I tried compiling using GCC. First, I changed config.site to:
~/R-3.2.2$ svn diff config.site
Index: config.site
===================================================================
--- config.site (revision 69236)
+++ config.site (working copy)
@@ -278,3 +278,8 @@
## Path to the version of pkg-config to be used for locating cairographics.
## PKGCONF =
+F77=gfortran48
+FC=${F77}
+CC=gcc48
+CXX=g++48
+OBJC=gcc48
Then plain-vanilla configure && make worked without a hitch:
~/R-3.2.2$ ./configure
[...]
R is now configured for x86_64-unknown-freebsd10.2
Source directory: .
Installation directory: /usr/local
C compiler: gcc48 -std=gnu99 -g -O2
Fortran 77 compiler: gfortran48 -g -O2
C++ compiler: g++48 -g -O2
C++ 11 compiler: g++48 -std=c++11 -g -O2
Fortran 90/95 compiler: gfortran48 -g -O2
Obj-C compiler: gcc48 -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
"make" completes, and "make check" again fails in datetime.R:
> Sys.setenv(TZ = "Europe/London") # pretty much portable.
> (z <- as.POSIXct("1848-01-01 12:00"))
Error in as.POSIXlt.character(x, tz, ...) :
character string is not in a standard unambiguous format
The next date check is fine, though:
> (z <- as.POSIXct("2040-01-01 12:00"))
[1] "2040-01-01 12:00:00 GMT"
as was the 1848 one when TZ="UTC":
> Sys.setenv(TZ = "UTC")
> (z <- as.POSIXct("1848-01-01 12:00"))
[1] "1848-01-01 12:00:00 UTC"
This is probably a quirk of FreeBSD's datetime support, I'll see what
the port used to do for 3.0.2.
Also, there is an issue tracking updating the port to the current
release: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=195783. I've
posted the summary of this thread there, thanks for your help.
Davor
Prof Brian Ripley writes:
> 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.
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