Opened 5 years ago

Closed 5 years ago

#18254 closed defect (fixed)

osx R spkg error: expected ',' or '}' before '__attribute__'

Reported by: buck Owned by:
Priority: major Milestone: sage-6.7
Component: packages: standard Keywords:
Cc: vbraun Merged in:
Authors: Buck Evan Reviewers: John Palmieri, Volker Braun
Report Upstream: N/A Work issues:
Branch: 3c5cd0f (Commits) Commit: 3c5cd0f74446992a2b98f84c34043cfa181b68b4
Dependencies: Stopgaps:

Description

The sage-support discussion is here: https://groups.google.com/forum/#!topic/sage-support/9m5N0KUqkWo

I'm on OS X 10.10.3. I've removed homebrew from any part of the build. I've updated sage to the develop branch.

The error still persists: (full output)

gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c devQuartz.c -o devQuartz.o
In file included from /usr/include/Availability.h:153:0,
                 from /usr/include/stdio.h:65,
                 from ../../../../include/Rinternals.h:37,
                 from ../../../include/Defn.h:80,
                 from devQuartz.c:30:
/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h:486:41: error: expected ',' or '}' before '__attribute__'
   kFSEventStreamEventFlagItemIsHardlink __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_9_0) = 0x00100000,

I suspect this needs another patch to fix up inappropriate objective-c in the C code, similar to what was done for dispatch/object.h, but I might be off base.

Attachments (3)

Availability.h (9.0 KB) - added by buck 5 years ago.
Availability.h from Xcode 6.3
AvailabilityInternal.h (642.7 KB) - added by buck 5 years ago.
AvailabilityInternal?.h from Xcode 6.3
Screen Shot 2015-04-22 at 10.53.37 AM.png (117.7 KB) - added by buck 5 years ago.
my xcode and clt versions

Download all attachments as: .zip

Change History (69)

comment:1 Changed 5 years ago by buck

Just to make double-sure, I tried one more time with an essentially empty environment from the develop branch. I get the same error:

$ env
PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin
PWD=/Users/buck/trees/mine/sage
HOME=/Users/buck
SHLVL=1
_=/usr/bin/env

$ ./src/bin/sage-spkg r 2>&1 | tee r.log.3
Found local metadata for r-3.1.2.p0
Found local sources at /Users/buck/trees/mine/sage/upstream/r-3.1.2.tar.gz
Checksum: 93809368e5735a630611633ac1fa99010020c5d6 vs 93809368e5735a630611633ac1fa99010020c5d6
r-3.1.2.p0
====================================================
Setting up build directory for r-3.1.2.p0
Finished set up
****************************************************
Host system:
Darwin YELP-BUCK.lan 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64 x86_64
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/Users/buck/trees/mine/sage/local/libexec/gcc/x86_64-apple-darwin14.3.0/4.9.2/lto-wrapper
Target: x86_64-apple-darwin14.3.0
Configured with: ../src/configure --prefix=/Users/buck/trees/mine/sage/local --with-local-prefix=/Users/buck/trees/mine/sage/local --with-gmp=/Users/buck/trees/mine/sage/local --with-mpfr=/Users/buck/trees/mine/sage/local --with-mpc=/Users/buck/trees/mine/sage/local --with-system-zlib --disable-multilib --disable-nls --enable-languages=c,c++,fortran --disable-libitm --without-isl --without-cloog  
Thread model: posix
gcc version 4.9.2 (GCC) 
****************************************************
Copying fake java and javac compiler on OS X
Configuring R without ATLAS for OS X
patching file src/scripts/R.sh.in
patching file configure
Hunk #1 succeeded at 22880 (offset 3 lines).
Hunk #2 succeeded at 23236 (offset 3 lines).
patching file configure.ac
Hunk #1 succeeded at 1324 (offset 14 lines).
patching file configure
Hunk #1 succeeded at 26317 (offset 4 lines).
patching file src/library/parallel/src/fork.c
Hunk #1 succeeded at 229 (offset 2 lines).
patching file src/scripts/Makefile.in
configure: WARNING: you should use --build, --host, --target
configure: WARNING: you should use --build, --host, --target
checking build system type... x86_64-apple-darwin14.3.0
checking host system type... x86_64-apple-darwin14.3.0
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... no
checking for tar... /usr/bin/tar
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 ginstall-info... no
checking for install-info... /usr/bin/install-info
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/texbin/kpsewhich
checking for latex inconsolata package... found zi4.sty
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /Users/buck/trees/mine/sage/local/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 realpath... false
checking for pkg-config... /Users/buck/trees/mine/sage/local/bin/pkg-config
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether gcc needs -traditional... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
no
checking how to run the C preprocessor... cpp
defining F77 to be gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... no
checking whether gcc accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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/cc accepts -g... yes
checking for Objective C++ compiler... trying some possibilities
checking whether /usr/bin/c++ can compile ObjC++... yes
/usr/bin/c++
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 gcc... ld
checking if the linker (ld) 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 ld 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 gcc 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 g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether gfortran accepts -g... (cached) yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.3.0 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 g++... ld
checking if the linker (ld) is GNU ld... no
checking whether the g++ linker (ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.3.0 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 gfortran option to produce PIC... -fno-common
checking if gfortran PIC flag -fno-common works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.3.0 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 langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.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 sched.h usability... yes
checking sched.h presence... yes
checking for sched.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 uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
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 gcc option to accept ISO C99... -std=gnu99
checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
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 size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes
checking for gcc -std=gnu99 option to support OpenMP... -fopenmp
checking how to get verbose linking output from gfortran... -###
checking for Fortran 77 libraries of gfortran...  -L/Users/buck/trees/mine/sage/local/lib/ -L/Users/buck/trees/mine/sage/local/lib -L/Users/buck/trees/mine/sage/local/lib/gcc/x86_64-apple-darwin14.3.0/4.9.2 -L/Users/buck/trees/mine/sage/local/lib/gcc/x86_64-apple-darwin14.3.0/4.9.2/../../.. -lgfortran -lquadmath -lm
checking how to get verbose linking output from gcc -std=gnu99... -###
checking for C libraries of gcc -std=gnu99...  -L/Users/buck/trees/mine/sage/local/lib/ -L/Users/buck/trees/mine/sage/local/lib -L/Users/buck/trees/mine/sage/local/lib/gcc/x86_64-apple-darwin14.3.0/4.9.2 -L/Users/buck/trees/mine/sage/local/lib/gcc/x86_64-apple-darwin14.3.0/4.9.2/../../.. -lSystem -lgcc_ext.10.5
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking whether gfortran appends underscores to external names... yes
checking whether gfortran appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether gfortran and gcc -std=gnu99 agree on int and double... yes
checking whether gfortran and gcc -std=gnu99 agree on double complex... yes
checking for gfortran option to support OpenMP... -fopenmp
checking whether g++ accepts -M for generating dependencies... yes
checking for g++ option to support OpenMP... -fopenmp
checking whether we can compute ObjC Make dependencies... yes, using /usr/bin/cc -MM
checking for ObjC runtime library... -lobjc
checking for ObjC runtime style... next
checking whether /usr/bin/cc accepts -fobjc-exceptions... yes
checking for cached Foundation settings... no
checking whether default Foundation framework works... no
checking whether -framework Foundation works... yes
checking for working Foundation implementation... yes
checking whether C runtime needs -D__NO_MATH_INLINES... no
checking for xmkmf... no
checking whether linker supports dynamic lookup... yes
checking whether g++  supports C++11 features by default... no
checking whether g++  supports C++11 features with -std=c++11... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log1pl exists and is declared... yes
checking whether log2 exists and is declared... yes
checking whether log10 exists and is declared... yes
checking whether nearbyint exists and is declared... yes
checking whether nearbyintl exists and is declared... yes
checking whether powl exists and is declared... yes
checking whether rint exists and is declared... yes
checking whether rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
checking sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking for cospi in -lsunmath... no
checking for atanpi... no
checking for atan2pi... no
checking for cospi... no
checking for exp10... no
checking for pown... no
checking for sinpi... no
checking for tanpi... no
checking for fseeko... yes
checking for ftello... yes
checking for matherr... yes
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
checking whether gmtime_r exists and is declared... yes
checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... no
checking whether sched_getaffinity exists and is declared... no
checking whether utime exists and is declared... yes
checking for clock_gettime in -lrt... no
checking whether clock_gettime exists and is declared... no
checking whether timespec_get exists and is declared... no
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... no
checking for realpath... yes
checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... no
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for __setfpucw... no
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... no
checking whether mktime works correctly outside 1902-2037... no
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for cblas_cdotu_sub in Accelerate framework... -framework Accelerate
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... in libiconv
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking for iconvlist... yes
checking for iconv... yes
checking for iconv declaration... 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... yes
checking wctype.h presence... yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether iswblank exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... no
checking for ucol_open in -licucore... yes
checking for X... disabled
using X11 ... no
checking whether pkg-config knows about cairo and pango... no
checking whether pkg-config knows about cairo... no
checking for CFStringGetSystemEncoding in CoreFoundation framework... -framework CoreFoundation
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories... /usr/lib/tclConfig.sh
checking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories... /usr/lib/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking if jpeglib version >= 6b... no
checking for main in -lz... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... no
checking tiffio.h usability... no
checking tiffio.h presence... no
checking for tiffio.h... no
checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
checking whether zlib support needs to be compiled... yes
checking mmap support for zlib... yes
checking whether bzip2 support needs to be compiled... yes
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... no
checking lzma.h presence... no
checking for lzma.h... no
checking whether PCRE support needs to be compiled... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for sys/time.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for struct stat.st_atim.tv_nsec... no
checking for struct stat.st_atimespec.tv_nsec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... yes
checking for lpr... lpr
checking for paperconf... false
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether gfortran accepts -g... (cached) yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fno-common
checking if gfortran PIC flag -fno-common works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin14.3.0 dyld
checking how to hardcode library paths into programs... immediate
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for gfortran option to support OpenMP... -fopenmp
checking for recommended packages... yes
checking whether NLS is requested... yes

Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... tools/install-sh -c -d
checking whether we are using the GNU C Library 2 or newer... no
checking for ranlib... (cached) ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking whether imported symbols can be declared weak... no
checking for multithread API to use... none
checking argz.h usability... no
checking argz.h presence... no
checking for argz.h... no
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) no
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... no
checking for argz_stringify... no
checking for argz_next... no
checking for __fsetlocking... no
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... no
checking for iconv... (cached) yes
checking for iconv declaration... (cached) 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... no
checking for bison... bison
checking version of bison... 2.3, ok
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... no
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... yes
checking for CFLocaleCopyCurrent... yes
checking for ptrdiff_t... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for shared library run path origin... done
checking for CFPreferencesCopyAppValue... (cached) yes
checking for CFLocaleCopyCurrent... (cached) yes
checking whether included gettext is requested... no
checking for GNU gettext in libc... no
checking for GNU gettext in libintl... no
checking whether to use NLS... yes
checking where the gettext function comes from... included intl directory
Finished configuring src/extra/intl directory

using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
config.status: creating Makeconf
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/manual/Makefile
config.status: creating etc/Makefile
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config.status: creating m4/Makefile
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config.status: creating src/extra/bzip2/Makefile
config.status: creating src/extra/intl/Makefile
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config.status: executing libtool commands
config.status: executing stamp-h commands

R is now configured for x86_64-apple-darwin14.3.0

  Source directory:          .
  Installation directory:    /Users/buck/trees/mine/sage/local

  C compiler:                gcc -std=gnu99  -g -O2 
  Fortran 77 compiler:       gfortran  -g -O2

  C++ compiler:              g++  -g -O2
  C++ 11 compiler:           g++  -std=c++11 -g -O2
  Fortran 90/95 compiler:    gfortran -g -O2 
  Obj-C compiler:	     /usr/bin/cc -g -O2 -fobjc-exceptions

  Interfaces supported:      aqua, tcltk
  External libraries:        readline
  Additional capabilities:   NLS, ICU
  Options enabled:           shared R library, shared BLAS, R profiling

  Capabilities skipped:      PNG, JPEG, TIFF, cairo
  Options not enabled:       memory profiling

