From ripley at stats.ox.ac.uk  Thu Jun  1 18:37:32 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 1 Jun 2006 17:37:32 +0100 (BST)
Subject: [Rd] package installation errors
In-Reply-To: <447F0F07.7090900@bank-banque-canada.ca>
References: <447F0F07.7090900@bank-banque-canada.ca>
Message-ID: <Pine.LNX.4.64.0606011731310.25888@gannet.stats.ox.ac.uk>

This is a report on a compiler error, not on R.  You could report it to 
RH, but it might be more effective to install gcc 3.4.6 (which works well 
on x86_64).

We've seen quite a few problems with early gcc versions on x86_64: that 
compiler is three years' old, which as I recall was early days for that 
architecture.  (We found it flaky in early 2004.)

On Thu, 1 Jun 2006, Paul Gilbert wrote:

> I installed R-2.3.1 and ran make check without problem, but I am having
> trouble installing several packages  using gcc (GCC) 3.2.3 20030502 (Red
> Hat Linux 3.2.3-53)
> on Red Hat Enterprise Linux AS release 3 (Taroon Update 7) Kernel
> 2.4.21-40.ELsmp on an x86_64
>
> Below are the messages from MCMCpack. Perhaps my systems are messed up?
>
> Paul Gilbert
>
> > install.packages("MCMCpack")
> Warning in install.packages("MCMCpack") : argument 'lib' is missing:
> using /home/mfa/gilp/toolchain/R/asd05546/R-2.3.1/site-library
> --- Please select a CRAN mirror for use in this session ---
> ....
>
> Selection: 3
> trying URL 'http://cran.at.r-project.org/src/contrib/MCMCpack_0.7-2.tar.gz'
> Content type 'application/x-tar' length 303618 bytes
> opened URL
> ==================================================
> downloaded 296Kb
>
> * Installing *source* package 'MCMCpack' ...
> checking for C++ compiler default output file name... a.out
> checking whether the C++ compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking for gcc... gcc
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking ieeefp.h usability... no
> checking ieeefp.h presence... no
> checking for ieeefp.h... no
> checking for trunc... no
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> g++ -I/home/mfa/gilp/toolchain/R/asd05546/R-2.3.1/include
> -I/home/mfa/gilp/toolchain/R/asd05546/R-2.3.1/include
> -I/usr/local/include  -DSCYTHE_COMPILE_DIRECT -DSCYTHE_NO_RANGE   -fpic
> -g -O2 -c distributions.cc -o distributions.o
> distributions.cc: In function `double SCYTHE::INTERNAL::dbinom_raw(const
>   double&, const double&, const double&, const double&)':
> distributions.cc:2048: could not split insn
> (insn:TI 454 450 91 (set (reg:DF 23 rxmm2 [58])
>        (if_then_else:DF (eq (mem:DF (reg/v/u/f:DI 3 rbx [59]) [5 S8 A64])
>                (reg:DF 23 rxmm2 [58]))
>            (reg:DF 21 rxmm0 [160])
>            (const_double:DF 0 [0x0] 0 [0x0] 0 [0x0]))) 660
> {*sse_movdfcc_const0_3} (insn_list 76 (insn_list 450 (nil)))
>    (expr_list:REG_DEAD (reg/v/u/f:DI 3 rbx [59])
>        (expr_list:REG_DEAD (reg:DF 21 rxmm0 [160])
>            (nil))))
> distributions.cc:2048: Internal compiler error in final_scan_insn, at
> final.c:
>   2624
> Please submit a full bug report,
> with preprocessed source if appropriate.
> See <URL:http://bugzilla.redhat.com/bugzilla/> for instructions.
> make: *** [distributions.o] Error 1
> chmod: failed to get attributes of
> `/home/mfa/gilp/toolchain/R/asd05546/R-2.3.1/site-library/MCMCpack/libs/*':
> No such file or directory
> ERROR: compilation failed for package 'MCMCpack'
> ** Removing
> '/home/mfa/gilp/toolchain/R/asd05546/R-2.3.1/site-library/MCMCpack'
>
> The downloaded packages are in
>    /tmp/RtmpZMSbbz/downloaded_packages
> Warning message:
> installation of package 'MCMCpack' had non-zero exit status in:
> install.packages("MCMCpack")
> >
> ====================================================================================
>
> La version fran?aise suit le texte anglais.
>
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>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


[Rd] package installation errors
Prof Brian Ripley