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

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Sat, 05 Apr 2008 20:03:02 +0100 (BST)

On Sat, 5 Apr 2008, Larry Snyder wrote:

> 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.

It should. One of the things recorded during the build is if -fvisibility=hidden works. So if the compiler has changed, that may have changed (but gcc 4.2.3 should support it). Another thing that is recorded is various paths, and quite possibly the reason this fails is because you are getting the wrong 'cc1' as a result. And definitely if you change your Fortran compiler you need to at least re-configure R, as the Fortran library paths are recorded -- so compiling any package with Fortran code would most likely not work.

(I have actually updated a compiler and found that -fvisibility=hidden was not longer supported -- but that was in the days of gcc3 and extensive RedHat modifications.)

>> 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
>

-- 
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

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Received on Sat 05 Apr 2008 - 19:07:09 GMT

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