  Recommended packages:      yes

make[1]: Nothing to be done for `R'.
make[1]: Nothing to be done for `R'.
make[2]: Nothing to be done for `R'.
creating src/scripts/R.fe
mkdir ../../bin
mkdir ../../include
mkdir ../../../include/R_ext
gfortran  -fopenmp -fPIC  -g -O2  -c blas.f -o blas.o
gfortran  -fopenmp -fPIC  -g -O2  -c cmplxblas.f -o cmplxblas.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -fopenmp -L/Users/buck/trees/mine/sage/local/lib/  -o libRblas.dylib blas.o  cmplxblas.o -install_name libRblas.dylib -headerpad_max_install_names -lgfortran -lquadmath -lm # xerbla.o
mkdir /Users/buck/trees/mine/sage/local/var/tmp/sage/build/r-3.1.2.p0/src/lib
making blocksort.d from blocksort.c
making bzlib.d from bzlib.c
making bzcompress.d from bzcompress.c
making crctable.d from crctable.c
making decompress.d from decompress.c
making huffman.d from huffman.c
making randtable.d from randtable.c
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c blocksort.c -o blocksort.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c bzlib.c -o bzlib.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c bzcompress.c -o bzcompress.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c crctable.c -o crctable.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c decompress.c -o decompress.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c huffman.c -o huffman.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c randtable.c -o randtable.o
rm -f libbz2.a
ar cr libbz2.a blocksort.o bzlib.o bzcompress.o crctable.o decompress.o huffman.o randtable.o
ranlib libbz2.a
making pcre_chartables.d from pcre_chartables.c
making pcre_compile.d from pcre_compile.c
making pcre_config.d from pcre_config.c
making pcre_exec.d from pcre_exec.c
making pcre_fullinfo.d from pcre_fullinfo.c
making pcre_get.d from pcre_get.c
making pcre_globals.d from pcre_globals.c
making pcre_jit_compile.d from pcre_jit_compile.c
making pcre_maketables.d from pcre_maketables.c
making pcre_newline.d from pcre_newline.c
making pcre_ord2utf8.d from pcre_ord2utf8.c
making pcre_refcount.d from pcre_refcount.c
making pcre_study.d from pcre_study.c
making pcre_tables.d from pcre_tables.c
making pcre_ucd.d from pcre_ucd.c
making pcre_valid_utf8.d from pcre_valid_utf8.c
making pcre_version.d from pcre_version.c
making pcre_xclass.d from pcre_xclass.c
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_chartables.c -o pcre_chartables.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_compile.c -o pcre_compile.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_config.c -o pcre_config.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_exec.c -o pcre_exec.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_fullinfo.c -o pcre_fullinfo.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_get.c -o pcre_get.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_globals.c -o pcre_globals.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_jit_compile.c -o pcre_jit_compile.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_maketables.c -o pcre_maketables.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_newline.c -o pcre_newline.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_ord2utf8.c -o pcre_ord2utf8.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_refcount.c -o pcre_refcount.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_study.c -o pcre_study.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_tables.c -o pcre_tables.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_ucd.c -o pcre_ucd.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_valid_utf8.c -o pcre_valid_utf8.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_version.c -o pcre_version.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c pcre_xclass.c -o pcre_xclass.o
rm -f libpcre.a
ar cr libpcre.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_jit_compile.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o
ranlib libpcre.a
making adler32.d from adler32.c
making compress.d from compress.c
making crc32.d from crc32.c
making deflate.d from deflate.c
making infback.d from infback.c
making inffast.d from inffast.c
making inflate.d from inflate.c
making inftrees.d from inftrees.c
making trees.d from trees.c
making uncompr.d from uncompr.c
making zutil.d from zutil.c
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c adler32.c -o adler32.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c compress.c -o compress.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c crc32.c -o crc32.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c deflate.c -o deflate.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c infback.c -o infback.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c inffast.c -o inffast.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c inflate.c -o inflate.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c inftrees.c -o inftrees.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c trees.c -o trees.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c uncompr.c -o uncompr.o
gcc -std=gnu99 -I.  -DUSE_MMAP -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c zutil.c -o zutil.o
rm -f libz.a
ar cr libz.a adler32.o compress.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
ranlib libz.a
making bindtextdom.d from bindtextdom.c
making dcgettext.d from dcgettext.c
making dgettext.d from dgettext.c
making gettext.d from gettext.c
making finddomain.d from finddomain.c
making loadmsgcat.d from loadmsgcat.c
making textdomain.d from textdomain.c
making l10nflist.d from l10nflist.c
making explodename.d from explodename.c
making dcigettext.d from dcigettext.c
making dcngettext.d from dcngettext.c
making dngettext.d from dngettext.c
making ngettext.d from ngettext.c
making plural.d from plural.c
making plural-exp.d from plural-exp.c
making langprefs.d from langprefs.c
making localcharset.d from localcharset.c
making localename.d from localename.c
making printf.d from printf.c
making osdep.d from osdep.c
making intl-compat.d from intl-compat.c
making hash-string.d from hash-string.c
making lock.d from lock.c
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c bindtextdom.c -o bindtextdom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c dcgettext.c -o dcgettext.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c dgettext.c -o dgettext.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c gettext.c -o gettext.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c finddomain.c -o finddomain.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c loadmsgcat.c -o loadmsgcat.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c textdomain.c -o textdomain.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c l10nflist.c -o l10nflist.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c explodename.c -o explodename.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c dcigettext.c -o dcigettext.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c dcngettext.c -o dcngettext.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c dngettext.c -o dngettext.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c ngettext.c -o ngettext.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c plural.c -o plural.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c plural-exp.c -o plural-exp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c langprefs.c -o langprefs.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c localcharset.c -o localcharset.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c localename.c -o localename.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c printf.c -o printf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c osdep.c -o osdep.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c intl-compat.c -o intl-compat.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c hash-string.c -o hash-string.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I.  -DLOCALEDIR=\"\" -DLOCALEALIAS_PATH=\"\" -DIN_LIBINTL -DHAVE_CONFIG_H -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c lock.c -o lock.o
rm -f libintl.a
ar cr libintl.a bindtextdom.o dcgettext.o dgettext.o gettext.o finddomain.o loadmsgcat.o textdomain.o l10nflist.o explodename.o dcigettext.o dcngettext.o dngettext.o ngettext.o plural.o plural-exp.o langprefs.o localcharset.o localename.o printf.o osdep.o intl-compat.o hash-string.o lock.o
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libintl.a(printf.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libintl.a(osdep.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libintl.a(lock.o) has no symbols
ranlib libintl.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libintl.a(printf.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libintl.a(osdep.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libintl.a(lock.o) has no symbols
making regcomp.d from regcomp.c
making regerror.d from regerror.c
making regexec.d from regexec.c
making tre-ast.d from tre-ast.c
making tre-compile.d from tre-compile.c
making tre-match-approx.d from tre-match-approx.c
making tre-match-backtrack.d from tre-match-backtrack.c
making tre-match-parallel.d from tre-match-parallel.c
making tre-mem.d from tre-mem.c
making tre-parse.d from tre-parse.c
making tre-stack.d from tre-stack.c
making xmalloc.d from xmalloc.c
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c regcomp.c -o regcomp.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c regerror.c -o regerror.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c regexec.c -o regexec.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c tre-ast.c -o tre-ast.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c tre-compile.c -o tre-compile.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c tre-match-approx.c -o tre-match-approx.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c tre-match-backtrack.c -o tre-match-backtrack.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c tre-match-parallel.c -o tre-match-parallel.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c tre-mem.c -o tre-mem.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c tre-parse.c -o tre-parse.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c tre-stack.c -o tre-stack.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c xmalloc.c -o xmalloc.o
rm -f libtre.a
ar cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o
ranlib libtre.a
making localtime.d from localtime.c
making strftime.d from strftime.c
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I. -I../../../src/main  -DHAVE_CONFIG_H  -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c localtime.c -o localtime.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I. -I../../../src/main  -DHAVE_CONFIG_H  -I/System/Library/Frameworks/CoreFoundation.framework/Headers  -fPIC  -g -O2    -c strftime.c -o strftime.o
ar cr libtz.a localtime.o strftime.o
touch stamp
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c alone_decoder.c -o alone_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c alone_encoder.c -o alone_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c arm.c -o arm.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c armthumb.c -o armthumb.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c auto_decoder.c -o auto_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c block_buffer_decoder.c -o block_buffer_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c block_buffer_encoder.c -o block_buffer_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c block_decoder.c -o block_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c block_encoder.c -o block_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c block_header_decoder.c -o block_header_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c block_header_encoder.c -o block_header_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c block_util.c -o block_util.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c check.c -o check.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c common.c -o common.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c crc32_fast.c -o crc32_fast.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c crc32_table.c -o crc32_table.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c crc64_fast.c -o crc64_fast.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c crc64_table.c -o crc64_table.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c delta_common.c -o delta_common.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c delta_decoder.c -o delta_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c delta_encoder.c -o delta_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c easy_buffer_encoder.c -o easy_buffer_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c easy_decoder_memusage.c -o easy_decoder_memusage.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c easy_encoder.c -o easy_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c easy_encoder_memusage.c -o easy_encoder_memusage.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c easy_preset.c -o easy_preset.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c fastpos_table.c -o fastpos_table.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c filter_buffer_decoder.c -o filter_buffer_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c filter_buffer_encoder.c -o filter_buffer_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c filter_common.c -o filter_common.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c filter_decoder.c -o filter_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c filter_encoder.c -o filter_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c filter_flags_decoder.c -o filter_flags_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c filter_flags_encoder.c -o filter_flags_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c ia64.c -o ia64.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c index.c -o index.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c index_decoder.c -o index_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c index_encoder.c -o index_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c index_hash.c -o index_hash.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lz_decoder.c -o lz_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lz_encoder.c -o lz_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lz_encoder_mf.c -o lz_encoder_mf.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lzma2_decoder.c -o lzma2_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lzma2_encoder.c -o lzma2_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lzma_decoder.c -o lzma_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lzma_encoder.c -o lzma_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lzma_encoder_optimum_fast.c -o lzma_encoder_optimum_fast.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lzma_encoder_optimum_normal.c -o lzma_encoder_optimum_normal.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c lzma_encoder_presets.c -o lzma_encoder_presets.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c powerpc.c -o powerpc.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c price_table.c -o price_table.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c sha256.c -o sha256.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c simple_coder.c -o simple_coder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c simple_decoder.c -o simple_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c simple_encoder.c -o simple_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c sparc.c -o sparc.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c stream_buffer_decoder.c -o stream_buffer_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c stream_buffer_encoder.c -o stream_buffer_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c stream_decoder.c -o stream_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c stream_encoder.c -o stream_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c stream_flags_common.c -o stream_flags_common.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c stream_flags_decoder.c -o stream_flags_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c stream_flags_encoder.c -o stream_flags_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c vli_decoder.c -o vli_decoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c vli_encoder.c -o vli_encoder.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c vli_size.c -o vli_size.o
gcc -std=gnu99 -I./api -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c x86.c -o x86.o
rm -f liblzma.a
ar cr liblzma.a alone_decoder.o alone_encoder.o arm.o armthumb.o auto_decoder.o block_buffer_decoder.o block_buffer_encoder.o block_decoder.o block_encoder.o block_header_decoder.o block_header_encoder.o block_util.o check.o common.o crc32_fast.o crc32_table.o crc64_fast.o crc64_table.o delta_common.o delta_decoder.o delta_encoder.o easy_buffer_encoder.o easy_decoder_memusage.o easy_encoder.o easy_encoder_memusage.o easy_preset.o fastpos_table.o filter_buffer_decoder.o filter_buffer_encoder.o filter_common.o filter_decoder.o filter_encoder.o filter_flags_decoder.o filter_flags_encoder.o ia64.o index.o index_decoder.o index_encoder.o index_hash.o lz_decoder.o lz_encoder.o lz_encoder_mf.o lzma2_decoder.o lzma2_encoder.o lzma_decoder.o lzma_encoder.o lzma_encoder_optimum_fast.o lzma_encoder_optimum_normal.o lzma_encoder_presets.o powerpc.o price_table.o sha256.o simple_coder.o simple_decoder.o simple_encoder.o sparc.o stream_buffer_decoder.o stream_buffer_encoder.o stream_decoder.o stream_encoder.o stream_flags_common.o stream_flags_decoder.o stream_flags_encoder.o vli_decoder.o vli_encoder.o vli_size.o x86.o
ranlib liblzma.a
making integrate.d from integrate.c
making interv.d from interv.c
making maxcol.d from maxcol.c
making optim.d from optim.c
making pretty.d from pretty.c
making uncmin.d from uncmin.c
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c integrate.c -o integrate.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c interv.c -o interv.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c maxcol.c -o maxcol.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c optim.c -o optim.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pretty.c -o pretty.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c uncmin.c -o uncmin.o
gfortran  -fopenmp -fPIC  -g -O2  -c dchdc.f -o dchdc.o
gfortran  -fopenmp -fPIC  -g -O2  -c dpbfa.f -o dpbfa.o
gfortran  -fopenmp -fPIC  -g -O2  -c dpbsl.f -o dpbsl.o
gfortran  -fopenmp -fPIC  -g -O2  -c dpoco.f -o dpoco.o
gfortran  -fopenmp -fPIC  -g -O2  -c dpodi.f -o dpodi.o
gfortran  -fopenmp -fPIC  -g -O2  -c dpofa.f -o dpofa.o
gfortran  -fopenmp -fPIC  -g -O2  -c dposl.f -o dposl.o
gfortran  -fopenmp -fPIC  -g -O2  -c dqrdc.f -o dqrdc.o
gfortran  -fopenmp -fPIC  -g -O2  -c dqrdc2.f -o dqrdc2.o
gfortran  -fopenmp -fPIC  -g -O2  -c dqrls.f -o dqrls.o
gfortran  -fopenmp -fPIC  -g -O2  -c dqrsl.f -o dqrsl.o
gfortran  -fopenmp -fPIC  -g -O2  -c dqrutl.f -o dqrutl.o
gfortran  -fopenmp -fPIC  -g -O2  -c dsvdc.f -o dsvdc.o
gfortran  -fopenmp -fPIC  -g -O2  -c dtrco.f -o dtrco.o
gfortran  -fopenmp -fPIC  -g -O2  -c dtrsl.f -o dtrsl.o
rm -f libappl.a
ar cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o 
ranlib libappl.a
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making expm1.d from expm1.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c mlutils.c -o mlutils.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c d1mach.c -o d1mach.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c i1mach.c -o i1mach.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c fmax2.c -o fmax2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c fmin2.c -o fmin2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c fprec.c -o fprec.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c fround.c -o fround.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c ftrunc.c -o ftrunc.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c sign.c -o sign.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c fsign.c -o fsign.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c imax2.c -o imax2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c imin2.c -o imin2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c chebyshev.c -o chebyshev.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c log1p.c -o log1p.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c expm1.c -o expm1.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c lgammacor.c -o lgammacor.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c gammalims.c -o gammalims.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c stirlerr.c -o stirlerr.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c bd0.c -o bd0.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c gamma.c -o gamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c lgamma.c -o lgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c gamma_cody.c -o gamma_cody.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c beta.c -o beta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c lbeta.c -o lbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c polygamma.c -o polygamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c cospi.c -o cospi.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c bessel_i.c -o bessel_i.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c bessel_j.c -o bessel_j.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c bessel_k.c -o bessel_k.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c bessel_y.c -o bessel_y.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c choose.c -o choose.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c snorm.c -o snorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c sexp.c -o sexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dgamma.c -o dgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pgamma.c -o pgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qgamma.c -o qgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rgamma.c -o rgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dbeta.c -o dbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pbeta.c -o pbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qbeta.c -o qbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rbeta.c -o rbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dunif.c -o dunif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c punif.c -o punif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qunif.c -o qunif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c runif.c -o runif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dnorm.c -o dnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pnorm.c -o pnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qnorm.c -o qnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rnorm.c -o rnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dlnorm.c -o dlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c plnorm.c -o plnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qlnorm.c -o qlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rlnorm.c -o rlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c df.c -o df.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pf.c -o pf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qf.c -o qf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rf.c -o rf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dnf.c -o dnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dt.c -o dt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pt.c -o pt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qt.c -o qt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rt.c -o rt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dnt.c -o dnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dchisq.c -o dchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pchisq.c -o pchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qchisq.c -o qchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rchisq.c -o rchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rnchisq.c -o rnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dbinom.c -o dbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pbinom.c -o pbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qbinom.c -o qbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rbinom.c -o rbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rmultinom.c -o rmultinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dcauchy.c -o dcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pcauchy.c -o pcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qcauchy.c -o qcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rcauchy.c -o rcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dexp.c -o dexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pexp.c -o pexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qexp.c -o qexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rexp.c -o rexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dgeom.c -o dgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pgeom.c -o pgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qgeom.c -o qgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rgeom.c -o rgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dhyper.c -o dhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c phyper.c -o phyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qhyper.c -o qhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rhyper.c -o rhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dnbinom.c -o dnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pnbinom.c -o pnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qnbinom.c -o qnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rnbinom.c -o rnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dpois.c -o dpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c ppois.c -o ppois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qpois.c -o qpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rpois.c -o rpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dweibull.c -o dweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pweibull.c -o pweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qweibull.c -o qweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rweibull.c -o rweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dlogis.c -o dlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c plogis.c -o plogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qlogis.c -o qlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rlogis.c -o rlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dnchisq.c -o dnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pnchisq.c -o pnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qnchisq.c -o qnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dnbeta.c -o dnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pnbeta.c -o pnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qnbeta.c -o qnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pnf.c -o pnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c pnt.c -o pnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qnf.c -o qnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qnt.c -o qnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c ptukey.c -o ptukey.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qtukey.c -o qtukey.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c toms708.c -o toms708.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c wilcox.c -o wilcox.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c signrank.c -o signrank.o
