[Rcpp-devel] undefined symbol: clock_gettime in Rcpp 0.10.2

Martin Morgan mtmorgan at fhcrc.org
Mon Dec 24 09:32:10 CET 2012

On 12/23/2012 10:08 PM, Yan Zhou wrote:
> Just a guess.
> Is it possible that this is caused by the way how R was built? Since you are
> using clang and R unstable, it is clear that you build R yourself.

I usually build with

~/bin$ CC=clang CFLAGS=-g -O0 CXX=clang++ ~/src/R-devel/configure 
--enable-memory-profiling --enable-R-shlib --disable-byte-compiled-packages

Looking at R's config.log carefully, I eventually spotted a difference depending 
on compilation with -O0 (when the symbol is not found) and -O2 (when everything 
is fine). The essence of the test is

~/tmp$ clang -O0 conftest.c
/tmp/conftest-hn9uU6.o: In function `main':
conftest.c:(.text+0x9): undefined reference to `clock_gettime'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
~/tmp$ clang -O2 conftest.c

for either gcc or clang, in R-2-15 or R-devel. conftest.c is, at the end of the day

#include <time.h>

main ()
#ifndef clock_gettime
   char *p = (char *) clock_gettime;

   return 0;

with -O2 succeeding because, well, the 'check' is optimized out (right?). This 
is from R-devel/configure.ac:1835

R_CHECK_FUNCS([clock_gettime timespec_get], [#include <time.h>])
if test "${ac_cv_have_decl_clock_gettime}" = "yes"; then
AC_CHECK_LIB(rt, clock_gettime)

I'm not completely sure of this...


> From the error message, it happens when  "testing if installed package can be
> loaded" and trying to load Rcpp.so through dyn.load. I am not very sure how
> dyn.load works (and thus please ignore me if I am talking non-sense), but
> from the help page it seems that it loads additional shared object into the
> executing R image. On my machine, R was built as a shared library, and ldd
> libR.so shows among other things librt. In other words, librt was loaded when
> R was started. However building Rcpp only builds libraries rather than
> executables, and thus there shouldn't be errors when building Rcpp while
> loading Rcpp may cause errors unless librt was already loaded or linked to
> libRcpp.so
> Another reason that I suspect that this is not a problem with compiler but
> how R is built is that, try the following program,
> #include <time.h>
> int main () { clock_gettime(0,0); }
> with either g++ or clang++, without explicit linking to -lrt, the same
> undefined symbol error occurs. For instance, on my RHEL, with g++ 4.4, $ g++
> -o foo foo.cpp /tmp/ccKB2Ftv.o: In function `main': foo.cpp:(.text+0xf):
> undefined reference to `clock_gettime' collect2: ld returned 1 exit status
> Change main to say, foo, and build a shared or static library without linking
> to librt causes no problems at all (though loading that library will cause
> problems as usual).
> If so far what I am talking is not non-sense, then I suggest you find your
> libR.so library, and check if it indeed does not link to librt. If that is
> the case, we need to find out how to build R to trigger the linking to librt
> (build R with profiling, which is the default?)
> Anyway, as Dirk said, linking to librt is harmless on Linux nonetheless, so
> that is perhaps the easiest 'fix'.
> Best,
> Yan Zhou
> On Dec 24, 2012, at 1:11 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
>> On 23 December 2012 at 18:31, Martin Morgan wrote: | When trying to install
>> Rcpp 0.10.2 with | | $ R --version | R Under development (unstable)
>> (2012-12-18 r61372) -- "Unsuffered Consequences" | $ clang++ --version |
>> Ubuntu clang version 3.0-6ubuntu3 (tags/RELEASE_30/final) (based on LLVM
>> 3.0) | Target: x86_64-pc-linux-gnu | Thread model: posix
>> I just upgraded my r-devel version today; the one I used to test 0.10.2
>> was probably a week or at the most two weeks old. I did quite a few R CMD
>> check runs; they all passed -- but I only used g++.
>> Methinks I could have caught that if I had used clang.
>> | I get | | $ R CMD INSTALL Rcpp_0.10.2.tar.gz | ... | clang++
>> -I/home/mtmorgan/bin/R-devel/include -DNDEBUG -I../inst/include/ |
>> -I/usr/local/include    -fpic  -g -O2  -c Timer.cpp -o Timer.o | ... | **
>> testing if installed package can be loaded | Error in dyn.load(file,
>> DLLpath = DLLpath, ...) : |    unable to load shared object |
>> '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/2.16/Rcpp/libs/Rcpp.so':
|    /home/mtmorgan/R/x86_64-unknown-linux-gnu-library/2.16/Rcpp/libs/Rcpp.so:
>> | undefined symbol: clock_gettime | Error: loading failed | |  From man
>> clock_gettime I have | | ... |         Link with -lrt. | | and adding
>> PKG_LIBS += -lrt to src/Makevars addresses the problem for me, but | I'm
>> not sure that is a universal solution? Also, I had an identical problem
>> with | another package (Matrix, since corrected) so there is perhaps
>> something | a-typical about my configuration.
>> I don't think so. The internal-to-Rcpp Timer class is new in 0.10.2.  And
>> Yan is (as usual) correct, -lrt is AFACR specific to Linux. I needed that
>> in the past when using the kernel-based high-res timer.
>> So this is something we need to figure out. So we seem to know that
>> r-devel and clang need it. Can you check if r-release needs it?  With g++,
>> neither R versions seems to need it.
>> OTOH I don't think adding -lrt does any harm so maybe we'll add "in
>> general". Might run this by Simon too....  This needs more work.
>> Thanks so much for the heads-up!
>> Dirk
>> | | Martin | -- | Computational Biology / Fred Hutchinson Cancer Research
>> Center | 1100 Fairview Ave. N. | PO Box 19024 Seattle, WA 98109 | |
>> Location: Arnold Building M1 B861 | Phone: (206) 667-2793 |
>> _______________________________________________ | Rcpp-devel mailing list |
>> Rcpp-devel at lists.r-forge.r-project.org |
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>> -- Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
>> _______________________________________________ Rcpp-devel mailing list
>> Rcpp-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel

Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

More information about the Rcpp-devel mailing list