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

[Larry Snyder]

On Sat, 5 Apr 2008, Prof Brian Ripley wrote:

> Why are you asking here if you should submit a bug report on your compiler?

I was asking so that I'd get exactly this answer back!

More seriously, I thought there was a chance that the problem was 
specific to the particular compilation, but I know nothing about gcc
and R compilation, so I'm happy to take your word that -

> 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.

I didn't do that.  That shouldn't have anything to do with this problem 
though, right?  But I suppose it's a good idea regardless.  Thanks.


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

Thanks for that, too!

larry



>
>
> 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
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> 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
>

-- 
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