rm -rf libnmath.a
ar cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libnmath.a(mlutils.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libnmath.a(log1p.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libnmath.a(expm1.o) has no symbols
ranlib libnmath.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libnmath.a(mlutils.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libnmath.a(log1p.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libnmath.a(expm1.o) has no symbols
config.status: creating src/unix/Makefile
making Rembedded.d from Rembedded.c
making dynload.d from dynload.c
making system.d from system.c
making sys-unix.d from sys-unix.c
making sys-std.d from sys-std.c
making X11.d from X11.c
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c Rembedded.c -o Rembedded.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dynload.c -o dynload.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c system.c -o system.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c sys-unix.c -o sys-unix.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c sys-std.c -o sys-std.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c X11.c -o X11.o
rm -rf libunix.a
ar cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o
ranlib libunix.a
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -L/Users/buck/trees/mine/sage/local/lib/  -DR_HOME='"/Users/buck/trees/mine/sage/local/var/tmp/sage/build/r-3.1.2.p0/src"' \
	  -o Rscript ./Rscript.c
config.status: creating src/main/Makefile
making CommandLineArgs.d from CommandLineArgs.c
making Rdynload.d from Rdynload.c
making Renviron.d from Renviron.c
making RNG.d from RNG.c
making agrep.d from agrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making vfonts.d from vfonts.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c CommandLineArgs.c -o CommandLineArgs.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c Rdynload.c -o Rdynload.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c Renviron.c -o Renviron.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c RNG.c -o RNG.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c agrep.c -o agrep.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c apply.c -o apply.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c arithmetic.c -o arithmetic.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c array.c -o array.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c attrib.c -o attrib.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c bind.c -o bind.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c builtin.c -o builtin.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c character.c -o character.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c coerce.c -o coerce.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c colors.c -o colors.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c complex.c -o complex.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c connections.c -o connections.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c context.c -o context.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c cum.c -o cum.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dcf.c -o dcf.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c datetime.c -o datetime.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c debug.c -o debug.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c deparse.c -o deparse.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c devices.c -o devices.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dotcode.c -o dotcode.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dounzip.c -o dounzip.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c dstruct.c -o dstruct.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c duplicate.c -o duplicate.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c edit.c -o edit.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c engine.c -o engine.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c envir.c -o envir.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c errors.c -o errors.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c eval.c -o eval.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c format.c -o format.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c gevents.c -o gevents.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c gram.c -o gram.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c gram-ex.c -o gram-ex.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c graphics.c -o graphics.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c grep.c -o grep.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c identical.c -o identical.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c inlined.c -o inlined.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c inspect.c -o inspect.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c internet.c -o internet.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c iosupport.c -o iosupport.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c lapack.c -o lapack.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c list.c -o list.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c localecharset.c -o localecharset.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c logic.c -o logic.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c main.c -o main.o
main.c: In function 'dummy_ii':
main.c:1594:5: warning: function returns address of local variable [-Wreturn-local-addr]
     return (uintptr_t) ⅈ
     ^
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c mapply.c -o mapply.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c match.c -o match.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c memory.c -o memory.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c names.c -o names.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c objects.c -o objects.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c options.c -o options.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c paste.c -o paste.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c platform.c -o platform.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c plot.c -o plot.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c plot3d.c -o plot3d.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c plotmath.c -o plotmath.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c print.c -o print.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c printarray.c -o printarray.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c printvector.c -o printvector.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c printutils.c -o printutils.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c qsort.c -o qsort.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c random.c -o random.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c raw.c -o raw.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c registration.c -o registration.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c relop.c -o relop.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c rlocale.c -o rlocale.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c saveload.c -o saveload.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c scan.c -o scan.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c seq.c -o seq.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c serialize.c -o serialize.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c sort.c -o sort.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c source.c -o source.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c split.c -o split.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c sprintf.c -o sprintf.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c startup.c -o startup.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c subassign.c -o subassign.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c subscript.c -o subscript.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c subset.c -o subset.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c summary.c -o summary.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c sysutils.c -o sysutils.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c times.c -o times.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c unique.c -o unique.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c util.c -o util.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c version.c -o version.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c vfonts.c -o vfonts.o
gfortran  -fopenmp -fPIC  -g -O2  -c xxxpr.f -o xxxpr.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -fopenmp -L/Users/buck/trees/mine/sage/local/lib/  -install_name libR.dylib -compatibility_version 3.1.0  -current_version 3.1.2  -headerpad_max_install_names -o libR.dylib CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o vfonts.o xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a ../extra/tre/libtre.a  ../extra/xz/liblzma.a ../extra/intl/libintl.a ../extra/tzone/libtz.a -L../../lib -lRblas -lgfortran -lquadmath -lm    -Wl,-framework -Wl,CoreFoundation -lreadline  -licucore -lm -liconv  
mkdir /Users/buck/trees/mine/sage/local/var/tmp/sage/build/r-3.1.2.p0/src/bin/exec
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra  -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c Rmain.c -o Rmain.o
gcc -std=gnu99 -fopenmp  -L../../lib -L/Users/buck/trees/mine/sage/local/lib/  -o R.bin Rmain.o  -lR -lRblas
making Rhttpd.d from Rhttpd.c
making Rsock.d from Rsock.c
making internet.d from internet.c
making nanoftp.d from nanoftp.c
making nanohttp.d from nanohttp.c
making sock.d from sock.c
making sockconn.d from sockconn.c
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c Rhttpd.c -o Rhttpd.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c Rsock.c -o Rsock.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c internet.c -o internet.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c nanoftp.c -o nanoftp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c nanohttp.c -o nanohttp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c sock.c -o sock.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2    -c sockconn.c -o sockconn.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L../../../lib -L/Users/buck/trees/mine/sage/local/lib/  -o internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o sockconn.o -lR   -Wl,-framework -Wl,CoreFoundation
mkdir /Users/buck/trees/mine/sage/local/var/tmp/sage/build/r-3.1.2.p0/src/modules
making Lapack.d from Lapack.c
gfortran -fPIC  -g -O2 -ffloat-store -c dlamch.f -o dlamch.o
gfortran  -fopenmp -fPIC  -g -O2  -c dlapack.f -o dlapack.o
gfortran  -fopenmp -fPIC  -g -O2  -c cmplx.f -o cmplx.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -fopenmp -L/Users/buck/trees/mine/sage/local/lib/  -o libRlapack.dylib dlamch.o dlapack.o cmplx.o  -install_name libRlapack.dylib -compatibility_version 3.1.0 -current_version 3.1.2  -headerpad_max_install_names -L../../../lib -lRblas -lgfortran -lquadmath -lm  -L../../../lib -lR
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c Lapack.c -o Lapack.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L../../../lib -L/Users/buck/trees/mine/sage/local/lib/  -o lapack.so  Lapack.o  -lR  -Wl,-framework -Wl,CoreFoundation -L../../../lib -lRlapack -L../../../lib -lRblas -lgfortran -lquadmath -lm
/Users/buck/trees/mine/sage/local/var/tmp/sage/build/r-3.1.2.p0/src/lib/libRlapack.dylib is unchanged
making g_alab_her.d from g_alab_her.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making g_her_glyph.d from g_her_glyph.c
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c g_alab_her.c -o g_alab_her.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c g_cntrlify.c -o g_cntrlify.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c g_fontdb.c -o g_fontdb.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2   -c g_her_glyph.c -o g_her_glyph.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L../../../lib -L/Users/buck/trees/mine/sage/local/lib/  -o vfonts.so g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o -lR   -Wl,-framework -Wl,CoreFoundation
mkdir ../../library
building system startup profile
mkdir ../../../library/base
mkdir ../../../library/base/R
building package 'translations'
mkdir ../../../library/translations
building package 'base'
mkdir ../../../library/base/demo
building package 'tools'
mkdir ../../../library/tools
mkdir ../../../library/tools/R
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
making signals.d from signals.c
making install.d from install.c
making getfmts.d from getfmts.c
making http.d from http.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c text.c -o text.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c Rmd5.c -o Rmd5.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c md5.c -o md5.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c signals.c -o signals.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c install.c -o install.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c getfmts.c -o getfmts.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c http.c -o http.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c gramLatex.c -o gramLatex.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main     -fPIC  -g -O2   -c gramRd.c -o gramRd.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L../../../../lib -L/Users/buck/trees/mine/sage/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 -L../../../../lib -lR -Wl,-framework -Wl,CoreFoundation
mkdir ../../../../library/tools/libs
Warning messages:
1: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'America/Los_Angeles'
2: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'GMT'
3: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'America/New_York'
Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
2: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/New_York'
building package 'compiler'
mkdir ../../../library/compiler
mkdir ../../../library/compiler/R
Warning messages:
1: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'America/Los_Angeles'
2: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'GMT'
3: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'America/New_York'
Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
2: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/New_York'
byte-compiling package 'compiler'
Warning messages:
1: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'America/Los_Angeles'
2: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'GMT'
3: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'America/New_York'
byte-compiling package 'base'
Warning messages:
1: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'America/Los_Angeles'
2: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'GMT'
3: In strptime(paste(.leap.seconds, "23:59:60"), "%Y-%m-%d %H:%M:%S") :
  unknown timezone 'America/New_York'
byte-compiling package 'tools'
building package 'utils'
mkdir ../../../library/utils
mkdir ../../../library/utils/doc
mkdir ../../../library/utils/R
Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/Los_Angeles'
2: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
3: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/New_York'
4: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
5: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/New_York'
mkdir ../../../library/utils/Sweave
mkdir ../../../library/utils/misc
making init.d from init.c
making io.d from io.c
making size.d from size.c
making sock.d from sock.c
making stubs.d from stubs.c
making utils.d from utils.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/extra/xz/api     -fPIC  -g -O2   -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/extra/xz/api     -fPIC  -g -O2   -c io.c -o io.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/extra/xz/api     -fPIC  -g -O2   -c size.c -o size.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/extra/xz/api     -fPIC  -g -O2   -c sock.c -o sock.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/extra/xz/api     -fPIC  -g -O2   -c stubs.c -o stubs.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/extra/xz/api     -fPIC  -g -O2   -c utils.c -o utils.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L../../../../lib -L/Users/buck/trees/mine/sage/local/lib/ -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR -Wl,-framework -Wl,CoreFoundation
mkdir ../../../../library/utils/libs
byte-compiling package 'utils'
building package 'grDevices'
mkdir ../../../library/grDevices
mkdir ../../../library/grDevices/R
Warning messages:
1: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/Los_Angeles'
2: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
3: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/New_York'
4: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
5: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'America/New_York'
mkdir ../../../library/grDevices/afm
mkdir ../../../library/grDevices/enc
mkdir ../../../library/grDevices/icc
making axis_scales.d from axis_scales.c
making chull.d from chull.c
making devices.d from devices.c
making init.d from init.c
making stubs.d from stubs.c
making colors.d from colors.c
making devCairo.d from devCairo.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
making devQuartz.d from devQuartz.c
making qdBitmap.d from qdBitmap.c
making qdPDF.d from qdPDF.c
making qdCocoa.d from qdCocoa.m
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c axis_scales.c -o axis_scales.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c chull.c -o chull.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c devices.c -o devices.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c stubs.c -o stubs.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c colors.c -o colors.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c devCairo.c -o devCairo.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c devPicTeX.c -o devPicTeX.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c devPS.c -o devPS.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c devQuartz.c -o devQuartz.o
In file included from /usr/include/Availability.h:153:0,
                 from /usr/include/stdio.h:65,
                 from ../../../../include/Rinternals.h:37,
                 from ../../../include/Defn.h:80,
                 from devQuartz.c:30:
/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h:486:41: error: expected ',' or '}' before '__attribute__'
   kFSEventStreamEventFlagItemIsHardlink __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_9_0) = 0x00100000,
                                         ^
devQuartz.c: In function 'RQuartz_Font':
devQuartz.c:646:13: warning: 'ATSFontFindFromName' is deprecated (declared at /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803) [-Wdeprecated-declarations]
             atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
             ^
devQuartz.c:648:17: warning: 'ATSFontFindFromPostScriptName' is deprecated (declared at /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:820) [-Wdeprecated-declarations]
                 atsFont = ATSFontFindFromPostScriptName(cfFontName, kATSOptionFlagsDefault);
                 ^
devQuartz.c:675:17: warning: 'ATSFontFindFromName' is deprecated (declared at /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803) [-Wdeprecated-declarations]
                 atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                 ^
devQuartz.c:676:17: warning: 'ATSFontFindFromPostScriptName' is deprecated (declared at /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:820) [-Wdeprecated-declarations]
                 if (!atsFont) atsFont = ATSFontFindFromPostScriptName(cfFontName, kATSOptionFlagsDefault);
                 ^
devQuartz.c:682:25: warning: 'ATSFontFindFromName' is deprecated (declared at /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803) [-Wdeprecated-declarations]
                         atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                         ^
devQuartz.c:688:29: warning: 'ATSFontFindFromName' is deprecated (declared at /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803) [-Wdeprecated-declarations]
                             atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                             ^
devQuartz.c:696:25: warning: 'ATSFontFindFromName' is deprecated (declared at /System/Library/Frameworks/ApplicationServices.framework/Frameworks/ATS.framework/Headers/ATSFont.h:803) [-Wdeprecated-declarations]
                         atsFont = ATSFontFindFromName(cfFontName, kATSOptionFlagsDefault);
                         ^
devQuartz.c:715:5: warning: 'CGFontCreateWithPlatformFont' is deprecated (declared at /System/Library/Frameworks/CoreGraphics.framework/Headers/CGFont.h:61) [-Wdeprecated-declarations]
     return CGFontCreateWithPlatformFont(&atsFont);
     ^
devQuartz.c: In function 'RQuartz_Text':
devQuartz.c:997:5: warning: 'CGContextShowGlyphsWithAdvances' is deprecated (declared at /System/Library/Frameworks/CoreGraphics.framework/Headers/CGContext.h:1023) [-Wdeprecated-declarations]
     CGContextShowGlyphsWithAdvances(ctx,glyphs, g_adv, len);
     ^
make[5]: *** [devQuartz.o] Error 1
make[4]: *** [mksrc] Error 1
make[3]: *** [all] Error 2
make[2]: *** [R] Error 1
make[1]: *** [R] Error 1
make: *** [R] Error 1
Error building R.

