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

From: Larry Snyder <larry_at_eye-hand.wustl.edu>
Date: Sat, 05 Apr 2008 08:12:32 -0500 (CDT)

>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 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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Received on Sat 05 Apr 2008 - 13:24:11 GMT

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