[R-sig-Debian] configure: error: linking to Fortran libraries from C fails

[Matt Dowle]

Hi all,

Nice one for a Friday afternoon ...

I'm trying to follow this section of the manual :

http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Using-Undefined-Behaviour-Sanitizer

to build R-devel (as of a few hours ago: rev 66684) with 
-fsanitize=undefined,address.

My OS is Linux Mint Debian Edition.  To get gcc-4.9 I added Debian 
testing to my apt sources and ran :

    sudo apt-get install gcc-4.9, g++-4.9 gfortran-4.9

in the root of a clean Rtrunk.  I then started simple with just ASAN 
first of all :

./configure CC="gcc-4.9 -std=gnu99 -fsanitize=address" 
CFLAGS="-fno-omit-frame-pointer -O0 -g -Wall -pedantic -mtune=native" 
--without-recommended-packages --enable-strict-barrier 
--disable-byte-compiled-packages

This runs for a while and then returns the following error :

checking for dummy main to link with Fortran 77 libraries... unknown
configure: error: in `/home/mdowle/R/Rtrunk':
configure: error: linking to Fortran libraries from C fails
See `config.log' for more details

Looking in config.log there are a lot of errors but I believe that's the 
way it works as it tests what is available on the system.  If I change 
"gcc-4.9" to "gcc" (which is 4.8.2 on my system), then it works fine 
(but then I won't be able to do UBSAN with gcc).

Looking at the last error in config.log,  it seems to be this :

configure:23682: gcc-4.9 -std=gnu99 -fsanitize=address -o conftest 
-fno-omit-frame-pointer -O0 -g -Wall -pedantic -mtune=native 
-I/usr/local/include -L/usr/local/lib conftest.c -ldl -lm 
-L/usr/lib/gcc/x86_64-linux-gnu/4.8 -lgfortran -lm -lquadmath >&5
/usr/lib/gcc/x86_64-linux-gnu/4.9/libasan_preinit.o:(.preinit_array+0x0): undefined 
reference to `__asan_init_v3'
/tmp/cchWOhDV.o: In function `_GLOBAL__sub_I_00099_0__main':
/home/mdowle/R/Rtrunk/conftest.c:113: undefined reference to 
`__asan_init_v3'
collect2: error: ld returned 1 exit status
configure:23682: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "R"
| #define PACKAGE_TARNAME "R"
| #define PACKAGE_VERSION "3.2.0"
| #define PACKAGE_STRING "R 3.2.0"
| #define PACKAGE_BUGREPORT "http://bugs.r-project.org"
| #define PACKAGE_URL "http://www.r-project.org"
| #define PACKAGE "R"
| #define VERSION "3.2.0"
| #define R_PLATFORM "x86_64-unknown-linux-gnu"
| #define R_CPU "x86_64"
| #define R_VENDOR "unknown"
| #define R_OS "linux-gnu"
| #define Unix 1
| #define TESTING_WRITE_BARRIER 1
| #define R_ARCH ""
| #define HAVE_VISIBILITY_ATTRIBUTE 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define __EXTENSIONS__ 1
| #define _ALL_SOURCE 1
| #define _GNU_SOURCE 1
| #define _POSIX_PTHREAD_SEMANTICS 1
| #define _TANDEM_SOURCE 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_LIBM 1
| #define HAVE_LIBDL 1
| #define HAVE_READLINE_HISTORY_H 1
| #define HAVE_READLINE_READLINE_H 1
| #define HAVE_LIBREADLINE 1
| #define HAVE_HISTORY_TRUNCATE_FILE 1
| #define HAVE_RL_COMPLETION_MATCHES 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_WAIT_H 1
| #define HAVE_ARPA_INET_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_ELF_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FPU_CONTROL_H 1
| #define HAVE_GLOB_H 1
| #define HAVE_GRP_H 1
| #define HAVE_LANGINFO_H 1
| #define HAVE_NETDB_H 1
| #define HAVE_NETINET_IN_H 1
| #define HAVE_PWD_H 1
| #define HAVE_SCHED_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_SYS_RESOURCE_H 1
| #define HAVE_SYS_SELECT_H 1
| #define HAVE_SYS_SOCKET_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_SYS_TIMES_H 1
| #define HAVE_SYS_UTSNAME_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_UTIME_H 1
| #define HAVE_ERRNO_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_LOCALE_H 1
| #define HAVE_STDARG_H 1
| #define HAVE_STDBOOL_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STRING_H 1
| #define HAVE_DECL_SIGSETJMP 1
| #define HAVE_DECL_SIGLONGJMP 1
| #define HAVE_POSIX_SETJMP 1
| #define HAVE_GLIBC2 1
| #define RETSIGTYPE void
| #define HAVE_INT64_T 1
| #define HAVE_INT_FAST64_T 1
| #define HAVE_DECL_SIZE_MAX 1
| #define R_SOCKLEN_T socklen_t
| #define HAVE_STACK_T 1
| #define HAVE_INTPTR_T 1
| #define HAVE_UINTPTR_T 1
| #define R_INLINE inline
| #define SIZEOF_INT 4
| #define INT_32_BITS 1
| #define SIZEOF_LONG 8
| #define SIZEOF_LONG_LONG 8
| #define SIZEOF_DOUBLE 8
| #define SIZEOF_SIZE_T 8
| #define HAVE_LONG_DOUBLE 1
| #define SIZEOF_LONG_DOUBLE 16
| /* end confdefs.h.  */
| #define F77_DUMMY_MAIN _main
| #ifdef F77_DUMMY_MAIN
|
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int F77_DUMMY_MAIN() { return 1; }
|
| #endif
| int
| main ()
| {
|
|   ;
|   return 0;
| }
configure:23698: result: unknown
configure:23715: error: in `/home/mdowle/R/Rtrunk':
configure:23717: error: linking to Fortran libraries from C fails
See `config.log' for more details

I've searched for the error messages but no luck so far.  Can anyone see 
what I've done wrong?

I just installed  lib64gcc-4.9-dev  as well (includes quadmath and asan 
libraries) but that didn't help, same error as above.

Thanks!
Matt