real	4m58.277s
user	4m10.787s
sys	0m42.757s
************************************************************************
Error installing package r-3.1.2.p0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
  /Users/buck/trees/mine/sage/logs/pkgs/r-3.1.2.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/Users/buck/trees/mine/sage/local/var/tmp/sage/build/r-3.1.2.p0 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
  (cd '/Users/buck/trees/mine/sage/local/var/tmp/sage/build/r-3.1.2.p0' && '/Users/buck/trees/mine/sage/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
Version 0, edited 5 years ago by buck (next)

comment:2 Changed 5 years ago by vbraun

Those are warnings, not errors. The buildbot log shows the same warnings ( http://build.sagedev.org/release/builders/%20%20fast%20Volker%20MiniMac%20%28OSX%2010.10%20x86_64%29%20full/builds/42/steps/compile_1/logs/r-project). Do you have -Werror or something like that in CFLAGS/CXXFLAGS/...? This looks like a problem with your environment variables.

comment:3 Changed 5 years ago by buck

@vbraun: I showed all my environment above:

$ env
PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin
PWD=/Users/buck/trees/mine/sage
HOME=/Users/buck
SHLVL=1
_=/usr/bin/env

There's definitely an error:

gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -g -O2   -c devQuartz.c -o devQuartz.o
In file included from /usr/include/Availability.h:153:0,
                 from /usr/include/stdio.h:65,
                 from ../../../../include/Rinternals.h:37,
                 from ../../../include/Defn.h:80,
                 from devQuartz.c:30:
/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h:486:41:
error: expected ',' or '}' before '__attribute__'
   kFSEventStreamEventFlagItemIsHardlink __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_9_0) = 0x00100000,
                                         ^
...
Error installing package r-3.1.2.p0
Last edited 5 years ago by buck (previous) (diff)

comment:4 Changed 5 years ago by buck

The error I've pointed out does not show in your buildbot log.

comment:5 Changed 5 years ago by buck

On osx 10.10, __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_9_0) expands to __attribute__((availability(macosx,introduced=10.10))), which helps explain the error message..

I expect the difference is that your buildbot is not 10.10.

comment:6 Changed 5 years ago by jhpalmieri

I'm guessing that this has to do with Xcode, and in particular the fact that its most recent version is broken.

comment:7 Changed 5 years ago by vbraun

Sage sets MACOSX_DEPLOYMENT_TARGET=10.9 on 10.10 to work around Apple's broken toolchain so the conditional should be false. Though the error is about what is before the __OSX_AVAILABLE_STARTING. What are the relevant lines in your Availability.h?

I thought we had established that he is using Xcode < 6.3 on the mailinglist? With Xcode 6.3 he should't have gotten this far, the compilation pretty much dies immediately.

comment:8 Changed 5 years ago by vbraun

PS: The buildbot most certainly is on OSX 10.10.3

comment:9 Changed 5 years ago by jhpalmieri

On a machine on which I upgraded Xcode, I run into the same problem, and that machine built Sage fine before the upgrade.

comment:10 Changed 5 years ago by buck

Here's the gcc version you asked for:

$ which gcc
/usr/bin/gcc

$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.3.0
Thread model: posix

The XCode GUI reports "Version 6.3 (6D570)".

Changed 5 years ago by buck

Availability.h from Xcode 6.3

Changed 5 years ago by buck

AvailabilityInternal?.h from Xcode 6.3

comment:11 Changed 5 years ago by buck

I've attached the entire files just in case I've gotten it wrong, but I believe these are the relevant lines.

Availability.h:

162 #elif defined(__MAC_OS_X_VERSION_MIN_REQUIRED)
163     #define __OSX_AVAILABLE_STARTING(_osx, _ios) __AVAILABILITY_INTERNAL##_osx

AvailabilityInternal?.h:

5513 #define __AVAILABILITY_INTERNAL__MAC_10_10
                  __attribute__((availability(macosx,introduced=10.10)))
Last edited 5 years ago by buck (previous) (diff)

comment:12 Changed 5 years ago by vbraun

  • Milestone changed from sage-6.7 to sage-duplicate/invalid/wontfix

Xcode 6.3 isn't going to work (#18156). Propose to close as duplicate.

comment:13 Changed 5 years ago by vbraun

  • Status changed from new to needs_review

comment:14 Changed 5 years ago by buck

While both these issues may be caused by xcode-6.3, they look like separate bugs, separate pieces of work to me.

I upgraded my Xcode at the recommendation of one of the guys at sage days :( Shall I downgrade to 6.2?

comment:15 Changed 5 years ago by vbraun

yes, downgrade to 6.2

comment:16 Changed 5 years ago by buck

I've downgraded to 6.2, with no change in behavior D:

$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.3.0
Thread model: posix

The GUI reports "Version 6.2 (6C131e)".

