From ripley at stats.ox.ac.uk  Tue Sep  1 07:50:52 2015
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 1 Sep 2015 06:50:52 +0100
Subject: [Rd] R doesn't compile on FreeBSD 10.2
In-Reply-To: <86si6zzdg5.fsf@stat.ubc.ca>
References: <86fv302hft.fsf@stat.ubc.ca> <55E449DF.7010403@stats.ox.ac.uk>
	<86si6zzdg5.fsf@stat.ubc.ca>
Message-ID: <55E53CBC.1020004@stats.ox.ac.uk>

On 31/08/2015 16:26, Davor Cubranic wrote:
> Prof Brian Ripley writes:
>
>> Second, we don't have all the pertinent information such as the
>> configure options used and the architecture (x86_64?).  I am going to
>> have to guess none as none were mentioned, but using --enable-R-shlib
>> would be pertinent.
>>
>> On 31/08/2015 05:47, Davor Cubranic wrote:
>>> On FreeBSD 10.2, I get the following error when compiling R from the
>>> Subversion trunk (with "configure && make"):
>>
>> You have not told us which revision.  A basic check is to see if you can
>> build the latest released version, as the trunk is 'Under development'.
>
> As suggested, I tried compiling from Subversion tag 3.2.2 (r69054).
> I used no command-line options to 'configure', as mentioned in my
> previous email, and this is the output:
>
>    R is now configured for x86_64-unknown-freebsd10.2
>
>      Source directory:          .
>      Installation directory:    /usr/local
>
>      C compiler:                cc  -g -O2
>      Fortran 77 compiler:       gfortran48  -g -O2
>
>      C++ compiler:              c++  -g -O2
>      C++ 11 compiler:           c++  -std=c++11 -g -O2
>      Fortran 90/95 compiler:    gfortran48 -g -O2
>      Obj-C compiler:	     cc -g -O2 -fobjc-exceptions
>
>      Interfaces supported:      X11, tcltk
>      External libraries:        readline, zlib, bzlib, lzma, PCRE, curl
>      Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
>      Options enabled:           shared BLAS, R profiling
>
>      Capabilities skipped:
>      Options not enabled:       memory profiling
>
>      Recommended packages:      yes
>
> (I thought this, and more, would be included in config.log, but please
> let me know if there is other place to get the configuration details
> that are relevant.)

You need to tell us exactly which commands you used: nowhere records 
everything.

>
> Still the same error:
>
>    --- tools.so ---
>    cc -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o
>    --- all ---
>    --- shlib ---
>    mkdir ../../../../library/tools/libs
>    --- sysdata ---
>    installing 'sysdata.rda'
>    Error in dyn.load(file, DLLpath = DLLpath, ...) :
>      unable to load shared object '/usr/home/davor/R-3.2.2/library/tools/libs/tools.so':
>      /usr/home/davor/R-3.2.2/library/tools/libs/tools.so: Undefined symbol "R_ClassSymbol"
>    Error: unable to load R code in package 'tools'
>    Execution halted
>
>> Here is a series of checks for that symbol (results from a working Linux
>> system):
>>
>> auk% nm -g bin/exec/R  | grep R_ClassSymbol
>> 0000000000962ec0 B R_ClassSymbol
>>
>> auk% nm -g src/main/main.o | grep R_ClassSymbol
>> 0000000000000008 C R_ClassSymbol
>>
>> auk% nm -g library/tools/libs/tools.so  | grep R_ClassSymbol
>>                    U R_ClassSymbol
>>
>> auk% nm -g src/library/tools/src/gramRd.o | grep R_ClassSymbol
>>                    U R_ClassSymbol
>
> Interestintly, checking for R_ClassSymbol gives the same output as on
> your working Linux system:
>
>    ~/R-3.2.2$ nm -g bin/exec/R | grep R_ClassSymbol
>    00000000008f8ff8 B R_ClassSymbol
>
>    ~/R-3.2.2$ nm -g src/main/main.o | grep R_ClassSymbol
>    0000000000000008 C R_ClassSymbol
>
>    ~/R-3.2.2$ nm -g library/tools/libs/tools.so | grep R_ClassSymbol
>                     U R_ClassSymbol
>
>    ~/R-3.2.2$ nm -g src/library/tools/src/gramRd.o | grep R_ClassSymbol
>                     U R_ClassSymbol
>
>> So R_ClassSymbol is unresolved in the tools package and should be
>> resolved by loading into the main R executable. On Linux that is
>> achieved by the linker flag
>>
>> -Wl,--export-dynamic
>>
>> as part of MAIN_LDFLAGS in Makeconf in the top-level directory.  We have
>> in configure.ac
>>
>>     freebsd*)
>>       main_ldflags="-export-dynamic"
>>       shlib_ldflags="-shared"
>>
>> but those were from the days when FreeBSD used gcc, and it is possible
>> that your use of clang[*] requires -Wl,--export-dynamic . If so, add to
>> config.site
>>
>> MAIN_LDFLAGS="-Wl,--export-dynamic"
>>
>> It would also be worth trying a build with --enable-R-shlib, as that
>> resolves R_ClassSymbol and similar differently.
>
> I tried 'configure --enable-R-shlib', still the same error.
>
> I then tried adding MAIN_LDFLAGS as you suggested, and the install
> worked. Thanks you very much! ("make check" fails in datetime.R, but
> that's something I'll follow up in a separate email.)
>
> Should configure.ac be changed to account for this on FreeBSD's using
> clang? (I should probably also try compiling with GCC, which I had to
> install anyways for gfortran.)

It is more complicated than that, in the absence of any definitive 
FreeBSD documentation.  There are five possibilities:

-export-dynamic
-rdynamic
-Wl,--export-dynamic
-Wl,-export-dynamic
-Wl,-E

The first two work for GCC (and have for a long time, although only the 
second is currently documented) and are accepted by compilers claiming 
to be GCC-compliant (clang and icc).  That clang does nothing with the 
first seems a clear bug in clang (at least on some OSes (which from the 
sources do include FreeBSD) it does support the second and maps it to 
the fourth).  Not least as a compiler called 'gcc' may not be 
GCC-compliant (that on OS X is based on clang).

It seems the GNU linker supports all -WL forms (but only the first and 
last are documented): some other linkers require the fourth line.  And 
that means that GCC's -rdynamic on ELF platforms is documented to 
generate a linker flag, -export-dynamic, that the GNU linker is not 
documented to support.

If FreeBSD continues to use ELF and GNU ld, -Wl,--export-dynamic seems 
the safest choice, but if they change linker (and there are/will be 
alternatives such as gold and lld) -rdynamic might be more future-proof.

It seems R has very few FreeBSD users.  The core team cannot be expected 
to support all minority platforms and we rely on the OS teams to inform 
us what is required.  Now it seems that there *is* a FreeBSD port for R: 
https://www.freebsd.org/ports/math.html albeit at R 3.0.2 but updated 
for texinfo 6.0 a couple of months ago, so that is the place to get 
needed changes recorded.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK



[Rd] R doesn't compile on FreeBSD 10.2
Prof Brian Ripley