[R] bug? nlme 3.1-88 compilation under linx

[Prof Brian Ripley]

Why are you asking here if you should submit a bug report on your 
compiler?  This is not a bug in R, but in your compilation enviroment.

If you update your compiler you may well need to reinstall R -- you did 
not mention that you did so.

BTW, R is not setting '-mcpu=i686 -pipe', but your Linux distro may be.


On Sat, 5 Apr 2008, Larry Snyder wrote:

>
>> From http://bugs.r-project.org/cgi-bin/R:
>
>   If you are not sure whether you have observed a bug or not, it is a good
>   idea to ask on the mailing list R-Help by sending an e-mail to
>   r-help at stat.math.ethz.ch rather than submitting a bug report.
>
> I'm wondering whether to submit a bug report on this:
>
> ==============================================================
>> install.packages("nlme")
>   ((several lines removed))
> * Installing *source* package 'nlme' ...
> ** libs
> i686-pc-linux-gnu-gcc -I/usr/lib/R/include -I/usr/lib/R/include
> -I/usr/local/include   -fvisibility=hidden -fPIC  -O2 -mcpu=i686 -pipe
> -std=gnu99 -c corStruct.c -o corStruct.o
> cc1: error: unrecognized option `-fvisibility=hidden'
> make: *** [corStruct.o] Error 1
> ERROR: compilation failed for package 'nlme'
> ==============================================================
>
> Here's my configuration:
>
>> uname -a
>> Linux conception.wustl.edu 2.6.12-gentoo-r9 #3 SMP Mon Aug 29 14:00:05
>> CDT 2005 i686 Intel(R) Pentium(R) 4 CPU 2.80GHz GenuineIntel GNU/Linux
>
> This error occurred after I upgraded my gcc to the newest version (it
> also occurred with the previous version):
>
>> gcc-config -c
>> i686-pc-linux-gnu-4.2.3
>
> To see if the "-fvisibility=hidden" problem was a bug in gcc, I tried
> using it in a toy compilation:
>
>> echo 'main() { }' > in.c
>> gcc  -fvisibility=hidden in.c
>
> This returned without an error.
>
> Then I tried:
>
>> i686-pc-linux-gnu-gcc -I/usr/lib/R/include -I/usr/lib/R/include
>   -I/usr/local/include   -fvisibility=hidden -fPIC  -O2 -mcpu=i686 -pipe
>   -std=gnu99 -c in.c
>> `-mcpu=' is deprecated. Use `-mtune=' or '-march=' instead.
>> in.c:1: warning: return type defaults to 'int'
>
> Conclusion: my gcc seems to accept -fvisibility=hidden.
>
> So: Should I submit a bug report on this?  Thanks -
>
> larry
>
>
>
> --
> Larry Snyder                                  larry at eye-hand.wustl.edu
> Associate Professor of Neurobiology             www.eye-hand.wustl.edu
> Washington University, School of Medicine      Office:  (314) 747-3530
> Dept of Anatomy & Neurobiology,  Box 8108      Lab:     (314) 747-4095
> 660 S Euclid Ave, St. Louis, MO 63110          Fax:     (314) 747-4370
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
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