_eT& in, const typename arma_not_cx<out_eT>::result* junk1 = 0,
const typename arma_not_cx< in_eT>::result* junk2 = 0);
include/armadillo_bits/arrayops_proto.hpp: convert_cx_scalar(out_eT& out,
const std::complex<in_T>& in, const typename arma_not_cx<out_eT>::result*
junk = 0);
include/armadillo_bits/compiler_setup.hpp: #define ARMA_GCC_VERSION
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
include/armadillo_bits/compiler_setup.hpp: #if (ARMA_GCC_VERSION >= 40200)
include/armadillo_bits/compiler_setup.hpp: #if (ARMA_GCC_VERSION >= 40300)
include/armadillo_bits/compiler_setup.hpp: #undef ARMA_GCC_VERSION
include/armadillo_bits/debug.hpp: const char* nickname =
ARMA_VERSION_NAME;
include/armadillo_bits/debug.hpp: << arma_version::major <<
'.' << arma_version::minor << '.' << arma_version::patch
.
.
.
On 4/28/11 4:14 PM, "Douglas Bates" <bates at stat.wisc.edu> wrote:
> 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
>> Œ/home/bates/R/x86_64-unknown-linux-gnu-library/2.13¹
>> (as Œlib¹ 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 ŒRcppArmadillo¹ ...
>> ** 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/RcppA
>> rmadillo.so':
>> /home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo/libs/RcppA
>> rmadillo.so:
>> undefined symbol: _ZN4arma12arma_version5majorE
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> * removing
>> Œ/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo¹
>> * restoring previous
>> Œ/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo¹
>>
>> The downloaded packages are in
>> Œ/tmp/RtmpoJ3I0u/downloaded_packages¹
>> 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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