mxcl/homebrew — Issue #10420: brew install R fails
Author: crd1859
Created: 2012-02-23 07:32:05+00:00
State: open

Recently switched to Command Line Tools for Xcode. Any suggestions would be very welcome.

crd1859$ brew install R
==> Downloading http://cran.r-project.org/src/base/R-2/R-2.14.1.tar.gz
File already downloaded in /Users/crd1859/Library/Caches/Homebrew
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environme
==> ./configure --prefix=/usr/local/Cellar/r/2.14.1 --with-aqua --enable-R-framework --with-l
checking build system type... x86_64-apple-darwin11.3.0
checking host system type... x86_64-apple-darwin11.3.0
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether ln -s works... yes
checking for bison... bison -y
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /usr/bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... /usr/bin/gnutar
checking for tex... /usr/texbin/tex
checking for pdftex... /usr/texbin/pdftex
checking for pdflatex... /usr/texbin/pdflatex
checking for makeindex... /usr/texbin/makeindex
checking for makeinfo... /usr/bin/makeinfo
checking whether makeinfo version is at least 4.7... yes
checking for install-info... /usr/bin/install-info
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/texbin/kpsewhich
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for firefox... no
checking for mozilla... no
checking for galeon... no
checking for opera... no
checking for xdg-open... no
checking for kfmclient... no
checking for gnome-moz-remote... no
checking for open... /usr/bin/open
using default browser ... /usr/bin/open
checking for acroread... no
checking for acroread4... no
checking for xdg-open... no
checking for evince... no
checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... no
checking for okular... no
checking for kpdf... no
checking for open... /usr/bin/open
checking for notangle... false
checking for pkg-config... /usr/local/bin/pkg-config
checking for gcc... /usr/bin/clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/clang accepts -g... yes
checking for /usr/bin/clang option to accept ISO C89... none needed
checking how to run the C preprocessor... /usr/bin/clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether /usr/bin/clang needs -traditional... no
checking how to run the C preprocessor... /usr/bin/clang -E
defining F77 to be /usr/local/bin/gfortran
checking whether we are using the GNU Fortran 77 compiler... no
checking whether /usr/local/bin/gfortran accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/clang++ accepts -g... yes
checking how to run the C++ preprocessor... /usr/bin/clang++ -E
checking whether __attribute__((visibility())) is supported... no
checking whether /usr/bin/clang accepts -fvisibility... yes
checking whether /usr/local/bin/gfortran accepts -fvisibility... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether we are using the GNU Objective C compiler... yes
checking whether /usr/bin/clang accepts -g... yes
checking for Objective C++ compiler... trying some possibilities
checking whether /usr/bin/clang++ can compile ObjC++... yes
/usr/bin/clang++
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by /usr/bin/clang... /usr/bin/clang
checking if the linker (/usr/bin/clang) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/clang option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from /usr/bin/clang object... ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether /usr/bin/clang++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... /usr/bin/clang++ -E
checking whether we are using the GNU Fortran 77 compiler... (cached) no
checking whether /usr/local/bin/gfortran accepts -g... (cached) yes
checking for objdir... .libs
checking if /usr/bin/clang supports -fno-rtti -fno-exceptions... yes
checking for /usr/bin/clang option to produce PIC... -fno-common -DPIC
checking if /usr/bin/clang PIC flag -fno-common -DPIC works... yes
checking if /usr/bin/clang static flag -static works... no
checking if /usr/bin/clang supports -c -o file.o... yes
checking if /usr/bin/clang supports -c -o file.o... (cached) yes
checking whether the /usr/bin/clang linker (/usr/bin/clang) supports shared libraries... yes
checking dynamic linker characteristics... darwin11.3.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by /usr/bin/clang++... /usr/bin/clang
checking if the linker (/usr/bin/clang) is GNU ld... no
checking whether the /usr/bin/clang++ linker (/usr/bin/clang) supports shared libraries... yes
checking for /usr/bin/clang++ option to produce PIC... -fno-common -DPIC
checking if /usr/bin/clang++ PIC flag -fno-common -DPIC works... yes
checking if /usr/bin/clang++ static flag -static works... no
checking if /usr/bin/clang++ supports -c -o file.o... yes
checking if /usr/bin/clang++ supports -c -o file.o... (cached) yes
checking whether the /usr/bin/clang++ linker (/usr/bin/clang) supports shared libraries... yes
checking dynamic linker characteristics... darwin11.3.0 dyld
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for /usr/local/bin/gfortran option to produce PIC...
checking if /usr/local/bin/gfortran static flag works... no
checking if /usr/local/bin/gfortran supports -c -o file.o... no
checking if /usr/local/bin/gfortran supports -c -o file.o... (cached) no
checking whether the /usr/local/bin/gfortran linker (/usr/bin/clang) supports shared libraries... no
checking dynamic linker characteristics... darwin11.3.0 dyld
checking how to hardcode library paths into programs... immediate
checking for sin in -lm... yes
checking for library containing dlopen... none required
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking whether rl_completion_matches exists and is declared... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking dl.h usability... no
checking dl.h presence... no
checking for dl.h... no
checking for dlfcn.h... (cached) yes
checking elf.h usability... no
checking elf.h presence... no
checking for elf.h... no
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking fpu_control.h usability... no
checking fpu_control.h presence... no
checking for fpu_control.h... no
checking glob.h usability... yes
checking glob.h presence... yes
checking for glob.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking for strings.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... no
checking return type of signal handlers... void
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for /usr/bin/clang option to accept ISO C99... none needed
checking for /usr/bin/clang option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of long double... 16
checking size of size_t... 8
checking whether we can compute C Make dependencies... yes, using /usr/bin/clang -MM
checking whether /usr/bin/clang supports -c -o FILE.lo... yes
checking for /usr/bin/clang option to support OpenMP... unsupported
checking how to get verbose linking output from /usr/local/bin/gfortran... configure: WARNING: compilation failed