The error looks exactly the same to me, but here it is, for completeness:

$ ./src/bin/sage-spkg
Found local metadata for r-3.1.2.p0
Found local sources at /Users/buck/trees/mine/sage/upstream/r-3.1.2.tar.gz
Checksum: 93809368e5735a630611633ac1fa99010020c5d6 vs 93809368e5735a630611633ac1fa99010020c5d6
r-3.1.2.p0
====================================================
Setting up build directory for r-3.1.2.p0
Finished set up
****************************************************
Host system:
Darwin MacBookPro-7831C1F266DE.local 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64 x86_64
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/Users/buck/trees/mine/sage/local/libexec/gcc/x86_64-apple-darwin14.3.0/4.9.2/lto-wrapper
Target: x86_64-apple-darwin14.3.0
Configured with: ../src/configure --prefix=/Users/buck/trees/mine/sage/local --with-local-prefix=/Users/buck/trees/mine/sage/local --with-gmp=/Users
/buck/trees/mine/sage/local --with-mpfr=/Users/buck/trees/mine/sage/local --with-mpc=/Users/buck/trees/mine/sage/local --with-system-zlib --disable-
multilib --disable-nls --enable-languages=c,c++,fortran --disable-libitm --without-isl --without-cloog
Thread model: posix
gcc version 4.9.2 (GCC)
****************************************************
Copying fake java and javac compiler on OS X
Configuring R without ATLAS for OS X
patching file src/scripts/R.sh.in
patching file configure
<snip>
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib     -fPIC  -
g -O2   -c devQuartz.c -o devQuartz.o
In file included from /usr/include/Availability.h:153:0,
                 from /usr/include/stdio.h:65,
                 from ../../../../include/Rinternals.h:37,
                 from ../../../include/Defn.h:80,
                 from devQuartz.c:30:
/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h:486:41: error: expected ',' or '}' before '__attr
ibute__'
   kFSEventStreamEventFlagItemIsHardlink __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_9_0) = 0x00100000,
                                         ^
<snip>

comment:17 Changed 5 years ago by vbraun

Did you compile from scratch (make distclean && make)?

comment:18 Changed 5 years ago by jhpalmieri

I know you weren't asking me, but a further data point: I did not compile from scratch. On one machine, I had updated to OS X 10.10.3 and the most recent Xcode, and I got this error. On a second machine, I just updated to OS X 10.10.3 but did not update Xcode, and I was able to install R (with sage -f r) successfully. Now on that same machine I'm also trying a build from scratch, but from the experiments so far, it really looks like a manifestation of a problem with the most recent Xcode.

Note that I have not yet tried upgrading Xcode and then downgrading it.

comment:19 Changed 5 years ago by buck

I've made distclean, and still get the same dang behavior D:

Found local metadata for r-3.1.2.p0
Found local sources at /Users/buck/trees/mine/sage/upstream/r-3.1.2.tar.gz
Checksum: 93809368e5735a630611633ac1fa99010020c5d6 vs 93809368e5735a630611633ac1fa99010020c5d6
r-3.1.2.p0
====================================================
Setting up build directory for r-3.1.2.p0
Finished set up
****************************************************
Host system:
Darwin 140-sfoeng50-54.clients.corp.yelpcorp.com 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~
5/RELEASE_X86_64 x86_64
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/Users/buck/trees/mine/sage/local/libexec/gcc/x86_64-apple-darwin14.3.0/4.9.2/lto-wrapper
Target: x86_64-apple-darwin14.3.0
Configured with: ../src/configure --prefix=/Users/buck/trees/mine/sage/local --with-local-prefix=/Users/buck/trees/mine/sage/local --wit
h-gmp=/Users/buck/trees/mine/sage/local --with-mpfr=/Users/buck/trees/mine/sage/local --with-mpc=/Users/buck/trees/mine/sage/local --wit
h-system-zlib --disable-multilib --disable-nls --enable-languages=c,c++,fortran --disable-libitm --without-isl --without-cloog
Thread model: posix
gcc version 4.9.2 (GCC)
****************************************************
Copying fake java and javac compiler on OS X
Configuring R without ATLAS for OS X
<snip>
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib
    -fPIC  -g -O2   -c devQuartz.c -o devQuartz.o
In file included from /usr/include/Availability.h:153:0,
                 from /usr/include/stdio.h:65,
                 from ../../../../include/Rinternals.h:37,
                 from ../../../include/Defn.h:80,
                 from devQuartz.c:30:
/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h:486:41: 
error: expected ',' or '}' before '__attribute__'
   kFSEventStreamEventFlagItemIsHardlink __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_9_0) = 0x00100000,
Last edited 5 years ago by buck (previous) (diff)

comment:20 Changed 5 years ago by jhpalmieri

Whereas I downloaded a fresh 6.7.beta1 tarball and built it successfully on the machine running OS X 10.10.3 and Xcode 6.2. On another machine on which I've installed Xcode 6.3, I may try downgrading that to see if I can build there.

comment:21 follow-up: Changed 5 years ago by buck

I asked gcc for an expansion of the file in question and got this:

# 309 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h" 3
enum {
  kFSEventStreamEventFlagNone = 0x00000000,
# 330 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h" 3
  kFSEventStreamEventFlagMustScanSubDirs = 0x00000001,
# 345 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h" 3
  kFSEventStreamEventFlagUserDropped = 0x00000002,
<snip>
  kFSEventStreamEventFlagItemIsSymlink = 0x00040000,
  kFSEventStreamEventFlagOwnEvent = 0x00080000,
  kFSEventStreamEventFlagItemIsHardlink __attribute__((weak_import)) = 0x00100000,
  kFSEventStreamEventFlagItemIsLastHardlink __attribute__((weak_import)) = 0x00200000,
};

@jhpalmieri Show me what you get for this command?

gcc -E /System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h | grep kFSEventStreamEventFlagNone -B20 -A150 | grep -v '^$' | sed -n '/enum {/,/}/p'

comment:22 Changed 5 years ago by buck

Unsetting MACOSX_DEPLOYMENT_TARGET makes the .o file build fine...

Reproduction procedure:

cd 'local/var/tmp/sage/build/r-3.1.2.p0' && '../../../../../../sage' --sh
cd src/src/library/grDevices/src
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib -fPIC  -g -O2   -c devQuartz.c -o devQuartz.o
#syntax error explosion
env | grep MACOSX
#MACOSX_DEPLOYMENT_TARGET=10.9
unset MACOSX_DEPLOYMENT_TARGET
env | grep MACOSX
#no output
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/extra/zlib -fPIC  -g -O2   -c devQuartz.c -o devQuartz.o
#several warnings, but no error

comment:23 in reply to: ↑ 21 ; follow-up: Changed 5 years ago by jhpalmieri

Replying to buck:

@jhpalmieri Show me what you get for this command?

gcc -E /System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h | grep kFSEventStreamEventFlagNone -B20 -A150 | grep -v '^$' | sed -n '/enum {/,/}/p'

enum {
  kFSEventStreamEventFlagNone = 0x00000000,
# 330 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h"
  kFSEventStreamEventFlagMustScanSubDirs = 0x00000001,
# 345 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h"
  kFSEventStreamEventFlagUserDropped = 0x00000002,
  kFSEventStreamEventFlagKernelDropped = 0x00000004,
  kFSEventStreamEventFlagEventIdsWrapped = 0x00000008,
# 367 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h"
  kFSEventStreamEventFlagHistoryDone = 0x00000010,
# 380 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h"
  kFSEventStreamEventFlagRootChanged = 0x00000020,
# 395 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h"
  kFSEventStreamEventFlagMount = 0x00000040,
# 408 "/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h"
  kFSEventStreamEventFlagUnmount = 0x00000080,
  kFSEventStreamEventFlagItemCreated __attribute__((availability(macosx,introduced=10.7))) = 0x00000100,
  kFSEventStreamEventFlagItemRemoved __attribute__((availability(macosx,introduced=10.7))) = 0x00000200,
  kFSEventStreamEventFlagItemInodeMetaMod __attribute__((availability(macosx,introduced=10.7))) = 0x00000400,
  kFSEventStreamEventFlagItemRenamed __attribute__((availability(macosx,introduced=10.7))) = 0x00000800,
  kFSEventStreamEventFlagItemModified __attribute__((availability(macosx,introduced=10.7))) = 0x00001000,
  kFSEventStreamEventFlagItemFinderInfoMod __attribute__((availability(macosx,introduced=10.7))) = 0x00002000,
  kFSEventStreamEventFlagItemChangeOwner __attribute__((availability(macosx,introduced=10.7))) = 0x00004000,
  kFSEventStreamEventFlagItemXattrMod __attribute__((availability(macosx,introduced=10.7))) = 0x00008000,
  kFSEventStreamEventFlagItemIsFile __attribute__((availability(macosx,introduced=10.7))) = 0x00010000,
  kFSEventStreamEventFlagItemIsDir __attribute__((availability(macosx,introduced=10.7))) = 0x00020000,
  kFSEventStreamEventFlagItemIsSymlink __attribute__((availability(macosx,introduced=10.7))) = 0x00040000,
  kFSEventStreamEventFlagOwnEvent __attribute__((availability(macosx,introduced=10.9))) = 0x00080000
};
enum {
    kFSEventStreamEventIdSinceNow = 0xFFFFFFFFFFFFFFFFULL
};

comment:24 in reply to: ↑ 23 Changed 5 years ago by buck

Replying to jhpalmieri:

Replying to buck:

@jhpalmieri Show me what you get for this command?

gcc -E /System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h | grep kFSEventStreamEventFlagNone -B20 -A150 | grep -v '^$' | sed -n '/enum {/,/}/p'

enum {
  kFSEventStreamEventFlagOwnEvent __attribute__((availability(macosx,introduced=10.9))) = 0x00080000
};

This looks entirely different from mine. Describe this environment for me? It looks like 10.9.

comment:25 Changed 5 years ago by jhpalmieri

It is running 10.10, according to "About my Mac" and uname:

$ uname -v
Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64

I have Xcode 6.2. No homebrew or anything similar. What else would you like to know?

comment:26 Changed 5 years ago by jhpalmieri

Do you have Xcode installed, or just the command line tools? Here's what happened on one machine:

  • I had Xcode 6.3 installed. Sage would not build and I saw the above error.
  • I downloaded the older version of the command-line tools, installed it, and tried again. Still no luck.
  • Then I deleted the Xcode app and things now work.

So try deleting the Xcode app and see if that helps.

comment:27 follow-up: Changed 5 years ago by vbraun

Also note that xcode and clt (command line tools) are separate packages and you can easily have different versions installed...

comment:28 in reply to: ↑ 27 Changed 5 years ago by jhpalmieri

Replying to vbraun:

Also note that xcode and clt (command line tools) are separate packages and you can easily have different versions installed...

Although in my case, it seems that there is some shadowing (if that is the right word) if you have Xcode 6.3 and an earlier version of the command line tools.

comment:29 Changed 5 years ago by buck

@vbraun: Where's the ticket that induced you (plural) to twiddle the MACOSX_DEPLOYMENT_TARGET ?

comment:30 Changed 5 years ago by buck

It's this one: http://trac.sagemath.org/ticket/17204

That ticket doesn't describe how to reproduce the relevant issue, or how to check my libtool version. The version I find doesn't seem to be in the same scheme as the one mentioned (2.4.3).

