From ripley at stats.ox.ac.uk  Sun Apr 20 13:10:49 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sun, 20 Apr 2008 12:10:49 +0100 (BST)
Subject: [Rd] Fortran underscore problem persists on Linux x86/64
 (PR#11206)
In-Reply-To: <480B1D8D.2080808@biomserv.univ-lyon1.fr>
References: <20080419181513.6E73D2834154@mail.pubhealth.ku.dk>
	<480AFDDF.7060905@biomserv.univ-lyon1.fr>
	<alpine.LFD.1.10.0804201023270.31126@gannet.stats.ox.ac.uk>
	<480B1D8D.2080808@biomserv.univ-lyon1.fr>
Message-ID: <alpine.LFD.1.10.0804201141590.3204@auk.stats.ox.ac.uk>

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 Biom?trie et Biologie Evolutive
> Universite Lyon 1
> 43 bd du 11 novembre 1918
> 69622 Villeurbanne Cedex
> T?l. : 04.72.43.29.35
> Fax : 04.72.43.13.88
> jombart at biomserv.univ-lyon1.fr
> http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
> http://adegenet.r-forge.r-project.org/
>
>

-- 
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


[Rd] Fortran underscore problem persists on Linux x86/64 (PR#11206)
Prof Brian Ripley