On Sun, 20 Apr 2008, Thibaut Jombart wrote:
Prof Brian Ripley wrote:
And your machine is? -- you haven't given the 'at a minimum' information
asked for in the posting guide.
Neither example is reproducible on my Fedora 8 x86_64 systems (nor in the
case of tripack, on CRAN's). It will need someone with an affected system
to debug this. One possibility is that they are using double underscores,
where the code does not look right to me -- but few systems do and this
code is the same as in 2.6.2.
For the record, 'iniaqua' is a not a valid Fortran entry point, and all
these issues will go away if you register your package's symbols.
What does nm -g report on the affected DSOs?
My mistake, I thought sessionInfo() would be enough. My system is an Ubuntu
Dapper Drake (6.06.2 LTS, 64 bits version). R installed from the sources,
same for the packages, using install.packages (one warning for tripack: an
unmatched right brace in a manpage). My fortran and C compilers are
respectively g77 and gcc:
g77 -dumpversion
GNU Fortran (GCC) 3.4.6 (Ubuntu 3.4.6-1ubuntu2)
gcc --version
gcc (GCC) 4.0.3 (Ubuntu 4.0.3-1ubuntu5)
Thanks, for code-compilation problems we need that level of detail.
Your problem appears to be that you are mixing gcc4 and g77 (not
recommended), and g77 does use extra underscores, I believe. I have
/* Define if your Fortran compiler appends an extra_underscore to external
names containing an underscore. */
/* #undef HAVE_F77_EXTRA_UNDERSCORE */
/* Define if your Fortran compiler appends an underscore to external
names. */
#define HAVE_F77_UNDERSCORE 1
in src/include/config.h. If the first of these is defined, please try
commenting it out and rebuilding R.
I've found an old Solaris box that still has g77 on, and I can reproduce
this there. I will patch the sources after further testing, but altering
src/include/config.h worked for me.
I was certainly not expecting Ubuntu 7.07 to be using g77, so we need
the same details from Thomas Petzoldt.
BDR
# This may be useful:
ld --version
GNU ld version 2.16.91 20060118 Debian GNU/Linux
# Your request:
nm -g /usr/local/lib64/R-rc/library/tripack/libs/tripack.so
0000000000001f40 T addcst_
0000000000002270 T addnod_
0000000000002820 T areap_
0000000000002890 T bdyadd_
00000000000029c0 T bnodes_
0000000000001cc0 T border_
000000000010c53c A __bss_start
0000000000002a40 T circum_
0000000000002c40 T crtri_
w __cxa_finalize@@GLIBC_2.2.5
0000000000002cd0 T delarc_
0000000000002eb0 T delnb_
0000000000003050 T delnod_
U do_fio
000000000010c53c A _edata
0000000000003910 T edge_
000000000010c568 A _end
U e_wsfe
000000000000a6c8 T _fini
0000000000004570 T getnp_
w __gmon_start__
0000000000005010 T indxcc_
0000000000001740 T inhull_
00000000000014c0 T _init
0000000000005090 T insert_
00000000000050c0 T intadd_
00000000000051f0 T intsec_
0000000000005370 T jrand_
w _Jv_RegisterClasses
0000000000005450 T left_
0000000000005490 T lstptr_
00000000000054c0 T nbcnt_
00000000000054e0 T nearnd_
0000000000001940 T onhull_
0000000000005910 T optim_
0000000000001d10 T qsort_
000000000000a620 T rmshnb_
000000000010c550 B stcom_
0000000000005b90 T store_
0000000000005ba0 T swap_
000000000010c560 B swpcom_
0000000000005d60 T swptst_
U s_wsfe
0000000000005e90 T trfind_
0000000000006730 T trlist_
0000000000006be0 T trlprt_
0000000000007080 T trmesh_
00000000000076a0 T trmshr_
0000000000009d80 T troutp_
0000000000009e80 T troutq_
0000000000008190 T trplot_
00000000000097e0 T trprnt_
0000000000009fc0 T voronoi_
I can see one single difference in the compilation logs for tripack using R
2.6.2 vs R-rc (2008-04-15 r45347), and the same sources:
in R 2.6.2, gcc uses the option -lgcc_s to produce the shared object, which
is not used in R-rc. Command in R 2.6.2 is:
[...]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o tripack.so inhull.o qsort.o tr
ipack.o troutp.o troutq.o voronoi.o -L/usr/lib/gcc/x86_64-linux-gnu/3.4.6
-lg2c -lm -lgcc_s
[...]
I hope this helps. I'd be glad to provide more details if needed.
Regards,
Thibaut.
> sessionInfo()
R version 2.7.0 RC (2008-04-15 r45347)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=fr_FR.UTF-8;LC_NUMERIC=C;LC_TIME=fr_FR.UTF-8;LC_COLLATE=fr_FR.UTF-8;LC_MONETARY=C;LC_MESSAGES=fr_FR.UTF-8;LC_PAPER=fr_FR.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=fr_FR.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tripack_1.2-11
loaded via a namespace (and not attached):
[1] tools_2.7.0
###
Best regards,
Thibaut.
--
######################################
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
http://adegenet.r-forge.r-project.org/
--
Brian D. Ripley, [EMAIL PROTECTED]
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
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