$ libtool -V
Apple Inc. version cctools-862

I'm interested because this patch *seems to* work, and I'm trying to see if I've thereby regressed #17204:

  • src/bin/sage-env

    diff --git a/src/bin/sage-env b/src/bin/sage-env
    index 43f265b..8b26eda 100644
    a b fi 
    268268
    269269# Mac OS X-specific setup
    270270if [ `uname` = "Darwin" ]; then
    271     # set MACOSX_DEPLOYMENT_TARGET -- if set incorrectly, this can
     271    # unset MACOSX_DEPLOYMENT_TARGET -- if set incorrectly, this can
    272272    # cause lots of random "Abort trap" issues on OSX. see trac
    273273    # #7095 for an example.
    274     MACOSX_VERSION=`uname -r | awk -F. '{print $1}'`
    275     MACOSX_DEPLOYMENT_TARGET=10.$[$MACOSX_VERSION-4]
    276     if [ $MACOSX_DEPLOYMENT_TARGET = '10.10' ]; then
    277         # Workaround for the libtool version detection bug
    278         # See http://trac.sagemath.org/ticket/17204
    279         MACOSX_DEPLOYMENT_TARGET=10.9
    280     fi
    281     export MACOSX_DEPLOYMENT_TARGET
     274    unset MACOSX_DEPLOYMENT_TARGET
    282275fi
    283276
    284277# Compile-time path for libraries.  This is the equivalent of

comment:31 Changed 5 years ago by buck

It seems like this bug has the reproduction information I was looking for: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63610

Because I was able to make distclean && make with no issues whatsoever, I think the libtool problem is gone, and the workaround should be removed, since it is the source of this bug at hand.

comment:32 Changed 5 years ago by buck

Sorry for the spam, but I keep learning things. =X

Even if the libtool issue still exists, the above patch would avoid it. It's an implementation of the alternative workaround suggested by gcc dev Jack Howarth at https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63610#c9

comment:33 Changed 5 years ago by buck

  • Branch set to u/buck/unset_macosx_deployment_target_18254
  • Commit set to 569f12d06763baf11bf341129a9b7312a2bceb24

New commits:

569f12dunset MACOSX_DEPLOYMENT_TARGET, rather than sometimes setting a bogus value

comment:34 Changed 5 years ago by vbraun

There is nothing bogus about setting an earlier MACOSX_DEPLOYMENT_TARGET, its commonly used to make binaries that in addition run on older versions.

Autotool-based projects are supposed to ship their own copy of libtool, not use the system libtool.

comment:35 Changed 5 years ago by buck

Well... that patch is bogus then.

It's still mysterious that unsetting it "solves" this problem.

Last edited 5 years ago by buck (previous) (diff)

comment:36 Changed 5 years ago by buck

  • Branch u/buck/unset_macosx_deployment_target_18254 deleted
  • Commit 569f12d06763baf11bf341129a9b7312a2bceb24 deleted

comment:37 Changed 5 years ago by vbraun

Have you tried an earlier MACOSX_DEPLOYMENT_TARGET, maybe 10.8? We just have to find a combination that circumvents all bugs in Xcode...

comment:38 Changed 5 years ago by buck

I tried with MACOSX_DEPLOYMENT_TARGET=10.10 and got a segfault, so I guess that bug is still around.

Why is unset MACOSX_DEPLOYMENT_TARGET a non-starter?

I'll try 10.8...

comment:39 Changed 5 years ago by buck

I've verified that anything other than MACOSX_DEPLOYMENT_TARGET=10.10 throws the OP error.

Can I change the if-10.10 to do an unset?

comment:40 Changed 5 years ago by buck

I've pared it down to this minimal reproduction:

$ echo '#include <ApplicationServices/ApplicationServices.h>' | MACOSX_DEPLOYMENT_TARGET=10.10 gcc -c -xc -
(it works, no output)

$ echo '#include <ApplicationServices/ApplicationServices.h>' | MACOSX_DEPLOYMENT_TARGET=10.9 gcc -c -xc -
In file included from /usr/include/Availability.h:153:0,
                 from /System/Library/Frameworks/ApplicationServices.framework/Headers/ApplicationServices.h:19,
                 from <stdin>:1:
/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h:486:41: error: expected ',' or '}' before '__attribute__'
   kFSEventStreamEventFlagItemIsHardlink __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_9_0) = 0x00100000,
                                         ^

comment:41 Changed 5 years ago by buck

This only reproduces with GNU gcc, not with /usr/bin/gcc.

gcc bug?

Last edited 5 years ago by buck (previous) (diff)

comment:42 Changed 5 years ago by buck

Even-more-minimal reproduction:

$ echo 'enum {a = 1, b __attribute__((availability(macosx,introduced=10.10))) = 1};' | /usr/bin/gcc -c -xc -
(no output, it works)

$ echo 'enum {a = 1, b __attribute__((availability(macosx,introduced=10.10))) = 1};' | gcc -c -xc -
<stdin>:1:16: error: expected ',' or '}' before '__attribute__'

comment:43 Changed 5 years ago by jhpalmieri

On a machine running 10.10.3 and Xcode 6.2, if I use unset MACOSX_DEPLOYMENT_TARGET, Sage builds but I get a lot of doctest errors:

----------------------------------------------------------------------
sage -t --long src/sage/plot/graphics.py  # Killed due to abort
sage -t --long src/sage/matrix/matrix2.pyx  # Killed due to abort
sage -t --long src/sage/schemes/elliptic_curves/height.py  # Killed due to abort
sage -t --long src/sage/crypto/mq/sr.py  # 5 doctests failed
sage -t --long src/sage/libs/ppl.pyx  # Killed due to abort
sage -t --long src/sage/symbolic/integration/integral.py  # Killed due to abort
sage -t --long src/sage/schemes/projective/projective_morphism.py  # Killed due to abort
sage -t --long src/sage/modular/modsym/ambient.py  # Killed due to abort
sage -t --long src/sage/schemes/elliptic_curves/ell_finite_field.py  # Killed due to abort
sage -t --long src/sage/functions/prime_pi.pyx  # Killed due to abort
sage -t --long src/sage/modular/modform/eisenstein_submodule.py  # Killed due to abort
sage -t --long src/sage/tests/french_book/calculus_doctest.py  # Killed due to abort
sage -t --long src/sage/interfaces/maxima_lib.py  # Killed due to abort
sage -t --long src/sage/coding/code_constructions.py  # Killed due to abort
sage -t --long src/sage/groups/generic.py  # Killed due to abort
sage -t --long src/sage/matrix/matrix_modn_dense_template.pxi  # Killed due to abort
sage -t --long src/sage/rings/polynomial/multi_polynomial_sequence.py  # 1 doctest failed
sage -t --long src/sage/matrix/matrix_cyclo_dense.pyx  # Killed due to abort
sage -t --long src/sage/calculus/functional.py  # Killed due to abort
sage -t --long src/doc/en/thematic_tutorials/coding_theory.rst  # Killed due to abort
sage -t --long src/sage/functions/min_max.py  # Killed due to abort
sage -t --long src/sage/rings/polynomial/pbori.pyx  # Killed due to abort
sage -t --long src/sage/rings/algebraic_closure_finite_field.py  # Killed due to abort
sage -t --long src/sage/functions/trig.py  # Killed due to abort
sage -t --long src/doc/de/tutorial/tour_advanced.rst  # Killed due to abort
sage -t --long src/doc/en/tutorial/tour_advanced.rst  # Killed due to abort
sage -t --long src/doc/ru/tutorial/tour_advanced.rst  # Killed due to abort
sage -t --long src/sage/modular/modsym/modsym.py  # Killed due to abort
sage -t --long src/doc/pt/tutorial/tour_advanced.rst  # Killed due to abort
sage -t --long src/doc/fr/tutorial/tour_advanced.rst  # Killed due to abort
sage -t --long src/sage/modular/abvar/homology.py  # Killed due to abort
sage -t --long src/sage/symbolic/function.pyx  # Killed due to abort
sage -t --long src/sage/algebras/finite_dimensional_algebras/finite_dimensional_algebra.py  # Killed due to\
 abort
sage -t --long src/sage/tests/french_book/linalg_doctest.py  # Killed due to abort
sage -t --long src/sage/rings/finite_rings/element_base.pyx  # Killed due to abort
----------------------------------------------------------------------

A typical such error says

------------------------------------------------------------------------
Unhandled SIGABRT: An abort() occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Sage will now terminate.
------------------------------------------------------------------------

comment:44 Changed 5 years ago by buck

@jhpalmieri That looks like the abort errors mentioned in sage-env. It says to look at #7095

One workaround is to configure R with --with-aqua=no, but I don't know if that's acceptable. I don't know what aqua is or what R might use it for.

comment:45 Changed 5 years ago by vbraun

I'm pretty sure that some old libtool versions still linger in third-party tarballs, so we'll need MACOSX_DEPLOYMENT_TARGET <= 10.9 for a while.

comment:46 Changed 5 years ago by vbraun

Disabling aqua (=OSX gui), at least until Apple publishes a working Xcode, is fine with me.

comment:47 Changed 5 years ago by jhpalmieri

I'm confused about the goal here. As far as I can tell, if you have Xcode 6.3, Sage won't build, and the problem won't be with R, but with gcc. If you delete Xcode 6.3 and install version 6.2 of the command-line tools, Sage will build. Is this reproducible by anyone else? If so, what problem are we trying to solve with this ticket?

comment:48 Changed 5 years ago by buck

You're mistaken. I've been running 6.2 this whole time.

comment:49 Changed 5 years ago by buck

I wish any of you were on IRC. This would all go so much more quickly.

Changed 5 years ago by buck

my xcode and clt versions

comment:50 Changed 5 years ago by jhpalmieri

The next question is whether anyone else can replicate your problems. By the way, does it help to delete the Xcode app and just install the command-line tools (via the link described in the top-voted answer to http://stackoverflow.com/questions/29529455/missing-c-header-debug-after-updating-osx-command-line-tools-6-3)?