checking for Fortran 77 libraries of /usr/local/bin/gfortran...
checking how to get verbose linking output from /usr/bin/clang... -v
checking for C libraries of /usr/bin/clang... -lcrt1.10.6.o -L/usr/local/Cellar/readline/6.2.2/lib -L/usr/X11/lib -lSystem /usr/bin/../lib/clang/3.1/lib/darwin/libclang_rt.osx.a
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... configure: error: in `/private/tmp/homebrew-r-2.14.1-orQV/R-2.14.1':
configure: error: cannot compile a simple Fortran program
See `config.log' for more details
==> Exit Status: 1
http://github.com/mxcl/homebrew/blob/master/Library/Formula/r.rb#L50
==> Environment
HOMEBREW_VERSION: 0.8.1
HEAD: 51d054c9a9616f0c5bba5955561b7486fc5cf139
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
Hardware: quad-core 64-bit sandybridge
OS X: 10.7.3
Kernel Architecture: x86_64
Xcode: 4.2
GCC-4.0: N/A
GCC-4.2: N/A
LLVM: build 2336
Clang: 3.1 build 318
MacPorts or Fink? false
X11 installed? true
System Ruby: 1.8.7-249
/usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
Which Perl: /usr/bin/perl
Which Python: /usr/bin/python
Which Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
==> Build Flags
CC: /usr/bin/clang
CXX: /usr/bin/clang++ => /usr/bin/clang
LD: /usr/bin/clang
CFLAGS: -Os -w -pipe -march=native -Qunused-arguments
CXXFLAGS: -Os -w -pipe -march=native -Qunused-arguments
CPPFLAGS: -I/usr/local/Cellar/readline/6.2.2/include -I/usr/X11/include
LDFLAGS: -L/usr/local/Cellar/readline/6.2.2/lib -L/usr/X11/lib
MAKEFLAGS: -j4
PKG_CONFIG_PATH: /usr/local/Cellar/readline/6.2.2/lib/pkgconfig

Error: Failed executing: ./configure --prefix=/usr/local/Cellar/r/2.14.1 --with-aqua --enable-R-framework --with-lapack