Edit: you originally had installed Xcode 6.3. I wonder if there are any traces of that left somewhere?

Last edited 5 years ago by jhpalmieri (previous) (diff)

comment:51 Changed 5 years ago by jhpalmieri

With the change

  • build/pkgs/r/spkg-install

    diff --git a/build/pkgs/r/spkg-install b/build/pkgs/r/spkg-install
    index 2bb904d..4bad9c8 100755
    a b if [ "$UNAME" = "Darwin" ]; then 
    8484    R_CONFIGURE="--enable-R-framework=no $R_CONFIGURE"
    8585fi
    8686
     87# OS X 10.10 and/or Xcode 6.3 broke the R installation. See
     88# http://trac.sagemath.org/ticket/18254.
     89if { uname -sr | grep 'Darwin 14\.' ;} &>/dev/null; then
     90    echo "OS X 10.10: Configuring R without aqua support."
     91    R_CONFIGURE="--with-aqua=no $R_CONFIGURE"
     92fi
     93
    8794if [ "$UNAME" = "CYGWIN" ]; then
    8895    # Cygwin libm does not provide "long double" functions
    8996    # and we do not install Cephes on Cygwin at the moment

along with the workaround for gcc at #18156, R builds and passes its test suite, and Sage passes all tests, too. (This is with command line tools 6.3.1.)

comment:52 follow-up: Changed 5 years ago by vbraun

There is a new R release at #18229, does it change anything?

comment:53 in reply to: ↑ 52 Changed 5 years ago by jhpalmieri

Replying to vbraun:

There is a new R release at #18229, does it change anything?

Yes. Without the change here, I get the same failure. With the change here, I get a new failure:

gcc -std=gnu99 -I/Users/palmieri/Desktop/Sage_stuff/git/sage/local/var/tmp/sage/build/r-3.2.0.p0/src/include -DNDEBUG      -fPIC  -g -O2   -c init.c -o init.o
gcc -std=gnu99 -I/Users/palmieri/Desktop/Sage_stuff/git/sage/local/var/tmp/sage/build/r-3.2.0.p0/src/include -DNDEBUG      -fPIC  -g -O2   -c threeDplot.c -o threeDplot.o
gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/palmieri/Desktop/Sage_stuff/git/sage/local/var/tmp/sage/build/r-3.2.0.p0/src/lib -L/Users/palmieri/Desktop/Sage_stuff/git/sage/local/lib/ -o lattice.so init.o threeDplot.o -L/Users/palmieri/Desktop/Sage_stuff/git/sage/local/var/tmp/sage/build/r-3.2.0.p0/src/lib -lR -Wl,-framework -Wl,CoreFoundation
installing to /Users/palmieri/Desktop/Sage_stuff/git/sage/local/var/tmp/sage/build/r-3.2.0.p0/src/library/lattice/libs
** R
** data
*** moving datasets to lazyload DB
dyld: lazy symbol binding failed: Symbol not found: _BZ2_bzReadOpen
  Referenced from: /Users/palmieri/Desktop/Sage_stuff/git/sage/local/var/tmp/sage/build/r-3.2.0.p0/src/lib/libR.dylib
  Expected in: flat namespace

dyld: Symbol not found: _BZ2_bzReadOpen
  Referenced from: /Users/palmieri/Desktop/Sage_stuff/git/sage/local/var/tmp/sage/build/r-3.2.0.p0/src/lib/libR.dylib
  Expected in: flat namespace

/Users/palmieri/Desktop/Sage_stuff/git/sage/local/var/tmp/sage/build/r-3.2.0.p0/src/bin/INSTALL: line 34:  9807 Done                    echo 'tools:::.install_packages()'
      9808 Trace/BPT trap: 5       | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
make[5]: *** [lattice.ts] Error 1
make[4]: *** [recommended-packages] Error 2
make[3]: *** [stamp-recommended] Error 2
Error building vignettes.

comment:54 Changed 5 years ago by fbissey

Got there too. Like in #18254 libR.dylib is underlinked but somehow R.bin linked OK.

 otool -L /Users/fbissey/build/sage-6.6.beta5/local/var/tmp/sage/build/r-3.2.0.p0/src/lib/libR.dylib
/Users/fbissey/build/sage-6.6.beta5/local/var/tmp/sage/build/r-3.2.0.p0/src/lib/libR.dylib:
	libR.dylib (compatibility version 3.2.0, current version 3.2.0)
	libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Users/fbissey/build/sage-6.6.beta5/local/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
	/Users/fbissey/build/sage-6.6.beta5/local/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1153.18.0)
	/Users/fbissey/build/sage-6.6.beta5/local/lib/libreadline.6.dylib (compatibility version 6.0.0, current version 6.3.0)
	/Users/fbissey/build/sage-6.6.beta5/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 53.1.0)
	/usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
	/Users/fbissey/build/sage-6.6.beta5/local/lib/libgomp.1.dylib (compatibility version 2.0.0, current version 2.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
	/Users/fbissey/build/sage-6.6.beta5/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

libbz2 is missing. A gross hack that should get us past this would be to configure with --without-system-bzlib to force the use of the internal copy but it is quite curious we miss that linking on some platforms.

comment:55 Changed 5 years ago by fbissey

--without-system-bzlib did the trick. I also noticed that with r-3.1.2 bzip2 was not properly detected during configuration on my mac and therefore the internal copy was used in that case too.

comment:56 Changed 5 years ago by jhpalmieri

That works for me, too. All tests pass.

comment:57 Changed 5 years ago by buck

Let's make the new R version and its attendant patch a separate issue and ship the patch shown in comment:51.

comment:58 Changed 5 years ago by buck

  • Branch set to u/buck/18254_osx_R_noaqua
  • Commit set to ad87162c8b4b7ccef0553ad66d9a6b2e112c8f48

New commits:

ad87162skip R-aqua on osx 10.10. see #18254

comment:59 Changed 5 years ago by git

  • Commit changed from ad87162c8b4b7ccef0553ad66d9a6b2e112c8f48 to 3c5cd0f74446992a2b98f84c34043cfa181b68b4

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

3c5cd0fskip R-aqua on osx 10.10. see #18254

comment:60 Changed 5 years ago by buck

As for upstream, I've gotten some good response on the osx-dev forums:

https://devforums.apple.com/message/1128923#1128923

tl;dr: Fixing this upstream involves enhancements to one of both gcc and clang:

comment:61 Changed 5 years ago by buck

Apple says they don't care about GNU-gcc bugs. Is there a good reason to use gnu-gcc for all of this?

Apple Developer Relations24-Apr-2015 02:40 PM
 
Engineering has determined that this is an issue for a third party to resolve.

We do not support GNU gcc.

If you have questions regarding the resolution of this issue, please update your bug report with them.

We are closing this report.

Please be sure to regularly check new Apple releases for any updates that might affect this issue.
 
Buck Golemon21-Apr-2015 10:54 PM
 
This is related to the fact that clang supports "enumeration attributes" but GNU gcc does not.
http://clang.llvm.org/docs/LanguageExtensions.html#attributes-on-enumerators
https://gcc.gnu.org/onlinedocs/gcc/Attribute-Syntax.html#Attribute-Syntax

I've opened a public question on the matter at: http://stackoverflow.com/questions/29788547/gcc-attribute-for-enum-members
 
Buck Golemon21-Apr-2015 10:03 PM
 
Summary:
Under GNU gcc, there's a syntax error in ApplicationServices.h if $MACOSX_DEPLOYMENT_TARGET has any value less than 10.10.

Steps to Reproduce:
```
$ echo '#include <ApplicationServices/ApplicationServices.h>' | MACOSX_DEPLOYMENT_TARGET=10.10 gcc -c -xc -
(it works, no output)

$ echo '#include <ApplicationServices/ApplicationServices.h>' | MACOSX_DEPLOYMENT_TARGET=10.9 gcc -c -xc -
In file included from /usr/include/Availability.h:153:0,
                 from /System/Library/Frameworks/ApplicationServices.framework/Headers/ApplicationServices.h:19,
                 from <stdin>:1:
/System/Library/Frameworks/CoreServices.framework/Frameworks/FSEvents.framework/Headers/FSEvents.h:486:41: error: expected ',' or '}' before '__attribute__'
   kFSEventStreamEventFlagItemIsHardlink __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_9_0) = 0x00100000,
                                         ^
```


Expected Results:
successful compilation

Actual Results:
compilation fails with a syntax error

Version:
osx 10.10.3 (14D131)
xcode Version 6.2 (6C131e)
gcc --version: gcc (GCC) 4.9.2

Notes:
Downstream ticket: http://trac.sagemath.org/ticket/18254

Configuration:


Attachments:

comment:62 Changed 5 years ago by fbissey

Summary of why we use gcc instead of clang.

  • We need a fortran compiler so we build gcc anyway
  • A lot of packages shipped with sage won't compile with clang
  • it is too hard to use clang for some and gcc for some other
  • some of the package broken with clang my be in the too hard basket

I expect one way or another most packages in sage will eventually compile with clang. I for one will work on this once gentoo-prefix on OS X finally gets its toolchain issues sorted and default to clang.

comment:63 Changed 5 years ago by jhpalmieri

  • Authors set to Buck Evan
  • Reviewers set to John Palmieri, Volker Braun
  • Status changed from needs_review to positive_review

Let's merge this. The change was first suggested in comment 44, so I've made buck the author.

comment:64 Changed 5 years ago by vbraun

Merge or close as invalid? Can you set the milestone if you actually want to merge the branch?

comment:65 Changed 5 years ago by jhpalmieri

  • Milestone changed from sage-duplicate/invalid/wontfix to sage-6.7

Sorry. I think you set the milestone a while ago, and no one reset it to match the new branch.

comment:66 Changed 5 years ago by vbraun

  • Branch changed from u/buck/18254_osx_R_noaqua to 3c5cd0f74446992a2b98f84c34043cfa181b68b4
  • Resolution set to fixed
  • Status changed from positive_review to closed
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